EXTRACELLULAR VESICLE COMPOSITIONS AND METHODS OF USE THEREOF

Information

  • Patent Application
  • 20220226384
  • Publication Number
    20220226384
  • Date Filed
    January 19, 2022
    3 years ago
  • Date Published
    July 21, 2022
    2 years ago
  • Inventors
  • Original Assignees
    • Evia Life Sciences Inc. (Seattle, WA, US)
Abstract
Compositions and methods for promoting generation or regeneration of the lymphatic system in a subject are provided. Compositions and methods for the treatment of lymphedema are also provided. The composition can include extracellular vesicles and a pharmaceutically acceptable carrier, and is typically cell-free. In some embodiments, the extracellular vesicles are formed by a method including culturing MSCs to produce media conditioned with the extracellular vesicles, and optionally, but preferably separating the extracellular vesicles from the media conditioned by the MSCs. In some embodiments, the extracellular vesicles include or consist of exosomes, microvesicles or a combination thereof, and they may have a size of between about 20 nm and about 500 nm. In some embodiments, extracellular vesicles include CD9, CD63, or a combination thereof and/or one or more of miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, miR-29c-3p, miR-658, miR-493-3p, miR-184, and miR-27a-3p.
Description
REFERENCE TO THE SEQUENCE LISTING

The Sequence Listing submitted as a text file named “EVIA_100_ST25” created on Jan. 18, 2022 and having a size of 15,353 bytes is hereby incorporated by reference pursuant to 37 C.F.R. § 1.52(e)(5).


FIELD OF THE INVENTION

The field of the invention generally relates to cell-free compositions including extracellular vesicles and methods of use thereof.


BACKGROUND OF THE INVENTION

Lymphedema is based on a chronic disorder of the lymphatic system and accumulation of interstitial protein-rich fluid in the limbs. Lymphedema patients demonstrate chronic inflammation, and disorders of sensory and motor systems. Generally, lymphedema can be divided into primary and secondary types depending on the etiology. Primary lymphedema results from anatomic or functional defects, whereas secondary lymphedema is due to mainly infection or surgical resection of the lymph node for cancer therapy. It is estimated that approximately 30% of patients who undergo breast cancer surgery may develop lymphedema and 6% of cases of sentinel navigation surgery in the breast progress to lymphedema (DiSipio et al., Lancet Once, 14, 500-515 (2013)). In gynecologic cancers, approximately 10 to 30% of patients may develop lymphedema, depending on the cancer type, age, surgical approach. Furthermore, postoperative radiation increases the proportion of lymphedema to over 35% (Beesley et al., Cancer, 109, 2607-2614 (2007), Tada et al., BMC Cancer, 9, 47 (2009)). Because lymphedema disturbs the quality of life and elevates risks of recurrent cellulitis and secondary malignancy, the urgent development of effective treatment options is an important clinical goal.


To date, the treatment options are mainly limited to physiotherapy and surgical treatments. These methods require proper compliance and lifelong care. As the conventional treatment option, compression therapy using bandages or stockings is still used all over the world. Compression therapy can increase the internal pressure of the lymphatic systems. Thus, interstitial fluid could go into the lymphatic systems. Ideally, patients are required to wear thick garments or stockings every day even in summer; however, for most of the patients, full compliance is hard to achieve. In recent years, with the development of techniques using microsurgery and supermicrosurgery, surgical interventions such as lymphatico-venous anastomosis (LVA) have been attempted worldwide, with consistently favorable results. The long-term outcome of lymphatic microsurgery is also reported to be favorable in 24 to 48 months (Pedro, et al., Microsurgery, 40(2):130-136 (2020), and Antonio, et al., Gland Surg., 9(2):539-544 (2020)). However, these techniques are not easy to perform and are therefore not widely used in conventional clinical settings. Furthermore, it is still controversial whether the effect of surgical interventions lasts for an extended period. Moreover, such interventions cannot always stop the progress of the disease in severe cases. Regeneration of the lymphatic system is a hopeful treatment for the disease. Recent reports indicate that transplantation of mesenchymal stem cells (MSCs), such as adipose-derived mesenchymal stem cells (ADSCs) or bone-marrow mesenchymal stem cells (BMMSCs), promotes tissue regeneration including the lymphatic system by paracrine factors secreted by MSCs (Maertens et al., PLoS One, September 15;9(9):e106976 (2014), Shimizu et al., J Am Heart Assoc., August;1(4):e000877 (2012), Spees, et al., Stem Cell Res Ther., (7:125 (2016)). Diseases involving vascular and lymphatic systems such as ischemic heart failure, ischemic limb, DM foot necrosis, and lymphedema are possible disease indications. Transplantation of MSCs into damaged tissue has been shown to induce endothelial cell growth and enhance new blood vessel formation, with secreting paracrine factors as the predominant mechanism (Zhang, et al., J Transl Med. (13:49) (2015)).


As for inducing lymphangiogenesis, MSCs including ADSCs or BMMSCs have been shown to secrete many growth factors and cytokines that have effects on cells in their vicinity (Hwang, et al., Biomaterials, (32(19):4415-23 (2011)). For example, ADSCs can restore the lymphatic vascular network in a secondary mouse lymphedema model with increased collecting lymphatic vessels, mainly based on paracrine effects of ADSCs (Yoshida et al., Regen Med., 10(5):549-62 (2015)). In addition, it has been shown that BMMSCs play a role in lymphatic regeneration in a mouse tail lymphedema model (Conrad et al., Circulation, January 20;119(2):281-9 (2009)). In a clinical trial, BMMSCs were used for 10 post-mastectomy lymphedema patients, and the results indicate that BMMSC injection reduces arm volume as well as associated co-morbidities of pain (Maldonado et al., Cytotherapy, November;13(10):1249-55 (2011), Maldonado, et al., Cytotherapy, (13(10):1249-55 (2011)). ADSCs have been also used in both animal and clinical trials, showing their lymphangiogenic activity and therapeutic efficacy without serious adverse events in the six months follow-up period (Toyserkani et al., Stem Cells Transl Med., August;6(8):1666-1672 (2017), Hwang et al., Biomaterials, July;32(19):4415-23 (2011)). Potential risks of previous cancer spreading after treatment using MSCs are thought to be low because lymphedema treatment normally starts several years after initial treatment. However, MSC transplantation has drawbacks such as poor engraftment efficiency, potential tumor formation, unwanted immune responses, non-specific differentiation, and the difficulty of quality control before administration (Zhang, et al., Cell Pro 49:3-13 (2016)). Thus, there remains a need for alternatives to cell transplantation.


Thus, it is an object of the invention to provide alternative compositions and methods to mesenchymal stem cell transplantation.


It is a further object of the invention to provide compositions and methods of use thereof to promote generation or regeneration of the lymphatic system, treat lymphedema, and combinations thereof.


SUMMARY OF THE INVENTION

Compositions and methods for promoting generation or regeneration of the lymphatic system in a subject are provided. Compositions and methods for the treatment of lymphedema are also provided. The compositions include extracellular vesicles, typically in a pharmaceutically acceptable carrier, and are typically cell-free. In some embodiments, the extracellular vesicles are formed by a method including culturing MSCs to produce media conditioned with the extracellular vesicles, and optionally, but preferably separating the extracellular vesicles from the conditioned media. Thus, in some embodiments, the composition does not include the media conditioned by the MSCs. The MSCs can be primary cells or a cell line. MSCs can be isolated or derived from, for example, bone barrow, placenta, umbilical cord blood, adipose tissue, adult muscle, corneal stroma, or the dental pulp of deciduous teeth. In a preferred embodiment, the composition includes extracellular vesicles formed by adipose-derived stem cells.


The extracellular vesicles can include or consist of ectosomes, microvesicles (MV), microparticles, exosomes, oncosomes, apoptotic bodies (AB), tunneling nanotubes (TNT), or a combination thereof. In some embodiments, the extracellular vesicles include or consist of exosomes, microvesicles or a combination thereof. The extracellular vesicles can include or consist of vesicles having a size of, for example, between about 20 nm and about 500 nm, or between about 20 nm and about 250 nm, or between about 20 nm and about 200 nm, or between about 20 nm and about 150 nm, or between about 20 nm and about 100 nm. In some embodiments, extracellular vesicles of the composition include CD9, CD63, or a combination thereof. In some embodiments, extracellular vesicles of the composition include one or more of miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, miR-29c-3p, miR-658, miR-493-3p, miR-184, and miR-27a-3p.


In some embodiments the composition can increase the proliferation, migration, and/or tube formation of lymphatic endothelial cells, increase expression of one or more lymphatic markers (e.g., hyaluronan receptor-1 (LYVE-1), vascular endothelial growth factor receptor-3 (VEGFR-3), prospero homeobox 1 (Prox1), and/or podoplanin) in lymphatic endothelial cells, increase angiogenesis, increase lymphangiogeneisis, reduce inflammatory response, decrease fibrosis formation, enlarge circumference and/or induce formation of capillary vessels and/or lymphatic vessels, induce formation of vessels that express both vascular and lymphatic markers, increase drainage routes (e.g., for accumulated fluids), increase HIF1-alpha expression and/or activity (e.g., in lymphatic endothelial cells), reduce Prohibitin (PHB) expression and/or activity (e.g., in lymphatic endothelial cells), or a combination thereof in the subject.


The methods typically include administering a subject in need thereof a composition having an effective amount of extracellular vesicles formed by mesenchymal stem cells (MSCs) to, for example, increase generation of the lymphatic system or reduce one or more symptoms of lymphedema. The subject can have lymphedema or one or more symptoms thereof such as swelling of part or all of the arm(s) and/or leg(s), a feeling of heaviness or tightness, restricted range of motion, aching or discomfort, recurring infections, and fibrosis in one or both arms and/or legs. The subject can have a blockage in the lymphatic system, optionally wherein the blockage prevents lymph fluid from draining well, and wherein the fluid buildup leads to swelling.


In some methods, the composition is administered by local injection or infusion at or adjacent to a site of interest, for example in one or both arms and/or legs. The site of interest can be a site of lymphatic blockage and/or lymphedema or another site in need of lymphatic system generation or regeneration. The composition can be administered by any suitable means including, but not limited to, intramuscular, intraperitoneal, intravenous, subcutaneous, or subdermal injection or infusion.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 is a plot showing nanotracking analysis of the size distribution of extracellular vesicles (EV) isolated from conditioned media of adipose-derived stem cells.



FIGS. 2A-2C are bar graphs showing proliferation (2A, WST-8 assay), migration (2B, Boyden chamber assay), and tube length (2C, pixel length per field (×40 magnification, 5 random fields)) of lymphatic endothelial cells (LECs) treated with PBS, HEK 293-EVs, VEGF-C, or adipose-derived stem cells (ADSC)-EVs. For FIGS. 2A and 2B, values are means (SD) (n=6, triplicate) (*P<0.05). For FIG. 2C, values are means (SD) (n=6, duplicate) (*P<0.05).



FIGS. 3A-3H are bar graphs showing mRNA expression levels of LYVE-1 (3A, 3E), VEGFR-3 (3B, 3F), Prox1 (3C, 3G) and podoplanin (3D, 3H) in LECs 12 hrs. (3A-3D) or 24 hrs (3E-3H) after treatment with PBS, VEGF-C, or ADSC-EVs. The samples were analyzed by qRT-PCR to evaluate the expression of genes. The data were normalized based on GAPDH expression and shown as changes relative to PBS group. Values are means (SD) (n=3, triplicate) (*P<0.05 vs PBS). GAPDH indicates glyceraldehyde-3-phosphate dehydrogenase.



FIG. 4A is a schematic illustrating a splinted lymphedema model. After x-ray irradiation in the bilateral inguinal region at 10 Gy in a single dose twice prior to the surgery, mice were subjected to circumferential incision in the inguinal region. After the resection of inguinal lymph nodes, a 3-mm-wide silicone splint was placed in the inguinal wound and then fixed to the skin and underlying muscle to prevent wound contraction and desiccation. As a therapeutic intervention, injection of PBS or ADSC-EVs (˜40 μg) or HEK293-EVs (˜40 μg) as a thin layer to the whole leg area was performed in postoperative day 7 and 14. FIG. 4B is a line graph showing the ratio of hindlimb circumference change over 4 weeks after injections of PBS or ADSC-EVs. FIG. 4C is a bar graph showing quantitation of computed tomographic images of indocyanine green (ICG) lymphography used to assess lymphatic function of the hindlimb, after indocyanine green injection of both feet.



FIGS. 5A-5C are bar graphs showing histological analysis of LYVE-1(+) area (%) (5A), CD31(+) area (%) (5B), CD31(+)/LYVE-1(+) overlap area (%) (5C) per 0.25 mm2 area (four random areas per limb) following treatment with PBS, HEK 293-EVs, or ADSC-EVs. All data represent mean±s.d. with P<0.05 considered as significant.



FIGS. 6A-6B are bar graphs showing collagen 1(+) area (%) (6A) and pSMAD3(+) area (%) (6B) per 0.25 mm2 area (four random areas per limb) after treatments of PBS, HEK293-EVs, or ADSC-EVs. All data represent mean±s.d. with P<0.05 considered as significant.



FIG. 7 is a gene interaction network map illustrating the results of an Ingenuity Pathway Analysis (IPA) evaluating the implications of miRNA expression found to be altered by ADSC-EVs treatment. This map provides the top ranked network found associated with the role of ADSC-EVs in lymphatic endothelial cells.





DETAILED DESCRIPTION OF THE INVENTION
I. Definitions

As used herein, the term “carrier” or “excipient” refers to an organic or inorganic ingredient, natural or synthetic inactive ingredient in a formulation, with which one or more active ingredients are combined.


As used herein, the term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients.


As used herein, the term “pharmaceutically acceptable carrier” encompasses any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water and emulsions such as an oil/water or water/oil emulsion, and various types of wetting agents. As used herein, the terms “effective amount” or “therapeutically effective amount” means a dosage sufficient to alleviate one or more symptoms of a disorder, disease, or condition being treated, or to otherwise provide a desired pharmacologic and/or physiologic effect. The precise dosage will vary according to a variety of factors such as subject-dependent variables (e.g., age, immune system health, etc.), the disease or disorder being treated, as well as the route of administration and the pharmacokinetics of the agent being administered.


As used herein, the term “prevention” or “preventing” means to administer a composition to a subject or a system at risk for or having a predisposition for one or more symptom caused by a disease or disorder to cause cessation of a particular symptom of the disease or disorder, a reduction or prevention of one or more symptoms of the disease or disorder, a reduction in the severity of the disease or disorder, the complete ablation of the disease or disorder, stabilization or delay of the development or progression of the disease or disorder.


As used herein, the terms “subject,” “individual,” and “patient” refer to any individual who is the target of treatment using the disclosed compositions. The subject can be a vertebrate, for example, a mammal. Thus, the subject can be a human. The subjects can be symptomatic or asymptomatic. The term does not denote a particular age or sex. Thus, adult and newborn subjects, whether male or female, are intended to be covered. A subject can include a control subject or a test subject. As used herein, “substantially changed” means a change of at least e.g. 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, or more relative to a control.


As used herein, the term “purified,” “isolated,” and like terms relate to the isolation of a molecule or compound in a form that is substantially free (at least 60% free, preferably 75% free, and most preferably 90% free) from other components normally associated with the molecule or compound in a native environment.


As used herein, the term “antibody” refers to natural or synthetic antibodies that bind a target antigen. The term includes polyclonal and monoclonal antibodies. In addition to intact immunoglobulin molecules, also included in the term “antibodies” are fragments or polymers of those immunoglobulin molecules, and human or humanized versions of immunoglobulin molecules that bind the target antigen.


As used herein, “treatment” refers to the medical management of a patient with the intent to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder. This term includes active treatment, that is, treatment directed specifically toward the improvement of a disease, pathological condition, or disorder, and also includes causal treatment, that is, treatment directed toward removal of the cause of the associated disease, pathological condition, or disorder. In addition, this term includes palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, pathological condition, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated disease, pathological condition, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated disease, pathological condition, or disorder.


As used herein, the terms “inhibit” or “reduce” means to decrease, hinder or restrain a particular characteristic such as an activity, response, condition, disease, or other biological parameter. It is understood that this is typically in relation to some standard or expected value, i.e., it is relative, but that it is not always necessary for the standard or relative value to be referred to. “Inhibits” or “reduce” can also mean to hinder or restrain the synthesis, expression or function of a protein relative to a standard or control. This can include, but is not limited to, the complete ablation of the activity, response, condition, or disease. Inhibition may also include, for example, a 10% reduction in the activity, response, condition, disease, or other biological parameter as compared to the native or control level. Thus, the reduction can be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100%, or any amount of reduction in between as compared to native or control levels.


Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. Use of the term “about” is intended to describe values either above or below the stated value in a range of approx. +/−10%; in other forms the values may range in value either above or below the stated value in a range of approx. +/−5%; in other forms the values may range in value either above or below the stated value in a range of approx. +/−2%; in other forms the values may range in value either above or below the stated value in a range of approx. +/−1%. The preceding ranges are intended to be made clear by context, and no further limitation is implied.


II. Compositions

In general, cell-based therapies have limitations such as uncontrolled differentiation, side effects, tumor formation, and incompatibility of allogenic use. On the contrary, regenerative therapy using extracellular vesicles (EVs) from MSCs have the possibility to overcome such disadvantages cell-based therapies have.


The conditioned medium which contains cultured MSCs secretion have also been reported to have lymphangiogenic effects and therapeutic potential (Takeda et al., Ann Plast Surg., June;74(6):728-36 (2015)). MSCs can secrete cytokines, chemokines, growth factors, and EVs (Katsuda et al., Proteomics, May;13(10-11) (2013)). These EVs are produced by a variety of cell types and may pay a role as intercellular transmitters of mRNA, microRNA, and proteins (Valadi et al., Nature Cell Biology volume 9, pages 654-659 (2007)). There is some evidence indicating that some of the regenerative properties previously credited to MSCs may be related to the secreted EVs (Lai et al., Stem Cell Res., May;4(3):214-22 (2010), Bruno et al., J Am Soc Nephrol., May;20(5):1053-67 (2009)). However, the experiments discussed in the Examples below investigate the therapeutic ability of EVs secreted from ADSCs using in vitro and in vivo experimental systems and demonstrate that ADSC-EVs can modulate the phenotype of lymphatic endothelial cells (LECs), which may contribute to several lymphatic pathophysiological processes. Results further demonstrate the therapeutic potential of ADSC-EVs in relief of lymphedema using a mouse hindlimb lymphedema model. Cell-free compositions including EVs and methods of use thereof are provided. The EVs can be part of a heterogeneous mixture of factors such as conditioned media, or a fraction isolated therefrom. In other embodiments, EVs, or one or more subtypes thereof, are isolated or otherwise collected from conditioned media. The EVs, or one or more subtypes thereof, can be suspended in a pharmaceutically acceptable composition, such as a carrier or matrix or depot, prior to administration to the subject.


A. Extracellular Vesicles


The disclosed compositions typically are or include extracellular vesicles derived from mesenchymal cells, or an isolated or fractionated subtype or subtypes thereof. Extracellular vesicles are lipid bilayer-delimited particles that are naturally released from a cell and, unlike a cell, cannot replicate. EVs range in diameter from near the size of the smallest physically possible unilamellar liposome (around 20-30 nanometers) to as large as 10 microns or more, although the vast majority of EVs are smaller than 200 nm. EVs secreted from MSCs play a role in MSC-mediated paracrine effects via transfer of miRNAs (Spees et al., Stem Cell Res Ther., 7:125 (2016)), and may have effects on wound healing (Zhang et al., J Transl Med., February 1;13:49 (2015)), skin rejuvenation (Kim et al., Biochem Biophys Res Commun., November 18;493(2):1102-1108 (2017)), angiogenesis (Gong et al., Oncotarget, July 11;8(28):45200-45212 (2017)), adjusting immunologic function (Zhao et al., Diabetes, February;67(2):235-247 (2018)), regeneration of damaged tissue (Lai et al., Stem Cell Res., May;4(3):214-22 (2010)) as well as relief neurological disorders (Katsuda et al., Proteomics, May;13(10-11) (2013)). Diverse EV subtypes have been proposed including ectosomes, microvesicles (MV), microparticles, exosomes, oncosomes, apoptotic bodies (AB), tunneling nanotubes (TNT), and more (Yáñez-Mó, et al., J Extracell Vesicles. 4: 27066 (2015) doi:10.3402/jev.v4.27066. PMC 4433489). These EV subtypes have been defined by various, often overlapping, definitions, based mostly on biogenesis (cell pathway, cell or tissue identity, condition of origin) (Théry, et al., J Extracell Vesicles. 7 (1): 1535750 (2018). doi:10.1080/20013078.2018.1535750). However, EV subtypes may also be defined by size, constituent molecules, function, or method of separation. According to minimal information from studies of extracellular vesicles 2018 (MISEV2018)12, EV is a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names (Clotilde, et al., J Extracell Vesicles, 7(1):1535750 (2018)). As discussed in Théry, et al., subtypes of EVs may be defined by:

    • a) physical characteristics of EVs, such as size (“small EVs” (sEVs) and “medium/large EVs” (m/lEVs), with ranges defined, for instance, respectively, <100 nm or <200 nm [small], or >200 nm [large and/or medium]) or density (low, middle, high, with each range defined);
    • b) biochemical composition (CD63+/CD81+−EVs, Annexin A5-stained EVs, etc.); or
    • c) descriptions of conditions or cell of origin (podocyte EVs, hypoxic EVs, large oncosomes, apoptotic bodies).


Thus, in some embodiments, the composition is or includes one or more EV subtypes defined according (a), (b), or (c) as discussed above.


In some embodiments, the vesicles are or include exosomes. Exosomes possess the surface proteins that promote endocytosis and they have the potential to deliver macromolecules. Also, if the exosomes are obtained from the same individual as they are delivered to, the exosomes will be immunotolerant. Due to the technical limitations, previous studies are not sufficient to conclude that exosomes have specific functions compared with other EVs (Clotilde, et al., J Extracell Vesicles, 7(1):1535750 (2018)).


Exosomes are vesicles with the size of 30-150 nm, often 40-100 nm, and are observed in most cell types. Exosomes are often similar to MVs with an important difference: instead of originating directly from the plasma membrane, they are generated by inward budding into multivesicular bodies (MVBs). The formation of exosomes includes three different stages: (1) the formation of endocytic vesicles from plasma membrane, (2) the inward budding of the endosomal vesicle membrane resulting in MVBs that consist of intraluminal vesicles (ILVs), and (3) the fusion of these MVBs with the plasma membrane, which releases the vesicular contents, known as exosomes.


Exosomes have a lipid bilayer with an average thickness of ˜5 nm (see e.g., Li, Theranostics, 7(3):789-804 (2017) doi: 10.7150/thno.18133).


The lipid components of exosomes include ceramide (sometimes used to differentiate exosomes from lysosomes), cholesterol, sphingolipids, and phosphoglycerides with long and saturated fatty-acyl chains. The outer surface of exosomes is typically rich in saccharide chains, such as mannose, polylactosamine, alpha-2,6 sialic acid, and N-linked glycans.


Many exosomes contain proteins such as platelet derived growth factor receptor, lactadherin, transmembrane proteins and lysosome associated membrane protein-2B, membrane transport and fusion proteins like annexins, flotillins, GTPases, heat shock proteins, tetraspanins, proteins involved in multivesicular body biogenesis, as well as lipid-related proteins and phospholipases. These characteristic proteins therefore serve as good biomarkers for the isolation and quantification of exosomes. Another key cargo that exosomes carry is nucleic acids including deoxynucleic acids (DNA), coding and non-coding ribonucleic acid (RNA) like messenger RNA (mRNA) and microRNA (miRNA).


In some embodiments, the vesicles include or are one or more alternative extracellular vesicles, such as ABs, MVs, TNTs, or others discussed herein or elsewhere.


ABs are heterogenous in size and originate from the plasma membrane. They can be released from all cell types and are about 1-5 μm in size.


MVs with the size of 20 nm-1 μm are formed due to blebbing with incorporation of cytosolic proteins. In contrast to ABs, the shape of MVs is homogenous. They originate from the plasma membrane and are observed in most cell types.


TNTs are thin (e.g., 50-700 nm) and up to 100 μm long actin containing tubes formed from the plasma membrane.


The Examples below show that EVs isolated from ADSC were physically homogeneous with a peak of 100 nm (FIG. 1). Thus, in some embodiments, the EVs are between about 20 nm and about 500 nm. In some embodiments, the EVs are between about 20 nm and about 250 nm or 200 nm or 150 nm or 100 nm.


The Examples below show that EVs isolated from ADSC include CD9 and CD63. Thus, in some embodiments, the EVs include CD9, CD63, or both.


The Examples below show that EVs isolated from ADSC include a number of miRNAs. In some embodiments, the EVs include one or more of the miRNA of Table 1. In some embodiments, the EVs include on or more of miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, miR-29c-3p, miR-658, miR-493-3p, miR-184, and miR-27a-3p.


B. Methods of Making Extracellular Vesicles


1. Sources of Cells for Making Extracellular Vesicles


As used herein, EVs, including AB, MV, exosomes, and TNT typically refer to lipid vesicles formed by cells or tissue. They can be isolated from tissue, cells, and fluid directly from a subject, including cultured and uncultured tissue, cells, or fluids, and fluid derived or conditioned by cultured cells (e.g., conditioned media). For example, exosomes are present in physiological fluids such as plasma, lymph liquid, malignant pleural effusion, amniotic liquid, breast milk, semen, saliva and urine, and are secreted into the media of cultured cells.


The EVs of the disclosed compositions are typically formed from mesenchymal cells, preferably mesenchymal stem cells. Mesenchymal stem cells (MSCs) are multipotent adult stem cells that are present in multiple tissues, including umbilical cord, bone marrow and fat tissue. Mesenchymal stem cells can self-renew by dividing and can differentiate into multiple tissues including bone, cartilage, muscle and fat cells, and connective tissue. Thus, mesenchymal cells include, for example, adipocytes, chondrocytes, osteoblasts, myocytes and tendon, and MSCs are multipotent stem cells that can differentiate in one or more of these cell types.


In some embodiments, the EVs are formed by MSCs. MSCs can be derived from bone barrow or other non-marrow tissues, such as placenta, umbilical cord blood, adipose tissue, adult muscle, corneal stroma or the dental pulp of deciduous (baby) teeth.


In some embodiments, the MSCs are derived from adipose tissue. Adipose tissue-derived MSCs (AdMSCs or ADSC), in addition to being easier and safer to isolate than bone marrow-derived MSCs, can be obtained in larger quantities.


Methods of isolating extracellular vesicles from tissue, cells, and fluid directly from a subject, including cultured and uncultured tissue, cells, or fluids, and fluid derived or conditioned by cultured cells (e.g., conditioned media) are known in the art.


See, for example, Li, Themaostics, 7(3):789-804 (2017) doi: 10.7150/thno.18133, Ha, et al., Acta Pharmaceutica Sinica B, 6(4):287-296 (2016) doi: 10.1016/j.apsb.2016.02.001, Skotland, et al., Progress in Lipid Research, 66:30-41 (2017) doi: 10.1016/j.plipres.2017.03.001, Phinney and Pittenger, Stem Cells, 35:851-858 (2017) doi: 10.1002/stem.2575, each of which is specifically incorporated by reference, and describes isolating extracellular vesicles, particularly exosomes.


The EVs can be collected from primary cells or tissue or fluid. In some embodiments, the vesicles are isolated from cells, tissue, or fluid of the subject to be treated. An advantage of utilizing EVs that are isolated from natural sources includes avoidance of immunogenicity that can be associated with artificially produced lipid vesicles.


The EVs can also be collected from cell lines or tissue. Exemplary cells lines are commercially available and include those various sources including human bone-marrow, human umbilical cord, human embryonic tissue, and human adipose including those derived from lipoaspirate or dedifferentiated from mature adipocytes.


2. Methods of Collecting Extracellular Vesicles


Extracellular vesicles, including exosomes, can be isolated using differential centrifugation, flotation density gradient centrifugation, filtration, high performance liquid chromatography, and immunoaffinity-capture.


For example, one of the most common isolation techniques for isolating exosomes from cell culture is differential centrifugation, whereby large particles and cell debris in the culture medium are separated using centrifugal force between 200-100,000×g and the exosomes are separated from supernatant by the sedimenting exosomes at about 100,000×g. Purity can be improved, however, by centrifuging the samples using flotation density gradient centrifugation with sucrose or Optiprep. Tangential flow filtration combined with deuterium/sucrose-based density gradient ultracentrifugation was employed to isolate therapeutic exosomes for clinical trials.


In the experiments provided below, EVs were isolated from ADSCs. After incubation for two days, the medium was collected and centrifuged at 2,000 g for 15 min at room temperature. To thoroughly remove cellular debris, the supernatant was filtered with a 0.22-mm filter unit. Then, the cultured media (CM) was ultracentrifuged at 110,000 g (35,000 rpm) for 70 min at 4° C.


Ultrafiltration and high-performance liquid chromatography (HPLC) are additional methods of isolating EVs based on their size differences. EVs prepared by HPLC are highly purified.


Hydrostatic filtration dialysis has been used for isolating extracellular vesicles from urine.


Other common techniques for EV collection involve positive and/or negative selection using affinity-based methodology. Antibodies can be immobilized in different media conditions and combined with magnetic beads, chromatographic matrix, plates, and microfluidic devices for separation. For example, antibodies against exosome-associated antigens—such as cluster of differentiation (CD) molecules CD63, CD81, CD82, CD9, epithelial cell adhesion molecule (EpCAM), and Ras-related protein (Rab5)—can be used for affinity-based separation of exosomes. Non-exosomes vesicles that carry these or different antigens can also be isolated in a similar way.


Microfluidics-based devices have also been used to rapidly and efficiently isolate EVs such as exosomes, tapping on both the physical and biochemical properties of exosomes at microscales. In addition to size, density, and immunoaffinity, sorting mechanisms such as acoustic, electrophoretic and electromagnetic manipulations can be implemented.


Methods of characterizing EVs including exosomes are also known in the art. Exosomes can be characterized based on their size, protein content, and lipid content. Exosomes are sphere-shaped structures with sizes between 40-100 nm and are much smaller compared to other systems, such as a microvesicle, which has a size range from 100-500 nm. Several methods can be used to characterize EVs, including flow cytometry, nanoparticle tracking analysis, dynamic light scattering, western blot, mass spectrometry, and microscopy techniques. EVs can also be characterized and marked based on their protein compositions. For example, integrins and tetraspanins are two of the most abundant proteins found in exosomes. Other protein markers include TSG101, ALG-2 interacting protein X (ALIX), flotillin 1, and cell adhesion molecules. Similar to proteins, lipids are major components of EVs and can be utilized to characterize them.


C. Pharmaceutical Compositions


Pharmaceutical compositions including EVs are also provided. Pharmaceutical compositions can be administered parenterally (intramuscular (IM), intraperitoneal (IP), intravenous (IV), subcutaneous injection (SubQ), subdermal), transdermally (either passively or using iontophoresis or electroporation), or by any other suitable means, and can be formulated in dosage forms appropriate for each route of administration.


In some embodiments, the compositions are administered systemically, for example, by intravenous or intraperitoneal administration, in an amount effective for delivery of the compositions to targeted cells.


In preferred embodiments, the compositions are administered locally, for example, by injection directly into, or adjacent to, a site to be treated. For example, in some embodiments such as for the treatment of lymphedema, the compositions are injected or otherwise administered directly to the lymphedemic area or the area adjacent thereto (e.g., in the arms or legs).


Typically, local injection causes an increased localized concentration of the compositions which is greater than that which can be achieved by systemic administration.


In some embodiments, the compositions are delivered locally to the appropriate cells by using a catheter or syringe. Other means of delivering such compositions locally to cells include using infusion pumps (for example, from Alza Corporation, Palo Alto, Calif.) or incorporating the compositions into polymeric implants (see, for example, P. Johnson and J. G. Lloyd-Jones, eds., Drug Delivery Systems: Fundamentals and Techniques (Chichester, England: Ellis Horwood Ltd., 1988 ISBN-10: 0895735806), which can effect a sustained release of the material to the immediate area of the implant.


The EV compositions can be provided to the cell either directly, such as by contacting it with the cell, or indirectly, such as through the action of any biological process. For example, the vesicles can be formulated in a physiologically acceptable carrier, and injected into a tissue or fluid surrounding the cell.


Exemplary dosage for in vivo methods are discussed in the experiments below. As further studies are conducted, information will emerge regarding appropriate dosage levels for treatment of various conditions in various patients, and the ordinary skilled worker, considering the therapeutic context, age, and general health of the recipient, will be able to ascertain proper dosing. The selected dosage depends upon the desired therapeutic effect, on the route of administration, and on the duration of the treatment desired.


Generally, for local injection or infusion, dosage may be lower. Generally, the total amount of the active agent administered to an individual using the disclosed vesicles can be less than the amount of unassociated active agent that must be administered for the same desired or intended effect and/or may exhibit reduced toxicity.


In a preferred embodiment the compositions are administered in an aqueous solution, by parenteral injection such as intramuscular, intraperitoneal, intravenous, subcutaneous, subdermal, etc.


The formulation can be in the form of a suspension or emulsion. In general, pharmaceutical compositions are provided including effective amounts of one or more active agents optionally include pharmaceutically acceptable diluents, preservatives, solubilizers, emulsifiers, adjuvants and/or carriers. Such compositions can include diluents, sterile water, buffered saline of various buffer content (e.g., Tris-HCl, acetate, phosphate) at various pHs and ionic strengths; and optionally, additives such as detergents and solubilizing agents (e.g., TWEEN® 20, TWEEN® 80 also referred to as polysorbate 20 or 80), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), and preservatives (e.g., Thimersol, benzyl alcohol) and bulking substances (e.g., lactose, mannitol). Examples of non-aqueous solvents or vehicles are propylene glycol, polyethylene glycol, vegetable oils, such as olive oil and corn oil, gelatin, and injectable organic esters such as ethyl oleate. The formulations may be lyophilized and redissolved/resuspended immediately before use. The formulation may be sterilized by, for example, filtration through a bacterium retaining filter, by incorporating sterilizing agents into the compositions, by irradiating the compositions, or by heating the compositions.


Transdermal formulations may also be prepared. These will typically be ointments, lotions, sprays, or patches, all of which can be prepared using standard technology. Transdermal formulations can include penetration enhancers. Chemical enhancers and physical methods including electroporation and microneedles can work in conjunction with this method.


III. Methods of Use

Methods of using the disclosed compositions are also provided. The experiments below illustrate that EVs from ADSCs promoted proliferation, migration, and tube formation activities, and upregulated gene expression of lymphatic markers in lymphatic endothelial cells. ADSC-EVs increased both LYVE-1 positive lymphatic endothelial cells and CD-31 positive vascular endothelial cells of injected limbs in vivo, and suppressed immunologic activities. These alterations induced by ADSC-EVs resulted in relief the condition of lymphedema.


Thus, in some embodiments, the disclosed compositions are administered to a subject in need thereof in an effective amount. In some embodiments, the amount is effective to increase the proliferation, migration, and/or tube formation of lymphatic endothelial cells, increase expression of one or more lymphatic makers (e.g., hyaluronan receptor-1 (LYVE-1), vascular endothelial growth factor receptor-3 (VEGFR-3), prospero homeobox 1 (Prox1), and/or podoplanin) in lymphatic endothelial cells, increase angiogenesis, increase lymphangiogeneisis, reduce inflammatory response, decrease fibrosis formation, enlarging circumference and/or inducing formation of capillary vessels and/or lymphatic vessels, induce formation of vessels that express both vascular and lymphatic markers, increase drainage routes (e.g., for accumulated fluids), increase HIF1-alpha expression and/or activity (e.g., in lymphatic endothelial cells), reduce Prohibitin (PHB) expression and/or activity (e.g., in lymphatic endothelial cells), or a combination thereof in a subject.


The disclosed compositions and methods are particularly useful for treating a subject having lymphedema, and/or symptoms associated therewith. Thus, in some embodiments, EVs or a subtype or subtypes thereof or a composition thereof, are administered to a subject in need thereof in an effective amount to treat lymphedema, or one or more symptoms associated therewith.


Lymphedema refers to swelling that generally occurs in one or both arms or legs. Lymphedema is generally caused by blockage the lymphatic system. The blockage prevents lymph fluid from draining well, and the fluid buildup leads to swelling.


Lymphedema signs and symptoms, which typically occur in the affected arm(s) and/or leg(s), include: swelling of part or all of the arm(s) and/or leg(s), including fingers or toes, a feeling of heaviness or tightness, restricted range of motion, aching or discomfort, recurring infections, hardening and thickening of the skin (fibrosis).


Draining excess lymphatic fluid is one of the main purposes of lymphedema treatment. To promote remaining drainage function, traditional compression care or microsurgical lymphatic system reconstruction has been performed for lymphedema management (Tashiro, et al., J Plast Reconstr Aesthet Surg., 69(3):368-75 (2016)). Recent advancement of surgical approach to lymphedema has been attempted to create lympho-venous shunts or healthy lymph nodes transplantation from other sites. Thus, in some embodiments, the disclosed methods are combined with one or more of these or other conventional methods of treating lymphedema.


In the studies below, the effects of ADSC-EVs treatment were investigated both in vitro and in vivo situations, and results indicate that inducing both angiogenesis and lymphangiogenesis may lead to the establishment of new connection between capillary vessels and lymphatic vessels. The existence of the route between capillary system and lymphatic system may work lifelong as drainage route of excess lymphatic fluid in affected tissues as a treatment option.


Lymphedema can be caused by the removal of, or damage to, lymph nodes as a part of cancer treatment. Thus, in some embodiments, the subject also has cancer. In some embodiments, the subject does not have cancer.


In some embodiments, the EVs are administered as part of a heterogeneous mixture of factors (e.g., conditioned media, or a fraction isolated therefrom). In some embodiments, EVs or more of more subtypes thereof are isolated or otherwise collected from conditioned media. The EVs or one or more subtypes thereof can be suspended in pharmaceutically acceptable composition, such as a carrier or matrix or depot, prior to administration to the subject.


EVs may possess the versatility and capacity to interact with multiple cell types immediately and remote areas to regulate cellular responses (Zhang et al., Cell Prolif., 49:3-13 (2016)). Thus, although regional or local administration to the site of interest (e.g., the site of lymphedema) or a site adjacent thereto is preferred, systemic administration is also contemplated. Furthermore, although lymphatic endothelial cells are a preferred target, the EVs may also affect other cells in the region of administration that effect the treatment outcome.


The frequency of administration of a method of treatment can be, for example, one, two, three, four or more times daily, weekly, every two weeks, or monthly. In some embodiments, the composition is administered to a subject once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 days. In some embodiments, the frequency of administration is once, twice or three times weekly, or is once, twice or three times every two weeks, or is once, twice or three times every four weeks. In some embodiments, the composition is administered to a subject 1-3 times, preferably 2 times, a week.


In some embodiments, the effect of the disclosed compositions and methods on a subject is compared to a control. For example, the effect of the composition on a particular symptom, pharmacologic, or physiologic indicator (including those mentioned above and elsewhere herein) can be compared to an untreated subject, or the condition of the subject prior to treatment. In some embodiments, the symptom, pharmacologic, or physiologic indicator is measured in a subject prior to treatment, and again one or more times after treatment is initiated. In some embodiments, the control is a reference level, or average determined based on measuring the symptom, pharmacologic, or physiologic indicator in one or more subjects that do not have the disease or condition to be treated (e.g., healthy subjects).


In some embodiments, the effect of the treatment is compared to a conventional treatment that is known in the art, such as one of those discussed herein.


IV. Kits

Dosage units including the disclosed compositions, for example, in a pharmaceutically acceptable carrier for shipping and storage and/or administration are also disclosed. Components of the kit may be packaged individually and can be sterile. In some embodiments, a pharmaceutically acceptable carrier containing an effective amount of the composition is shipped and stored in a sterile vial. The sterile vial may contain enough composition for one or more doses. The composition may be shipped and stored in a volume suitable for administration, or may be provided in a concentration that is diluted prior to administration. In another embodiment, a pharmaceutically acceptable carrier containing drug can be shipped and stored in a syringe.


Kits containing syringes of various capacities or vessels with deformable sides (e.g., plastic vessels or plastic-sided vessels) that can be squeezed to force a liquid composition out of an orifice are provided. The size and design of the syringe will depend on the route of administration. Any of the kits can include instructions for use.


The disclosed compositions and methods can be further understood through the following numbered paragraphs.


1. A method of promoting generation or regeneration of the lymphatic system in a subject comprising administering the subject a composition comprising an effective amount of extracellular vesicles formed by mesenchymal stem cells (MSCs) to increase generation of the lymphatic system. 2. A method of treating a subject for lymphedema comprising administering the subject an effective amount of a composition comprising extracellular vesicles formed by mesenchymal stem cells to increase generation of the lymphatic system.


3. The method of paragraphs 1 or 2, wherein the composition comprises a pharmaceutically acceptable carrier.


4. The method of any one of paragraphs 1-3, wherein the composition is cell-free.


5. The method of any one of paragraphs 1-4, wherein the extracellular vesicles are formed by a method comprising culturing MSCs to produce media conditioned with the extracellular vesicles.


6. The method of paragraph 5, wherein the method further comprises separating extracellular vesicles from the media conditioned by the MSCs.


7. The method of paragraph 6, wherein the composition does not comprise the media conditioned by the MSCs.


8. The method of any one of paragraphs 1-7, wherein the MSCs are primary cells or a cell line.


9. The method of any one of paragraphs 1-8, wherein the MSCs are from bone barrow, placenta, umbilical cord blood, adipose tissue, adult muscle, conical stroma, or the dental pulp of deciduous teeth.


10. The method of any one of paragraphs 1-9, wherein the MSCs are adipose-derived stem cells.


11. The method of any one of paragraphs 1-10, wherein the extracellular vesicles comprise or consist of ectosomes, microvesicles (MV), microparticles, exosomes, oncosomes, apoptotic bodies (AB), tunneling nanotubes (TNT), or a combination thereof.


12. The method of paragraph 11, wherein the extracellular vesicles comprise or consist of exosomes, microvesicles or a combination thereof.


13. The method of any one of paragraphs 1-12, wherein the extracellular vesicles comprise or consist of a vesicles having a size of between about 20 nm and about 500 nm, or between about 20 nm and about 250 nm, or between about 20 nm and about 200 nm, or between about 20 nm and about 150 nm, or between about 20 nm and about 100 nm.


14. The method of any one of paragraphs 1-13, wherein the extracellular vesicles comprise CD9, CD63, or a combination thereof 15. The method of any one of paragraphs 1-14, wherein the extracellular vesicles comprise one or more of miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, miR-29c-3p, miR-658, miR-493-3p, miR-184, and miR-27a-3p.


16. The method of any one of paragraphs 1-15 comprising increasing the proliferation, migration, and/or tube formation of lymphatic endothelial cells, increasing expression of one or more lymphatic markers (e.g., hyaluronan receptor-1(LYVE-1), vascular endothelial growth factor receptor-3 (VEGFR-3), prospero homeobox 1 (Prox1), and/or podoplanin) in lymphatic endothelial cells, increasing angiogenesis, increasing lymphangiogeneisis, reducing inflammatory response, decreasing fibrosis formation, enlarging circumference and/or inducing formation of capillary vessels and/or lymphatic vessels, inducing formation of vessels that express both vascular and lymphatic markers, increasing drainage routes (e.g., for accumulated fluids), increasing HIF1-alpha expression and/or activity, reducing Prohibitin (PHB) expression and/or activity, or a combination thereof in the subject.


17. The method of any one of paragraphs 1-16, wherein the subject has a blockage in the lymphatic system, optionally wherein the blockage prevents lymph fluid from draining well, and wherein the fluid buildup leads to swelling.


18. The method of any one of paragraphs 1-17, wherein the subject has one or more symptoms selected from swelling of part or all of the arm(s) and/or leg(s), a feeling of heaviness or tightness, restricted range of motion, aching or discomfort, recurring infections, and fibrosis in one or both arms and/or legs.


19. The method of any one of paragraphs 1-18, wherein the subject has been diagnosed with lymphedema.


20. The method of any one of paragraphs 1-19, wherein the composition is administered by local injection or infusion at or adjacent to a site of interest.


21. The method of paragraph 20, wherein the site of interest is in one or both arms and/or legs.


22. The method of paragraphs 20 or 21, wherein the site of interest is a site of lymphatic blockage and/or lymphedema.


23. The method of any one of paragraphs 1-22, wherein the composition is administered by intramuscular, intraperitoneal, intravenous, subcutaneous, or subdermal injection.


24. The composition of any one of paragraphs 1-23.


25. A composition comprising an effective amount of extracellular vesicles formed by mesenchymal stem cells (MSCs) suitable for use in the method of any one of paragraphs 1-23.


26. Use of the composition of paragraph 24 or 25 for promoting generation or regeneration of the lymphatic system.


27. Use of the composition of paragraph 24 or 25 for the manufacture of a medicament for promoting generation or regeneration of the lymphatic system.


28. Use of the composition of paragraph 24 or 25 for treating lymphedema.


29. Use of the composition of paragraph 24 or 25 for the manufacture of a medicament for treating lymphedema.


30. A composition, use, or method according to any of the disclosure herein including, but not limited to, the description, the experimental examples, and/or the figures and their descriptions.


EXAMPLES
Example 1
Characteristics of ADSC-Derived EVs Materials and Methods

Cell Culture and Preparation of EVs


Human adipose derived stem cells were purchased from Lonza (Basel, Switzerland) and cultured in Dulbecco's Modified Eagle Medium (DMEM; Nissui Pharmaceutical Co, Tokyo, Japan) supplemented with 10% fetal bovine serum. Primary cells were cultured for 7 days (passage 0), replacing the medium three times weekly. Cell passage was done each week in 0.25% trypsin/2 mM EDTA (37° C., 5 min). All ADSCs were used within the sixth passage.


At approximate 80% confluence, ADSCs were washed with PBS thrice and the culture media were replaced with DMEM containing 0.1% fetal bovine serum. After incubation for two days, the medium was collected and centrifuged at 2,000 g for 15 mM at room temperature. To thoroughly remove cellular debris, the supernatant was filtered with a 0.22-mm filter unit (Millipore). Then, the conditioned media (CM) was ultracentrifuged at 110,000 g (35,000 rpm) for 70 mM at 4° C. using an SW41 rotor (Beckman) (Clotilde, et al., J Extracell Vesicles, 7(1):1535750 (2018)). The pellets were washed with 11 ml PBS, and after ultracentrifugation, they were resuspended in PBS. The protein concentration of the putative EV fraction was determined using a Quant-iT Protein Assay with a Qubit 2.0 Fluorometer (Invitrogen). To determine the size distribution of the EVs, nanoparticle tracking analysis was carried out using the Nanosight system (NanoSight) on samples diluted 500- to 1,000-fold with PBS for analysis. The system focuses a laser beam through a suspension of the particles of interest. These are visualized by light scattering using a conventional optical microscope perpendicularly aligned to the beam axis, which collects light scattered from every particle in the field of view. A 60 s video recorded all events for further analysis by the nanoparticle tracking analysis software. The Brownian motion of each particle was tracked between frames to calculate its size using the Stokes-Einstein equation. Using same procedures and culture media, EVs derived from Human Embryonic Kidney 293 (HEK293) cells (KAC co ltd, Japan) were obtained.


PKH67-Labelled EVs Transfer


Purified EVs derived from ADSCs were labelled with a PKH67 green fluorescence labelling kit (Sigma-Aldrich, Mo., USA). EVs were incubated with 2 mM of PKH67 for 5 min and washed five times using a 100 kDa filter (Microcon YM-100, Millipore) to remove excess dye. PKH67-labelled EVs were used to assess EV uptake in vitro.


Results

Recently, it has been shown that EVs secreted by ADSCs contribute to their paracrine effects. To identify the angiogenic and lymphangiogenic capacity of ADSC-EVs, putative EV fractions were isolated from conditioned media of ADSCs. ADSC-EVs exhibited the characteristic round morphology with bilayer structure under a transmission electron microscope. Nano tracking analysis showed that the size distribution of the isolated EVs was physically homogeneous with a peak diameter of 82 nm (FIG. 1).


Immunoblot analyses showed that tetraspanin CD9 and CD63, reliable exosomal markers, were present in the EV fraction. Fluorescence microscopy analysis demonstrated that the PKH67-labelled EVs had been taken up and was transferred to perinuclear compartments, presumably representative of late endocytic compartments.


Example 2
ADSC-Derived EVs have Lymphangiogenic Effects
Materials and Methods

LEC Culture


Human dermal lymphatic microvascular endothelial cells (HMVEC-dLy Ad) were purchased from Lonza (Basel, Switzerland) and cultured in endothelial growth medium-2-MV(EGM-2-MV; Lonza) that consisted of endothelial basal medium-2 (EBM-2; Lonza) supplemented with 5% fetal bovine serum (FBS), human basic fibroblast growth factor (bFGF), human


VEGF, human insulin like growth factor-1 (IGF-1), human epidermal growth factor, hydrocortisone, ascorbic acid, and gentamicin and amphotericin (SingleQuots; Lonza), according to the manufacturer's instructions. Lymphatic endothelial cells between passages 3 and 6 were used for all experiments in this study.


Proliferation Assay


LEC proliferation assays were performed as previously described (Takeda, et al., Ann Plast Surg., 74(6):728-36 (2015)) LECs were treated with 100 μL of EBM-2 containing PBS, 10 ng/ml recombinant human VEGF-C (rVEGF-C) (R&D Systems, Minneapolis, Minn.), HEK293-EVs, or ADSC-EVs (10 μg/ml) for 48 hours at 37° C. in 5% CO2. Cell proliferation activity was measured using Cell Counting Kit-8 (Dojindo, Kumamoto, Japan), in which 10 μL of the WST-8 assay solution was added to each well and incubated for 4 hours. The absorbance was measured using a microplate reader (Bio-Rad, Hercules, Calif.) at a wavelength of 450 nm.


Migration Assay


LEC migration assays were performed using Transwell chambers with inserts with 8-μm pores (Corning Costar) as previously described (Takeda, et al., Ann Plast Surg., 74(6):728-36 (2015)). The lower chambers were filled with 700 μL of EBM-2 containing PBS, 10 ng/ml rVEGF-C, HEK293-EVs, or ADSC-EVs (10 μg/ml). After incubation for 16 hours at 37° C. in 5% CO2, the cells on the lower surface of the filter were stained using Diff-Quik (Sysmex, Hyogo, Japan).LECs were photographed through the pores at 100x magnification in 10 random fields, and the migrated cells were counted.


Tube Formation Assay


Matrigel tube formation assays were carried out as previously described (Takeda, et al., Ann Plast Surg., 74(6):728-36 (2015)). LECs were seeded onto the coated wells and cultured in 500 μL of EBM-2 containing PBS, 10 ng/ml rVEGF-C, HEK293-EVs, or ADSC-EVs (10 μg/ml). After incubation for 8 hours at 37° C. in 5% CO2, tube formation images were captured at 40× magnification in 5 random fields. For quantification, the tube length was measured using NIH ImageJ software.


Statistical Analysis


All statistical analyses were performed using GraphPad Prism 8 (GraphPad Software, Inc., La Jolla, Calif.). All data were expressed as mean±SEM, with the results in the three groups compared by one-way analysis of variance for more than three groups and t test for two groups, with a value of p<0.05 considered significant.


Results

To investigate the ability of ADSC-EVs to enhance lymphangiogenesis in vitro, the proliferation, migration, and tube formation was investigated in LECs, after addition of ADSC-EVs. Proliferation assay showed that ADSC-EVs markedly increased proliferation (absorbance: 1.51+−0.21, P<0.05) by up to one and one-half times compared with PBS treated group (absorbance: 1.095+−0.11). Similar tendency was observed in VEGF-C treated group (absorbance: 1.62+−0.19, P<0.05), although HEK293-EVs treated group showed no significant changes (absorbance: 1.15+−0.20, P>0.05) (FIG. 2A). Migration assay showed that ADSC-EVs significantly promoted LECs migration (120.1+−12.2, cells/field, P<0.05) compared with PBS treated group (90.2 +−11.2, cells/field), as well as VEGF-C treated group (125.3+−11.7, cells/field, P<0.05). HEK293-EVs did not show a significant difference (102.1+−13.3, cells/field, P>0.05) (FIG. 2B). The role of ADSC-EVs was further assessed in the regulation of LECs tube formation. Morphological analysis showed ADSC-EVs promote tube formation (2620.5+−321.3, pixel/field, P<0.05) of LECs compared with PBS treated group (1317.8+−500.8 pixel/field) (FIG. 2C). VEGF-C treated group showed a significant difference (2593.4+−156.2, pixel/field, P<0.05), however, HEK293-EVs showed no significant difference (1702.1+−280.3, pixel/field, P>0.05) (FIG. 2C) These results indicate that ADSC-EVs have lymphangiogenic molecules such as cytokines or miRNAs that stimulated proliferation, migration, and tube formation of LECs.


Example 3
qRT-PCR Analysis Shows Increased Expression of Lymphatic Marker mRNA after ADS C-Derived EVs Treatment
Materials and Methods

qRT-PCR


To assess the effect of ADSC-EVs on LECs, confluent LECs in 24-well plates were treated with 500 μl of EBM-2 containing PBS, rVEGF-C(10 ng/ml), or ADSC-EVs(10 μg/ml) for 12 or 24 hours. Total RNA was extracted from LECs cultured in each condition using a QIAzol and the miRNeasy Mini Kit (Qiagen, Holden, Germany) according to the manufacturer's protocols. For qRT-PCR analysis, complementary DNA was generated from 1 μg of total RNA using a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). Real-Time PCR system was subsequently performed in triplicate with a 1:15 dilution of cDNA using TaqMan Gene Expression Assays (Applied Biosystems) on a StepOne Real-Time PCR System (Applied Biosystems). Each Assay ID (Thermo Fisher Scientific) is LYVE-1 (Hs00272659_m1), VEFF-R3 (Hs01047677_m1), Prox1 (Hs00896293_m1), and podoplanin (Hs00366766_m1). All mRNA quantification data from cultured cells were normalized to the expression of glyceraldehydes 3-phosphate dehydrogenase (GAPDH).


Results

Lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1), vascular endothelial growth factor receptor-3 (VEGFR-3), prospero homeobox 1 (Prox1), and podoplanin are well known lymphatic markers in LECs. Therefore, expression levels of mRNA of LYVE-1, VEGFR-3, Prox1, and podoplanin in LECs were examined under conditions of PBS, VEGF-C, or ADSC-EVs treatment. The mRNA expression of LYVE-1 was slightly higher in both 12 and 24 hours in the ADSC-EVs treatment group compared to the PBS group. The VEGF-C group showed a similar trend to the ADSC-EVs treatment group. As for VEGFR-3 mRNA expression, it was almost four times higher in 12 hours and twice higher in 24 hours in the ADSC-EVs treatment group than the PBS treatment group. The VEGF-C treated group showed five to six times higher expression than the PBS treated group in 12 hours. The mRNA expression of Prox1 showed no significant differences in 12 hours, however, it was almost 2.5 times higher in the ADSC-EVs treatment group than PBS treatment group, after 24 hours. VEGF-C treatment group showed little expression changes compared to the ADSC-EVs treatment group. The expression levels of Podoplanin were increased 1.5 times higher in ADSC-EVs treatment group than PBS treatment group in 12 hours; however, it showed no significant differences in 24 hours. VEGF-C group showed the same trend as the ADSC-EVs treatment group. See FIGS. 3A-3H.


Example 4
ADSC-Derived EV Improved Hindlimbs Appearance in a Lymphedema Mouse Model
Materials and Methods

Lymphedema Mouse Model, Treatment and Edema Assessment


Lymphedema was established in the bilateral hindlimbs of 10-week-old female C57BL/6J mice (CLEA Japan, Inc., Tokyo, Japan) as previously described (Iwasaki, et al., Plast Reconstr Surg., 139(1):67e-78e (2017)). They were handled according to the guidelines established for animal care at the center and the protocol was approved by the Institutional Animal Care and Use Committee of Jichi Medical University. After gas anesthesia, the mice were subjected to x-ray irradiation in the bilateral inguinal region at 10 Gy in a single dose twice prior to the surgery. The radiation was emitted from an x-ray machine (MX-160Labo, mediXtec, Japan). One week later, mice were subjected to circumferential incision in the inguinal region to the muscle layer. The subiliac and popliteal lymph nodes and the lymphatic vessels entwined around the sciatic veins were removed. To block the superficial lymphatic system, a 3-mm-wide silicone splint was placed in the inguinal wound and then fixed to the skin and underlying muscle using interrupted 6-0 nylon sutures (Bear medic, Tokyo, Japan). This silicon splint placement prevented wound contraction and desiccation. As a therapeutic intervention, injection of PBS (25 μ1) or ADSC-EVs (˜40 μg) or HEK293-EVs (˜40 μg) as a thin layer to the whole leg area was performed in postoperative day 7 and 14. Hindlimb circumference measurements were performed by unblind reviewers at a point 6 mm proximal to the heel at various time points.


Fluorescence lymphography was used to compare the lymphatic structures in swollen hindlimbs treated with PBS or ADSC-EVs every 2 weeks postoperatively using a near-infrared fluorescence camera system (FLUORO, Toa Kogaku, Japan). To examine the thickness of soft tissue postoperatively, we used computed tomography (CT) imaging over 4 weeks postoperatively.


Edema Assessment


To measure the extent of postsurgical edema, hindlimb circumference measurements were performed at a point 6 mm proximal to the heel. In addition, to evaluate the state of lymphedema and the effect of injection of ADSC-EVs, hindlimb circumferences were determined at various time points. Fluorescence lymphography was used to compare lymphatic structures in swollen hindlimbs treated PBS or ADSC-EVs every 2 weeks postoperatively. The animals were clipped and residual hair was removed with a depilatory cream before imaging. Anesthetized mice with isoflurane were placed on a warming pad. A 5-μl volume of a 1-mg/ml solution of indocyanine green (Sigma-Aldrich, St. Louis, Mo.) dissolved in distilled water was injected subcutaneously into the dorsal aspect of both paws using a 26-gauge needle. Fluorescence images were acquired 15 mintes after indocyanine green injection using a near-infrared fluorescence camera system (FLUORO, Toa Kogaku, Japan). Computed tomography (CT) imaging was used to examine the thickness of soft tissue postoperatively, over 4 weeks. Anesthesized mice with isoflurane were placed inside the CT. After the CT images were acquired, the thickness of the soft tissue (length from bone to skin) was measured.


Results

All limbs demonstrated consistent enlargement after radiation, surgical removal of lymph nodes and lymphatic vessels and silicone fixation (FIG. 4A). Although the limb volumes did not return to preoperative levels in these animals, treatment with ADSC-EVs was highly effective in decreasing gross leg swelling (65.1% +−4.5%) as compared with controls (79.4% +−5.1%) (FIG. 4B).


To assess lymphatic function, indocyanine green lymphography of the hindlimb was performed. Using indocyanine green lymphography 4 weeks after the final treatment, clearance of accumulated lymphatic fluid and a clear linear sign of lymphatic channels in ADSC-EVs-treated legs. In contrast, control legs demonstrated pooling of ICG in the whole area and no transport across the zone of surgery (FIG. 4C). This finding was confirmed using computed tomographic (CT) images. The thickness of soft tissue area, which was defined between bone and skin, markedly decreased in the ADSC-EVs treated group compared with the controls, indicating that the excess amount of lymphatic fluid was drained into the venous system.


Example 5
ADSC-Derived EVs Promoted Angiogenesis and Lymphangiogenesis in the Affected Limb
Materials and Methods

Immunohistochemistry


The mice were sacrificed 4 weeks after the final injection of PBS or ADSC-EVs. Skin sections (5 μm) were generated from 6 mm distal to the inguinal wound and 6 mm proximal to the ankle. The tissues were stained with Hoechst 33342 (Dojindo, Tokyo, Japan), lymphatic vessel endothelial receptor-1 (LYVE-1) polyclonal antibodies (bs-1311R-A555, Bioss Antibodies, USA), anti-CD31 polyclonal antibodies (bs-0468R-A647, Bioss Antibodies, USA), SMAD3 polyclonal antibodies (bs-2225R-A488, Bioss Antibodies, USA), and collagen 1 polyclonal antibodies (bs-10423R-A488, Bioss Antibodies, USA). Stained slides were examined under a fluorescence microscope (Keyence, Osaka, Japan). Fluorescence images were captured at 40×magnification in 5 random fields. For quantification, each positive area was measured using NIH ImageJ software by unblind reviewers.


Results

To determine the lymphangiogenic and angiogenic effects of ADSC-EVs in lymphedema leg models in which drainage of lymphatic fluid is obstructed surgically, histologic changes of affected limbs were evaluated. Immunohistochemical analysis of LYVE-1+ vessel counts in the hindlimb tissues of experimental and control legs demonstrated that injection of ADSC-EVs group modestly but significantly increased the total number of capillary lymphatic vessels (25.3%+−5.2%, P<0.05) compared to PBS group and HEK293-EVs group (16.1%+−2.8%, 16.9%+−3.2% respectively) (FIG. 5A). Similarly, analysis of cross-sections obtained from the hindlimb in the mouse models demonstrated increase in the number of CD31+ endothelial cells in the hindlimb tissues treated with ADSC-EVs (12.3%+−3.9%) as compared with PBS or HEK293-EVs (7.7%+−3.3%, 10.2%+−2.2%, respectively) (FIG. 5B). Consistent with the increased number of vascular and lymphatic endothelial cells, an increase of the number of vessels which expressed both CD31+ and LYVE-1+ in tissue samples harvested from the ADSC-EVs(5.2%+−1.1%, P<0.05) group was noted compared to controls (2.1%+−0.2%, 2.3%+−0.3%) (FIG. 5C). These overlapping regions may be the newly connected bypass between lymphatics to capillary vessels, indicating that interstitial transport capacity is greatly increased after ADSC-EVs treatment.


Example 6
ADSC-Derived EVs Decreased Fibrosis After Lymphatic Injury

Because the degree of fibrosis in lymphedema patients correlates with the severity of disease, several markers of fibrosis were analyzed in hindlimbs to understand the effects of ADSC-EVs treatment. ADSC-EVs significantly decreased subdermal type I collagen deposition (32.5%+−4.4%, P<0.05) as compared with PBS group (45.8%+−5.1%) and HEK293-EVs group (42.2%+−4.5%) (FIG. 6A). ADSC-EVs treatment significantly decreased expression of phosphorylated SMAD3 (pSMAD-3) (17.1%+−9.2%, P<0.05), which is a downstream signaling molecule of pro-fibrotic growth factor, compared to PBS group(36.5%+−14.2%) and HEK293-EVs group (23.3%+−10.4%) (FIG. 6B). Taken together, these findings show that ADSC-EVs mitigate the formation of fibrotic response in the setting of lymphedema.


Example 7
ADSC-Derived EVs Contain Several miRNAs Targeting MDM2, HIF1a, and PHB
Materials and Methods

miRNA Expression Profiling by Real-Time PCR Arrays


Total RNA, including miRNA, was extracted from ADSC-EVs and HEK293-EVs using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instruction. From each sample, 15 μl of miRNAs were reverse-transcribed using a miRCURY LNA RT Kit (Qiagen, Netherlands). The cDNA was mixed with 2× PCR master mix (Qiagen, Netherlands). All the real-time PCR-based experiments using a


LightCycler 480 Instrument 2 according to the manufacturer's instructions. For normalization, miRNA expressions were compared between ADSC-EVs and HEK293-EVs. The cycle threshold (2-AACt) method was utilized to calculate the fold change.


mRNA Expression Profiling in LECs by Microarray


To perform a mRNA microarray, 5×10e4 LECs were seeded into 24-well plates and 12 h later EVs from ADSC or PBS as control were added to LECs. Total mRNAs were extracted from LECs 12 h after treatment with the EVs and PBS. For each hybridization, 0.60 μg of Cy3 labeled cRNA were fragmented, and hybridized at 65 degrees for 17 hours to an Agilent SurePrint G3 Human GE v3 8×60K Microarray (Design ID: 072363). After washing, microarrays were scanned using an Agilent DNA microarray scanner.


Intensity values of each scanned feature were quantified using Agilent feature extraction software version 11.5.1.1, which performs background subtractions. Only features that were flagged as no errors (Detected flags) were used and features that were not positive, not significant, not uniform, not above background, saturated, and population outliers (Not Detected and Compromised flags) were excluded. Normalization was performed using Agilent GeneSpring software version 14.9.1 (per chip:normalization to Quantile).


Results

To determine how ADSC-EVs regulate miRNAs associated with various processes, using a real-time RT-PCR-based miRNA array, the expression patterns of 752 different miRNAs were next profiled in ADSC-EVs. The expression patterns of the same miRNAs in HEK293 cells derived EVs were also analyzed as controls. The miRNA PCR array revealed that 396 differentially expressed miRNAs in ADSC-EVs compared to HEK293-EVs. miRNAs expressed over double fold in log2 ratio are shown in Table 1.


Bioinformatic analysis (Ingenuity Pathway Analysis, IPA), was performed to evaluate the implications of the altered miRNA expression. IPA revealed that the major networks which incorporate the predicted targets, include functions such as ‘Organismal injury and abnormalities’, ‘Reproductive system disease’, ‘Inflammatory disease’, and ‘Inflammatory response’.


The cargo of EVs, which includes miRNAs, mRNAs, proteins and other biological components, is transferred from the donor to recipient cells and influences the cellular phenotypes. Therefore, which genes are altered in the LECs treated with the ADSC-EVs or PBS as control were investigated.


Total RNA was extracted from treated LECs, and microarray analyses were performed. Results show that differentially expressed genes among treatments with ADSC-EVs and control PBS, there were clear differences in gene expression in the LECs.


A bioinformatic analysis was conducted using IPA for the relation between highly expressed miRNAs in ADSC-EVs and genes which showed expression changes in LECs after addition of ADSC-EVs (FIG. 7, Table 2). As a result, eight miRNAs such as miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, and miR-29c-3p were found to target and regulate the expression of mouse double minute 2 homolog (MDM2), which contributed to the stability of hypoxiainducible factor-1 alpha (HIF1a) and resulted in angiogenesis and lymphangiogenesis in LECs.. MDM2 is a cellular oncoprotein encoded by a gene located on chromosome 12q13-14. MDM2 can suppress p53, a cancer suppressor gene. Inhibition of MDM2 has anti-inflammatory effects and may lead to treatment of autoimmune diseases and cancer. Previous studies have shown that MDM2 negatively regulates the stability of hypoxia-inducible factor-1 alpha (HIF1a) in protein level. This investigation found that the expression level of HIF1a was elevated in LECs after addition of ADSC-EVs. HIF1a is a transcription factor that controls the cellular response to hypoxia. HIF1a promotes transcription of various proteins such as VEGF, Erythropoietin (EPO) and glucose transporters, and also plays a key role in lymphangiogenesis and angiogenesis. The result indicates that the reduced expression of MDM2 caused by miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, and miR-29c-3p in ADSC-EVs lead to elevation of HIF1a in LECs, which leads to angiogenesis and lymphangiogenesis.


Another target of four miRNAs such as miR-658, miR-493-3p, miR-184, and miR-27a-3p in ADSC-EVs was found to be Prohibitin (PHB). PHB is a membrane protein which regulates a variety of biological processes such as apoptosis, cell cycle, signal transduction and cellular senescence. The downregulation of PHB can lead to angiogenesis (Qian, et al., CNS Neurosci Ther., 19(10):804-12 (2013)).









TABLE 1







miRNAs expressed over double fold in log2 ratio










SEQ ID #
miRname
Log2 Ratio
target sequence













  1
hsa-miR-548c-3p
13.1573
CAAAAAUCUCAAUUACUUUUGC





  2
hsa-miR-214-5p
12.4406
UGCCUGUCUACACUUGCUGUGC





  3
hsa-miR-372-3p
12.4273
AAAGUGCUGCGACAUUUGAGCGU





  4
hsa-miR-206
12.0473
UGGAAUGUAAGGAAGUGUGUGG





  5
hsa-miR-337-5p
11.2373
GAACGGCUUCAUACAGGAGUU





  6
hsa-miR-199a-5p
10.2440
CCCAGUGUUCAGACUACCUGUUC





  7
hsa-miR-214-3p
9.2040
ACAGCAGGCACAGACAGGCAGU





  8
hsa-miR-199a-3p
8.9240
ACAGUAGUCUGCACAUUGGUUA





  9
hsa-miR-370-3p
8.4440
GCCUGCUGGGGUGGAACCUGGU





 10
hsa-miR-100-5p
7.2940
AACCCGUAGAUCCGAACUUGUG





 11
hsa-miR-145-5p
7.2440
GUCCAGUUUUCCCAGGAAUCCCU





 12
hsa-miR-199b-5p
7.1940
CCCAGUGUUUAGACUAUCUGUUC





 13
hsa-miR-143-3p
7.1640
UGAGAUGAAGCACUGUAGCUC





 14
hsa-miR-888-5p
7.0240
UACUCAAAAAGCUGUCAGUCA





 15
hsa-let-71-3p
6.8206
CUGCGCAAGCUACUGCCUUGCU





 16
hsa-let-7 a-2-3p
6.7106
CUGUACAGCCUCCUAGCUUUCC





 17
hsa-miR-137
6.6740
UUAUUGCUUAAGAAUACGCGUAG





 18
hsa-miR-337-3p
6.4640
CUCCUAUAUGAUGCCUUUCUUC





 19
hsa-miR-145-3p
6.3173
GGAUUCCUGGAAAUACUGUUCU





 20
hsa-miR-133b
6.2640
UUUGGUCCCCUUCAACCAGCUA





 21
hsa-miR-208b-3p
5.7706
AUAAGACGAACAAAAGGUUUGU





 22
hsa-miR-493-5p
5.6873
UUGUACAUGGUAGGCUUUCAUU





 23
hsa-let-7b-3p
5.6073
CUAUACAACCUACUGCCUUCCC





 24
hsa-let-71-5p
5.6040
UGAGGUAGUAGUUUGUGCUGUU





 25
hsa-miR-143-5p
5.5773
GGUGCAGUGCUGCAUCUCUGGU





 26
hsa-miR-675-5p
5.4673
UGGUGCGGAGAGGGCCCACAGUG





 27
hsa-miR-136-3p
5.4473
CAUCAUCGUCUCAAAUGAGUCU





 28
hsa-miR-133a-3p
5.3740
UUUGGUCCCCUUCAACCAGCUG





 29
hsa-miR-377-5p
5.2406
AGAGGUUGCCCUUGGUGAAUUC





 30
hsa-let-7b-5p
5.2340
UGAGGUAGUAGGUUGUGUGGUU





 31
hsa-miR-377-3p
5.1840
AUCACACAAAGGCAACUUUUGU





 32
hsa-miR-136-5p
5.1840
ACUCCAUUUGUUUUGAUGAUGGA





 33
hsa-miR-125b-1-3p
5.0673
ACGGGUUAGGCUCUUGGGAGCU





 34
hsa-miR-100-3p
5.040584
CAAGCUUGUAUCUAUAGGUAUG





 35
hsa-miR-125b-5p
4.9640
UCCCUGAGACCCUAACUUGUGA





 36
hsa-miR-127-3p
4.8840
UCGGAUCCGUCUGAGCUUGGCU





 37
hsa-miR-29a-5p
4.8673
ACUGAUUUCUUUUGGUGUUCAG





 38
hsa-miR-135a-3p
4.8106
UAUAGGGAUUGGAGCCGUGGCG





 39
hsa-miR-539-5p
4.7340
GGAGAAAUUAUCCUUGGUGUGU





 40
hsa-miR-424-3p
4.5773
CAAAACGUGAGGCGCUGCUAU





 41
hsa-miR-369-5p
4.5540
AGAUCGACCGUGUUAUAUUCGC





 42
hsa-miR-376a-3p
4.2940
AUCAUAGAGGAAAAUCCACGU





 43
hsa-miR-410-3p
4.2340
AAUAUAACACAGAUGGCCUGU





 44
hsa-miR-376c-3p
4.1940
AACAUAGAGGAAAUUCCACGU





 45
hsa-miR-154-5p
4.1840
UAGGUUAUCCGUGUUGCCUUCG





 46
hsa-miR-409-3p
4.1740
GAAUGUUGCUCGGUGAACCCCU





 47
hsa-miR-146a-5p
4.0940
UGAGAACUGAAUUCCAUGGGUU





 48
hsa-miR-29a-3p
4.0640
UAGCACCAUCUGAAAUCGGUUA





 49
hsa-miR-127-5p
3.9640
CUGAAGCUCAGAGGGCUCUGAU





 50
hsa-miR-382-5p
3.9540
GAAGUUGUUCGUGGUGGAUUCG





 51
hsa-miR-409-5p
3.9273
AGGUUACCCGAGCAACUUUGCAU





 52
hsa-miR-424-5p
3.8540
CAGCAGCAAUUCAUGUUUUGAA





 53
hsa-let-7f-1-3p
3.7873
CUAUACAAUCUAUUGCCUUCCC





 54
hsa-miR-485-3p
3.7140
GUCAUACACGGCUCUCCUCUCU





 55
hsa-miR-369-3p
3.6273
AAUAAUACAUGGUUGAUCUUU





 56
hsa-miR-376a-5p
3.6173
GUAGAUUCUCCUUCUAUGAGUA





 57
hsa-miR-1
3.5940
UGGAAUGUAAAGAAGUAUGUAU





 58
hsa-let-7d-3p
3.5340
CUAUACGACCUGCUGCCUUUCU





 59
hsa-miR-382-3p
3.4973
AAUCAUUCACGGACAACACUU





 60
hsa-miR-668-3p
3.4840
UGUCACUCGGCUCGGCCCACUAC





 61
hsa-miR-487b-3p
3.4340
AAUCGUACAGGGUCAUCCACUU





 62
hsa-miR-411-5p
3.4240
UAGUAGACCGUAUAGCGUACG





 63
hsa-miR-544a
3.4073
AUUCUGCAUUUUUAGCAAGUUC





 64
hsa-miR-889-3p
3.4073
UUAAUAUCGGACAACCAUUGU





 65
hsa-miR-329-3p
3.2840
AACACACCUGGUUAACCUCUUU





 66
hsa-miR-503-5p
3.2540
UAGCAGCGGGAACAGUUCUGCAG





 67
hsa-miR-30c-1-3p
3.2473
CUGGGAGAGGGUUGUUUACUCC





 68
hsa-miR-22-5p
3.1840
AGUUCUUCAGUGGCAAGCUUUA





 69
hsa-miR-658
3.1473
GGCGGAGGGAAGUAGGUCCGUUGGU





 70
hsa-miR-1185-5p
3.1773
AGAGGAUACCCUUUGUAUGUU





 71
hsa-miR-495-3p
3.1240
AAACAAACAUGGUGCACUUCUU





 72
hsa-miR-432-5p
3.1040
UCUUGGAGUAGGUCAUUGGGUGG





 73
hsa-miR-379-5p
3.1040
UGGUAGACUAUGGAACGUAGG





 74
hsa-miR-22-3p
3.0640
AAGCUGCCAGUUGAAGAACUGU





 75
hsa-miR-654-3p
3.0373
UAUGUCUGCUGACCAUCACCUU





 76
hsa-miR-365b-5p
3.0273
AGGGACUUUCAGGGGCAGCUGU





 77
hsa-miR-493-3p
2.9740
UGAAGGUCUACUGUGUGCCAGG





 78
hsa-miR-134-5p
2.9340
UGUGACUGGUUGACCAGAGGGG





 79
hsa-miR-154-3p
2.8740
AAUCAUACACGGUUGACCUAUU





 80
hsa-miR-411-3p
2.8273
UAUGUAACACGGUCCACUAACC





 81
hsa-miR-335-3p
2.7773
UUUUUCAUUAUUGCUCCUGACC





 82
hsa-miR-543
2.7573
AAACAUUCGCGGUGCACUUCUU





 83
hsa-miR-381-3p
2.6940
UAUACAAGGGCAAGCUCUCUGU





 84
hsa-miR-574-3p
2.6640
CACGCUCAUGCACACACCCACA





 85
hsa-miR-379-3p
2.6173
UAUGUAACAUGGUCCACUAACU





 86
hsa-miR-21-5p
2.6040
UAGCUUAUCAGACUGAUGUUGA





 87
hsa-miR-654-5p
2.6040
UGGUGGGCCGCAGAACAUGUGC





 88
hsa-miR-605-5p
2.5573
UAAAUCCCAUGGUGCCUUCUCCU





 89
hsa-miR-29c-3p
2.5440
UAGCACCAUUUGAAAUCGGUUA





 90
hsa-miR-184
2.5040
UGGACGGAGAACUGAUAAGGGU





 91
hsa-miR-193a-5p
2.4940
UGGGUCUUUGCGGGCGAGAUGA





 92
hsa-miR-541-5p
2.4773
AAAGGAUUCUGCUGUCGGUCCCACU





 93
hs a-miR-27 a-3p
2.4740
UUCACAGUGGCUAAGUUCCGC





 94
hsa-miR-494-3p
2.4240
UGAAACAUACACGGGAAACCUC





 95
hsa-miR-376b-3p
2.4140
AUCAUAGAGGAAAAUCCAUGUU





 96
hsa-miR- 144-5p
2.3673
GGAUAUCAUCAUAUACUGUAAG





 97
hsa-miR-1244
2.3473
AAGUAGUUGGUUUGUAUGAGAUGGUU





 98
hsa-miR-323a-3p
2.3440
CACAUUACACGGUCGACCUCU





 99
hsa-miR-335-5p
2.2940
UCAAGAGCAAUAACGAAAAAUGU





100
hsa-miR-21-3p
2.2640
CAACACCAGUCGAUGGGCUGU





101
hs a-let-7 d-5p
2.0940
AGAGGUAGUAGGUUGCAUAGUU





102
hsa-miR-487 a-3p
2.0773
AAUCAUACAGGGACAUCCAGUU
















TABLE 2







Differentially expressed genes in LEC for treatment of EVs or PBS














Fold
Log fold




Expression
change
change




compared to
(ADSC EV
(ADSC EV


GeneSymbol
GeneName
control
vs PBS)
vs PBS)














FOXB1
forkhead box B1
up
19.85
4.31


WWC2-AS1
WWC2 antisense RNA 1
up
19.66
4.30


CFAP61
cilia and flagella associated
up
14.71
3.88



protein 61


CHST10
carbohydrate sulfotransferase 10
up
13.57
3.76


HRK
harakiri, BCL2 interacting
up
12.81
3.68



protein


KLK8
kallikrein-related peptidase 8
up
12.43
3.64


MYHAS
myosin heavy chain gene cluster
up
12.15
3.60



antisense RNA


HTR4
5-hydroxytryptamine (serotonin)
up
11.96
3.58



receptor 4, G protein-coupled


ANAPC1
anaphase promoting complex
up
10.64
3.41



subunit 1


LYPD6B
LY6/PLAUR domain containing
up
9.75
3.29



6B


LIG3
ligase III, DNA, ATP-dependent
up
9.75
3.29


TSPEAR
thrombospondin-type laminin G
up
9.41
3.23



domain and EAR repeats


OR6A2
olfactory receptor, family 6,
up
9.28
3.21



subfamily A, member 2


GRIN2C
glutamate receptor, ionotropic,
up
9.21
3.20



N-methyl D-aspartate 2C


GPR141
G protein-coupled receptor 141
up
9.11
3.19


MUC7
mucin 7, secreted
up
8.51
3.09


ATXN8OS
ATXN8 opposite strand (non-
up
8.14
3.03



protein coding)


KLK13
kallikrein-related peptidase 13
up
8.05
3.01


ADAMTS8
ADAM metallopeptidase with
up
8.01
3.00



thrombospondin type 1 motif, 8


ILF2
interleukin enhancer binding
up
7.59
2.92



factor 2


RMDN2-AS1
RMDN2 antisense RNA 1
up
7.48
2.90


CD300C
CD300c molecule
up
7.44
2.90


LRP1
low density lipoprotein receptor-
up
7.25
2.86



related protein 1


CCDC13
coiled-coil domain containing 13
up
6.77
2.76


POLM
polymerase (DNA directed), mu
up
6.40
2.68


GPER1
G protein-coupled estrogen
up
6.37
2.67



receptor 1


SNORD77
small nucleolar RNA, C/D box
up
6.14
2.62



77


SDC2
syndecan 2
up
5.78
2.53


KRTAP22-1
keratin associated protein 22-1
up
5.76
2.53


SLITRK2
SLIT and NTRK-like family,
up
5.72
2.52



member 2


LRRC7
leucine rich repeat containing 7
up
5.51
2.46


CHRNA2
cholinergic receptor, nicotinic,
up
5.40
2.43



alpha 2 (neuronal)


SEPT3
septin 3
up
5.22
2.39


TSRM
zinc finger domain-related
up
5.14
2.36



protein TSRM


TRAPPC2
trafficking protein particle
up
5.03
2.33



complex 2


WDR5B
WD repeat domain 5B
up
4.97
2.31


PPP1R26-AS1
PPP1R26 antisense RNA 1
up
4.79
2.26


SAMD13
sterile alpha motif domain
up
4.71
2.23



containing 13


RNF180
ring finger protein 180
up
4.69
2.23


ZNF888
zinc finger protein 888
up
4.39
2.14


PTCD2
pentatricopeptide repeat domain
up
4.38
2.13



2


TM4SF5
transmembrane 4 L six family
up
4.37
2.13



member 5


PHGR1
proline/histidine/glycine-rich 1
up
4.33
2.11


LRRC10
leucine rich repeat containing 10
up
4.27
2.09


COL27A1
collagen, type XXVII, alpha 1
up
4.26
2.09


XKR7
XK, Kell blood group complex
up
4.16
2.06



subunit-related family, member 7


NOS1AP
nitric oxide synthase 1 (neuronal)
up
4.11
2.04



adaptor protein


ITLN2
intelectin 2
up
4.11
2.04


PTCD2
pentatricopeptide repeat domain
up
4.05
2.02



2


KRT8
keratin 8, type II
up
3.92
1.97


FAM150B
family with sequence similarity
up
3.85
1.94



150, member B


SNORD19B
small nucleolar RNA, C/D box
up
3.83
1.94



19B


MEGF10
multiple EGF-like-domains 10
up
3.76
1.91


LRIG2
leucine-rich repeats and
up
3.67
1.87



immunoglobulin-like domains 2


LRIT1
leucine-rich repeat,
up
3.62
1.86



immunoglobulin-like and



transmembrane domains 1


OR1L8
olfactory receptor, family 1,
up
3.56
1.83



subfamily L, member 8


CBX3P2
chromobox homolog 3
up
3.54
1.83



pseudogene 2


RAB11FIP4
RAB11 family interacting
up
3.50
1.81



protein 4 (class II)


FSD1L
fibronectin type III and SPRY
up
3.48
1.80



domain containing 1-like


ROR1
receptor tyrosine kinase-like
up
3.45
1.79



orphan receptor 1


CCDC17
coiled-coil domain containing 17
up
3.42
1.78


SLC7A14
solute carrier family 7, member
up
3.42
1.77



14


KCNS1
potassium voltage-gated channel,
up
3.41
1.77



modifier subfamily S, member 1


PRY2
PTPN13-like, Y-linked 2
up
3.40
1.76


TLCD2
TLC domain containing 2
up
3.40
1.76


CEP85L
centrosomal protein 85 kDa-like
up
3.34
1.74


CDC42EP3
CDC42 effector protein (Rho
up
3.29
1.72



GTPase binding) 3


PVRL3-AS1
PVRL3 antisense RNA 1
up
3.24
1.69


NT5DC4
5′-nucleotidase domain
up
3.23
1.69



containing 4


CNOT4
CCR4-NOT transcription
up
3.18
1.67



complex, subunit 4


POFUT1
protein O-fucosyltransferase 1
up
3.17
1.67


PTGER4P2-
PTGER4P2-CDK2AP2P2
up
3.17
1.66


CDK2AP2P2
readthrough transcribed



pseudogene


NCOA2
nuclear receptor coactivator 2
up
3.13
1.65


L2HGDH
L-2-hydroxyglutarate
up
3.12
1.64



dehydrogenase


SIRPG
signal-regulatory protein gamma
up
3.10
1.63


MID1
midline 1
up
3.10
1.63


WDR55
WD repeat domain 55
up
3.10
1.63


GATA6
GATA binding protein 6
up
3.09
1.63


RNF216
ring finger protein 216
up
3.06
1.61


CGN
cingulin
up
3.04
1.60


SERPINI1
serpin peptidase inhibitor, clade I
up
3.01
1.59



(neuroserpin), member 1


LCP1
lymphocyte cytosolic protein 1
up
3.01
1.59



(L-plastin)


NR2F2-AS1
NR2F2 antisense RNA 1
up
3.00
1.59


FLJ43315
asparagine synthetase
up
2.99
1.58



pseudogene


AADAC
arylacetamide deacetylase
up
2.99
1.58


NDUFA6-AS1
NDUFA6 antisense RNA 1 (head
up
2.98
1.57



to head)


PMFBP1
polyamine modulated factor 1
up
2.96
1.57



binding protein 1


RBM23
RNA binding motif protein 23
up
2.96
1.57


CALML3-AS1
CALML3 antisense RNA 1
up
2.96
1.56


CSRNP3
cysteine-serine-rich nuclear
up
2.96
1.56



protein 3


PCDHGC3
protocadherin gamma subfamily
up
2.95
1.56



C, 3


CCDC110
coiled-coil domain containing
up
2.95
1.56



110


SYDE2
synapse defective 1, Rho
up
2.94
1.56



GTPase, homolog 2 (C. elegans)


LRRC7
leucine rich repeat containing 7
up
2.92
1.54


SYNGAP1
synaptic Ras GTPase activating
up
2.91
1.54



protein 1


MMP25
matrix metallopeptidase 25
up
2.88
1.52


PLXDC1
plexin domain containing 1
up
2.87
1.52


SPIN3
spindlin family, member 3
up
2.87
1.52


SP2-AS1
SP2 antisense RNA 1
up
2.87
1.52


FAM178B
family with sequence similarity
up
2.87
1.52



178, member B


FAM104B
family with sequence similarity
up
2.86
1.52



104, member B


SSU72
SSU72 RNA polymerase II CTD
up
2.86
1.52



phosphatase homolog



(S. cerevisiae)


CALY
calcyon neuron-specific vesicular
up
2.86
1.52



protein


ACVR1B
activin A receptor, type IB
up
2.84
1.51


KCTD21-AS1
KCTD21 antisense RNA 1
up
2.84
1.50


GPR173
G protein-coupled receptor 173
up
2.84
1.50


LBX1-AS1
LBX1 antisense RNA 1 (head to
up
2.83
1.50



head)


SPDYE3
speedy/RINGO cell cycle
up
2.82
1.50



regulator family member E3


CHRDL1
chordin-like 1
up
2.82
1.50


CDK20
cyclin-dependent kinase 20
up
2.80
1.49


SLC51B
solute carrier family 51, beta
up
2.80
1.48



subunit


ZBED3-AS1
ZBED3 antisense RNA 1
up
2.78
1.48


ETV4
ets variant 4
up
2.77
1.47


KLHL15
kelch-like family member 15
up
2.75
1.46


TCTE3
t-complex-associated-testis-
up
2.75
1.46



expressed 3


MAGEA2B
melanoma antigen family A, 2B
up
2.74
1.46


SP2-AS1
SP2 antisense RNA 1
up
2.74
1.46


RPAP2
RNA polymerase II associated
up
2.74
1.45



protein 2


ITPK1-AS1
ITPK1 antisense RNA 1
up
2.73
1.45


ATP1A1-AS1
ATP1A1 antisense RNA 1
up
2.73
1.45


C2orf15
chromosome 2 open reading
up
2.72
1.44



frame 15


UBE2E4P
ubiquitin-conjugating enzyme
up
2.71
1.44



E2E 4 pseudogene


OCLN
occludin
up
2.71
1.44


CHAC1
ChaC glutathione-specific
up
2.70
1.43



gamma-glutamylcyclotransferase



1


SPOPL
speckle-type POZ protein-like
up
2.69
1.43


TMEM200B
transmembrane protein 200B
up
2.68
1.42


TMEM184B
transmembrane protein 184B
up
2.68
1.42


GLTPD2
glycolipid transfer protein
up
2.65
1.41



domain containing 2


OBP2B
odorant binding protein 2B
up
2.64
1.40


CYP4Z1
cytochrome P450, family 4,
up
2.64
1.40



subfamily Z, polypeptide 1


CASC11
cancer susceptibility candidate
up
2.63
1.40



11 (non-protein coding)


AHCTF1
AT hook containing transcription
up
2.63
1.40



factor 1


PFKFB2
6-phosphofructo-2-
up
2.62
1.39



kinase/fructose-2,6-



biphosphatase 2


FAM154B
family with sequence similarity
up
2.62
1.39



154, member B


SUPT3H
suppressor of Ty 3 homolog
up
2.61
1.39



(S. cerevisiae)


BAALC
brain and acute leukemia,
up
2.61
1.38



cytoplasmic


RIBC1
RIB43A domain with coiled-
up
2.59
1.37



coils 1


ZNF354C
zinc finger protein 354C
up
2.59
1.37


DIS3E2
DIS3 like 3′-5′ exoribonuclease 2
up
2.58
1.37


HIST1H2AA
histone cluster 1, H2aa
up
2.55
1.35


MYCNOS
MYCN opposite strand
up
2.55
1.35


PLA2G2D
phospholipase A2, group IID
up
2.54
1.34


ANKRD20A19P
ankyrin repeat domain 20 family,
up
2.52
1.33



member A19, pseudogene


SSPO
SCO-spondin
up
2.52
1.33


ARMCX4
armadillo repeat containing, X-
up
2.51
1.33



linked 4


SNAR-G1
small ILF3/NF90-associated
up
2.51
1.33



RNA G1


MYLK3
myosin light chain kinase 3
up
2.50
1.32


NPAS3
neuronal PAS domain protein 3
up
2.49
1.31


HS1BP3-IT1
HS1BP3 intronic transcript 1
up
2.49
1.31



(non-protein coding)


DTX3
deltex 3, E3 ubiquitin ligase
up
2.48
1.31


PGM5P4-AS1
PGM5P4 antisense RNA 1
up
2.46
1.30


SNORA14B
small nucleolar RNA, H/ACA
up
2.46
1.30



box 14B


SLC39A2
solute carrier family 39 (zinc
up
2.46
1.30



transporter), member 2


ZNF287
zinc finger protein 287
up
2.45
1.29


GS1-259H13.2
transmembrane protein 225-like
up
2.45
1.29


MRGPRG
MAS-related GPR, member G
up
2.45
1.29


LRRC17
leucine rich repeat containing 17
up
2.45
1.29


LANCL2
LanC lantibiotic synthetase
up
2.44
1.29



component C-like 2 (bacterial)


ANKEF1
ankyrin repeat and EF-hand
up
2.44
1.29



domain containing 1


PBX2
pre-B-cell leukemia homeobox 2
up
2.43
1.28


CCDC121
coiled-coil domain containing
up
2.42
1.28



121


CRYBA2
crystallin, beta A2
up
2.42
1.28


TMPO-AS1
TMPO antisense RNA 1
up
2.42
1.28


ACSBG1
acyl-CoA synthetase bubblegum
up
2.41
1.27



family member 1


MR1
major histocompatibility
up
2.41
1.27



complex, class I-related


PPIP5K1
diphosphoinositol
up
2.41
1.27



pentakisphosphate kinase 1


TRIM6
tripartite motif containing 6
up
2.41
1.27


CCDC121
coiled-coil domain containing
up
2.41
1.27



121


TUSC5
tumor suppressor candidate 5
up
2.40
1.26


XPO5
exportin 5
up
2.39
1.26


SPDYE8P
speedy/RINGO cell cycle
up
2.39
1.26



regulator family member E8,



pseudogene


CSRNP3
cysteine-serine-rich nuclear
up
2.39
1.26



protein 3


RBM33
RNA binding motif protein 33
up
2.37
1.25


B3GNT7
UDP-GlcNAc:betaGal beta-1,3-
up
2.37
1.24



N-acetylglucosaminyltransferase



7


NME9
NME/NM23 family member 9
up
2.36
1.24


CYP4V2
cytochrome P450, family 4,
up
2.36
1.24



subfamily V, polypeptide 2


CDSN
corneodesmosin
up
2.36
1.24


COL20A1
collagen, type XX, alpha 1
up
2.36
1.24


ZNF192P1
zinc finger protein 192
up
2.35
1.23



pseudogene 1


HERC6
HECT and RLD domain
up
2.35
1.23



containing E3 ubiquitin protein



ligase family member 6


SNORD25
small nucleolar RNA, C/D box
up
2.35
1.23



25


FRS3
fibroblast growth factor receptor
up
2.35
1.23



substrate 3


RGS5
regulator of G-protein signaling
up
2.33
1.22



5


RMST
rhabdomyosarcoma 2 associated
up
2.33
1.22



transcript (non-protein coding)


GAS2L2
growth arrest-specific 2 like 2
up
2.33
1.22


SGPP1
sphingosine-1-phosphate
up
2.32
1.21



phosphatase 1


NIPSNAP3B
nipsnap homolog 3B (C. elegans)
up
2.31
1.21


TAB3
TGF-beta activated kinase
up
2.31
1.21



1/MAP3K7 binding protein 3


RASSF10
Ras association (RalGDS/AF-6)
up
2.31
1.21



domain family (N-terminal)



member 10


PPIL6
peptidylprolyl isomerase
up
2.31
1.20



(cyclophilin)-like 6


MPP4
membrane protein, palmitoylated
up
2.30
1.20



4 (MAGUK p55 subfamily



member 4)


ZNF37A
zinc finger protein 37A
up
2.30
1.20


ATG10
autophagy related 10
up
2.29
1.20


FPR3
formyl peptide receptor 3
up
2.28
1.19


PDP2
pyruvate dehyrogenase
up
2.27
1.18



phosphatase catalytic subunit 2


ZFAND4
zinc finger, AN1-type domain 4
up
2.27
1.18


RHOT1
ras homolog family member T1
up
2.26
1.18


NKAPP1
NFKB activating protein
up
2.26
1.18



pseudogene 1


OPTC
opticin
up
2.26
1.18


FLT4
fms-related tyrosine kinase 4
up
2.26
1.18


OR2AG1
olfactory receptor, family 2,
up
2.26
1.17



subfamily AG, member 1



(gene/pseudogene)


C9orf72
chromosome 9 open reading
up
2.25
1.17



frame 72


PPIP5K1
diphosphoinositol
up
2.25
1.17



pentakisphosphate kinase 1


ASIC3
acid sensing (proton gated) ion
up
2.24
1.17



channel 3


PIK3CD
phosphatidylinositol-4,5-
up
2.24
1.16



bisphosphate 3-kinase, catalytic



subunit delta


FAAHP1
fatty acid amide hydrolase
up
2.24
1.16



pseudogene 1


ZNF641
zinc finger protein 641
up
2.24
1.16


SCN1B
sodium channel, voltage gated,
up
2.24
1.16



type I beta subunit


FCN1
ficolin (collagen/fibrinogen
up
2.22
1.15



domain containing) 1


HIST1H4G
histone cluster 1, H4g
up
2.22
1.15


CEBPA
CCAAT/enhancer binding
up
2.22
1.15



protein (C/EBP), alpha


ANKRD20A8P
ankyrin repeat domain 20 family,
up
2.22
1.15



member A8, pseudogene


MLYCD
malonyl-CoA decarboxylase
up
2.22
1.15


C5orf56
chromosome 5 open reading
up
2.22
1.15



frame 56


HERC6
HECT and RLD domain
up
2.22
1.15



containing E3 ubiquitin protein



ligase family member 6


PRKACB
protein kinase, cAMP-dependent,
up
2.22
1.15



catalytic, beta


SRP14-AS1
SRP14 antisense RNA1 (head to
up
2.22
1.15



head)


C1RL
complement component 1, r
up
2.21
1.15



subcomponent-like


EMR2
egf-like module containing,
up
2.21
1.15



mucin-like, hormone receptor-



like 2


ATPAF1
ATP synthase mitochondrial F1
up
2.21
1.15



complex assembly factor 1


ZNF222
zinc finger protein 222
up
2.20
1.14


SCGB1B2P
secretoglobin, family 1B,
up
2.20
1.14



member 2, pseudogene


CCDC113
coiled-coil domain containing
up
2.20
1.14



113


C15orf48
chromosome 15 open reading
up
2.20
1.14



frame 48


ETV3
ets variant 3
up
2.20
1.14


SCP2
sterol carrier protein 2
up
2.20
1.14


MGC34796
sepiapterin reductase (7,8-
up
2.19
1.13



dihydrobiopterin:NADP+



oxidoreductase) pseudogene


RAP1GAP
RAP1 GTPase activating protein
up
2.19
1.13


MAGOHB
mago-nashi homolog B
up
2.19
1.13



(Drosophila)


ZBED4
zinc finger, BED-type containing
up
2.19
1.13



4


FAM98B
family with sequence similarity
up
2.18
1.13



98, member B


EPHB1
EPH receptor B1
up
2.18
1.13


POM121
POM121 transmembrane
up
2.18
1.12



nucleoporin


SNX21
sorting nexin family member 21
up
2.18
1.12


OR6Y1
olfactory receptor, family 6,
up
2.18
1.12



subfamily Y, member 1


LMBRD2
LMBR1 domain containing 2
up
2.18
1.12


FLVCR2
feline leukemia virus subgroup C
up
2.17
1.12



cellular receptor family, member



2


LRRC15
leucine rich repeat containing 15
up
2.17
1.12


TGFBR3
transforming growth factor, beta
up
2.17
1.12



receptor III


NXT2
nuclear transport factor 2-like
up
2.17
1.11



export factor 2


HCRP1
hepatocellular carcinoma-related
up
2.17
1.11



HCRP1


HEPACAM
hepatic and glial cell adhesion
up
2.16
1.11



molecule


OBSCN
obscurin, cytoskeletal calmodulin
up
2.16
1.11



and titin-interacting RhoGEF


SQSTM1
sequestosome 1
up
2.16
1.11


LGALS8
lectin, galactoside-binding,
up
2.15
1.11



soluble, 8


RHBDL1
rhomboid, veinlet-like 1
up
2.15
1.11



(Drosophila)


KIF21B
kinesin family member 21B
up
2.15
1.10


CEP170
centrosomal protein 170 kDa
up
2.15
1.10


CYP51A1-AS1
CYP51A1 antisense RNA 1
up
2.15
1.10


LIMD1
LIM domains containing 1
up
2.15
1.10


ANKRD53
ankyrin repeat domain 53
up
2.14
1.10


INGX
inhibitor of growth family, X-
up
2.14
1.10



linked, pseudogene


CDH15
cadherin 15, type 1, M-cadherin
up
2.14
1.10



(myotubule)


APCS
amyloid P component, serum
up
2.14
1.10


SYN2
synapsin II
up
2.14
1.10


SMKR1
small lysine-rich protein 1
up
2.13
1.09


KCNK7
potassium channel, two pore
up
2.13
1.09



domain subfamily K, member 7


TEX28
testis expressed 28
up
2.13
1.09


DYNLRB2
dynein, light chain, roadblock-
up
2.13
1.09



type 2


CNNM2
cyclin and CBS domain divalent
up
2.13
1.09



metal cation transport mediator 2


RSG1
REM2 and RAB-like small
up
2.13
1.09



GTPase 1


FRMD8
FERM domain containing 8
up
2.13
1.09


STK33
serine/threonine kinase 33
up
2.13
1.09


OPLAH
5-oxoprolinase (ATP-
up
2.13
1.09



hydrolysing)


EFHC1
EF-hand domain (C-terminal)
up
2.13
1.09



containing 1


C16orf47
chromosome 16 open reading
up
2.13
1.09



frame 47


GSTO2
glutathione S-transferase omega
up
2.12
1.09



2


PTPLB
protein tyrosine phosphatase-like
up
2.12
1.09



(proline instead of catalytic



arginine), member b


HIST1H2APS1
histone cluster 1, H2a,
up
2.12
1.09



pseudogene 1


OR10W1
olfactory receptor, family 10,
up
2.12
1.08



subfamily W, member 1


PEX5
peroxisomal biogenesis factor 5
up
2.12
1.08


ASS1
argininosuccinate synthase 1
up
2.11
1.08


LRRC16B
leucine rich repeat containing
up
2.11
1.08



16B


CWC15
CWC15 spliceosome-associated
up
2.11
1.08



protein


SUV420H1
suppressor of variegation 4-20
up
2.11
1.08



homolog 1 (Drosophila)


TET3
tet methylcytosine dioxygenase 3
up
2.11
1.07


POLD2
polymerase (DNA directed),
up
2.10
1.07



delta 2, accessory subunit


CCDC169
coiled-coil domain containing
up
2.10
1.07



169


QRICH2
glutamine rich 2
up
2.10
1.07


SLC9A5
solute carrier family 9, subfamily
up
2.10
1.07



A (NHE5, cation proton



antiporter 5), member 5


CFAP69
cilia and flagella associated
up
2.10
1.07



protein 69


HSF1
heat shock transcription factor 1
up
2.09
1.07


ACTB
actin, beta
up
2.09
1.06


MYPOP
Myb-related transcription factor,
up
2.09
1.06



partner of profilin


HOXA11
homeobox A11
up
2.08
1.06


GNG12-AS1
GNG12 antisense RNA 1
up
2.08
1.06


TAPBP
TAP binding protein (tapasin)
up
2.08
1.06


DLEU2L
deleted in lymphocytic leukemia
up
2.08
1.06



2-like


TESC
tescalcin
up
2.08
1.06


ITGA8
integrin, alpha 8
up
2.08
1.05


PPARGC1B
peroxisome proliferator-activated
up
2.08
1.05



receptor gamma, coactivator 1



beta


FAM26E
family with sequence similarity
up
2.08
1.05



26, member E


OR2A9P
olfactory receptor, family 2,
up
2.08
1.05



subfamily A, member 9



pseudogene


WHAMMP3
WAS protein homolog associated
up
2.07
1.05



with actin, golgi membranes and



microtubules pseudogene 3


BTNL10
butyrophilin-like 10
up
2.07
1.05


PADI6
peptidyl arginine deiminase, type
up
2.07
1.05



VI


TMEM86A
transmembrane protein 86A
up
2.06
1.04


PARK2
parkin RBR E3 ubiquitin protein
up
2.06
1.04



ligase


MAPT
microtubule-associated protein
up
2.06
1.04



tau


MAGEC1
melanoma antigen family C, 1
up
2.06
1.04


PYCR1
pyrroline-5-carboxylate
up
2.06
1.04



reductase 1


CTBP1-AS2
CTBP1 antisense RNA 2 (head
up
2.05
1.04



to head)


GGCT
gamma-glutamylcyclotransferase
up
2.05
1.04


FAM25A
family with sequence similarity
up
2.05
1.03



25, member A


PTCH1
patched 1
up
2.05
1.03


ALDH5A1
aldehyde dehydrogenase 5
up
2.05
1.03



family, member A1


CCDC68
coiled-coil domain containing 68
up
2.05
1.03


DAB2IP
DAB2 interacting protein
up
2.05
1.03


ATAD3C
ATPase family, AAA domain
up
2.05
1.03



containing 3C


MARVELD2
MARVEL domain containing 2
up
2.04
1.03


KLC4
kinesin light chain 4
up
2.04
1.03


SREK1IP1
SREK1-interacting protein 1
up
2.04
1.03


CHAC2
ChaC, cation transport regulator
up
2.04
1.03



homolog 2 (E. coli)


HDHD3
haloacid dehalogenase-like
up
2.04
1.03



hydrolase domain containing 3


ELMO2
engulfment and cell motility 2
up
2.04
1.03


TMSB4Y
thymosin beta 4, Y-linked
up
2.04
1.03


CYP2B6
cytochrome P450, family 2,
up
2.03
1.02



subfamily B, polypeptide 6


EDNRB
endothelin receptor type B
up
2.03
1.02


ZNF660
zinc finger protein 660
up
2.03
1.02


SLC2A3
solute carrier family 2 (facilitated
up
2.03
1.02



glucose transporter), member 3


ZNF749
zinc finger protein 749
up
2.03
1.02


C2orf27A
chromosome 2 open reading
up
2.03
1.02



frame 27A


STRADA
STE20-related kinase adaptor
up
2.03
1.02



alpha


MIR99AHG
mir-99a-let-7c cluster host gene
up
2.03
1.02



(non-protein coding)


ZNF671
zinc finger protein 671
up
2.02
1.02


CEP44
centrosomal protein 44 kDa
up
2.02
1.02


VPS9D1-AS1
VPS9D1 antisense RNA 1
up
2.02
1.01


SMAD1-AS1
SMAD1 antisense RNA 1
up
2.02
1.01


UBE3C
ubiquitin protein ligase E3C
up
2.02
1.01


PRSS33
protease, serine, 33
up
2.02
1.01


TTC28
tetratricopeptide repeat domain
up
2.02
1.01



28


RASGRF1
Ras protein-specific guanine
up
2.01
1.01



nucleotide-releasing factor 1


CFH
complement factor H
up
2.01
1.01


GNG12-AS1
GNG12 antisense RNA 1
up
2.01
1.01


GUSBP5
glucuronidase, beta pseudogene
up
2.01
1.01



5


MMRN2
multimerin 2
up
2.00
1.00


HIF1A
hypoxia inducible factor 1, alpha
up
2.00
1.00



subunit (basic helix-loop-helix



transcription factor)


ZNF271P
zinc finger protein 271,
up
2.00
1.00



pseudogene


DBF4B
DBF4 zinc finger B
up
2.00
1.00


NRCAM
neuronal cell adhesion molecule
up
2.00
1.00


MKS1
Meckel syndrome, type 1
up
2.00
1.00


GAREML
GRB2 associated, regulator of
down
−6.04
−2.59



MAPK1-like


SNORA2A
small nucleolar RNA, H/ACA
down
−6.04
−2.59



box 2A


MUC3A
mucin 3A, cell surface associated
down
−6.04
−2.59


MAP3K10
mitogen-activated protein kinase
down
−6.12
−2.61



kinase kinase 10


SASS6
spindle assembly 6 homolog
down
−6.15
−2.62



(C. elegans)


BANP
BTG3 associated nuclear protein
down
−6.16
−2.62


TSPAN15
tetraspanin 15
down
−6.23
−2.64


SLC25A17
solute carrier family 25
down
−6.27
−2.65



(mitochondrial carrier;



peroxisomal membrane protein,



34 kDa), member 17


SLC5A1
solute carrier family 5
down
−6.36
−2.67



(sodium/glucose co transporter),



member 1


HYOU1
hypoxia up-regulated 1
down
−6.37
−2.67


MYH3
myosin, heavy chain 3, skeletal
down
−6.38
−2.67



muscle, embryonic


FCRL5
Fc receptor-like 5
down
−6.39
−2.67


DIS3L2
DIS3 like 3′-5′ exoribonuclease 2
down
−6.43
−2.69


SUCNR1
succinate receptor 1
down
−6.44
−2.69


NPBWR1
neuropeptides B/W receptor 1
down
−6.53
−2.71


MDM2
MDM2 proto-oncogene, E3
down
−6.56
−2.71



ubiquitin protein ligase


HIST1H2AC
histone cluster 1, H2ac
down
−6.56
−2.71


KLRC1
killer cell lectin-like receptor
down
−6.58
−2.72



subfamily C, member 1


CDCA7L
cell division cycle associated 7-
down
−6.59
−2.72



like


RNA28S5
RNA, 28S ribosomal 5
down
−6.65
−2.73


MAGT1
magnesium transporter 1
down
−6.68
−2.74


HYDIN
HYDIN, axonemal central pair
down
−6.68
−2.74



apparatus protein


FAM96B
family with sequence similarity
down
−6.70
−2.74



96, member B


FPGT
fucose-1-phosphate
down
−6.70
−2.74



guanylyltransferase


USP45
ubiquitin specific peptidase 45
down
−6.72
−2.75


FAM87A
family with sequence similarity
down
−6.72
−2.75



87, member A


LMO7DN
LMO7 downstream neighbor
down
−6.78
−2.76


LACC1
laccase (multicopper
down
−6.80
−2.77



oxidoreductase) domain



containing 1


BAIAP2-AS1
BAIAP2 antisense RNA 1 (head
down
−6.87
−2.78



to head)


CACNA1I
calcium channel, voltage-
down
−6.88
−2.78



dependent, T type, alpha 11



subunit


MB21D2
Mab-21 domain containing 2
down
−6.91
−2.79


AMOTL1
angiomotin like 1
down
−7.01
−2.81


PALLD
palladin, cytoskeletal associated
down
−7.02
−2.81



protein


HTT
huntingtin
down
−7.09
−2.83


CASC8
cancer susceptibility candidate 8
down
−7.14
−2.84



(non-protein coding)


C11orf68
chromosome 11 open reading
down
−7.20
−2.85



frame 68


ZNF778
zinc finger protein 778
down
−7.25
−2.86


FUT7
fucosyltransferase 7 (alpha (1,3)
down
−7.26
−2.86



fucosyltransferase)


CT55
cancer/testis antigen 55
down
−7.29
−2.87


ULK4
unc-51 like kinase 4
down
−7.51
−2.91


EIF2AK1
eukaryotic translation initiation
down
−7.53
−2.91



factor 2-alpha kinase 1


STON1
stonin 1
down
−7.56
−2.92


NOX1
NADPH oxidase 1
down
−7.63
−2.93


METAP1D
methionyl aminopeptidase type
down
−7.67
−2.94



1D (mitochondrial)


FAM120B
family with sequence similarity
down
−7.68
−2.94



120B


IMPG1
interphotoreceptor matrix
down
−7.76
−2.96



proteoglycan 1


PBX2
pre-B-cell leukemia homeobox 2
down
−7.77
−2.96


POLR2F
polymerase (RNA) II (DNA
down
−7.81
−2.97



directed) polypeptide F


GLI2
GLI family zinc finger 2
down
−7.93
−2.99


MRPL28
mitochondrial ribosomal protein
down
−7.94
−2.99



L28


STEAP3
STEAP family member 3,
down
−8.08
−3.01



metalloreductase


USP2
ubiquitin specific peptidase 2
down
−8.09
−3.02


SEL1L
sel-1 suppressor of lin-12-like
down
−8.21
−3.04



(C. elegans)


PCDH17
protocadherin 17
down
−8.25
−3.04


ASB1
ankyrin repeat and SOCS box
down
−8.30
−3.05



containing 1


PER2
period circadian clock 2
down
−8.39
−3.07


KRT8P12
keratin 8 pseudogene 12
down
−8.45
−3.08


SYNJ2-IT1
SYNJ2 intronic transcript 1 (non-
down
−8.46
−3.08



protein coding)


ADCK5
aarF domain containing kinase 5
down
−8.46
−3.08


ATP2B1
ATPase, Ca++ transporting,
down
−8.49
−3.09



plasma membrane 1


GEMIN2
gem (nuclear organelle)
down
−8.50
−3.09



associated protein 2


EIF4B
eukaryotic translation initiation
down
−8.54
−3.09



factor 4B


IFNK
interferon, kappa
down
−8.63
−3.11


SPATS2L
spermatogenesis associated,
down
−8.63
−3.11



serine-rich 2-like


SUCLG2-AS1
SUCLG2 antisense RNA 1 (head
down
−8.67
−3.12



to head)


OTUD7B
OTU deubiquitinase 7B
down
−8.67
−3.12


HAPLN2
hyaluronan and proteoglycan link
down
−8.69
−3.12



protein 2


TRMT13
tRNA methyltransferase 13
down
−8.72
−3.12



homolog (S. cerevisiae)


PRR27
proline rich 27
down
−8.73
−3.13


RCSD1
RCSD domain containing 1
down
−8.81
−3.14


FBXO24
F-box protein 24
down
−8.99
−3.17


SYK
spleen tyrosine kinase
down
−9.02
−3.17


TMEM129
transmembrane protein 129, E3
down
−9.04
−3.18



ubiquitin protein ligase


CDRT1
CMT1A duplicated region
down
−9.05
−3.18



transcript 1


CDK5RAP3
CDK5 regulatory subunit
down
−9.11
−3.19



associated protein 3


OPTN
optineurin
down
−9.13
−3.19


CYLC1
cylicin, basic protein of sperm
down
−9.21
−3.20



head cytoskeleton 1


CAPN3
calpain 3, (p94)
down
−9.35
−3.23


LARGE-AS1
LARGE antisense RNA 1
down
−9.36
−3.23


CXorf40B
chromosome X open reading
down
−9.44
−3.24



frame 40B


NINL
ninein-like
down
−9.44
−3.24


ETV5
ets variant 5
down
−9.45
−3.24


ZNF585A
zinc finger protein 585A
down
−9.59
−3.26


ARHGAP5-AS1
ARHGAP5 antisense RNA 1
down
−9.63
−3.27



(head to head)


ZNF594
zinc finger protein 594
down
−9.65
−3.27


ALS2
amyotrophic lateral sclerosis 2
down
−9.76
−3.29



(juvenile)


SNX10
sorting nexin 10
down
−9.76
−3.29


LGI2
leucine-rich repeat LGI family,
down
−9.80
−3.29



member 2


BTG3
BTG family, member 3
down
−9.93
−3.31


LCE2A
late cornified envelope 2A
down
−10.02
−3.32


CC2D1B
coiled-coil and C2 domain
down
−10.29
−3.36



containing 1B


DIP2A
DIP2 disco-interacting protein 2
down
−10.43
−3.38



homolog A (Drosophila)


RFNG
RFNG O-fucosylpeptide 3-beta-
down
−10.55
−3.40



N-acetylglucosaminyltransferase


SLN
sarcolipin
down
−10.56
−3.40


NUP98
nucleoporin 98 kDa
down
−10.65
−3.41


NSA2
NSA2 ribosome biogenesis
down
−10.70
−3.42



homolog (S. cerevisiae)


KIF1C
kinesin family member 1C
down
−10.72
−3.42


ZIC3
Zic family member 3
down
−11.34
−3.50


MFAP3
microfibrillar-associated protein
down
−11.37
−3.51



3


GNA15
guanine nucleotide binding
down
−11.46
−3.52



protein (G protein), alpha 15 (Gq



class)


MAGEA6
melanoma antigen family A, 6
down
−11.60
−3.54


MCAT
malonyl CoA:ACP
down
−11.65
−3.54



acyltransferase (mitochondrial)


MCFD2
multiple coagulation factor
down
−12.07
−3.59



deficiency 2


SNORD15A
small nucleolar RNA, C/D box
down
−12.11
−3.60



15A


KCNE5
potassium channel, voltage gated
down
−12.25
−3.61



subfamily E regulatory beta



subunit 5


MAGI2-AS3
MAGI2 antisense RNA 3
down
−12.33
−3.62


NAA60
N(alpha)-acetyltransferase 60,
down
−12.34
−3.63



NatF catalytic subunit


GABBR1
gamma-aminobutyric acid
down
−12.73
−3.67



(GABA) B receptor, 1


TGFB1I1
transforming growth factor beta
down
−12.84
−3.68



1 induced transcript 1


LPAR6
lysophosphatidic acid receptor 6
down
−13.11
−3.71


RNASE7
ribonuclease, RNase A family, 7
down
−13.47
−3.75


MAFG
v-maf avian musculoaponeurotic
down
−13.80
−3.79



fibrosarcoma oncogene homolog



G


COL6A4P1
collagen, type VI, alpha 4
down
−15.64
−3.97



pseudogene 1


NAV2-AS5
NAV2 antisense RNA 5
down
−15.83
−3.98


OR52B2
olfactory receptor, family 52,
down
−17.06
−4.09



subfamily B, member 2


SLC19A1
solute carrier family 19 (folate
down
−17.20
−4.10



transporter), member 1


HIST1H2BM
histone cluster 1, H2bm
down
−17.25
−4.11


LRRC17
leucine rich repeat containing 17
down
−17.46
−4.13


TNFRSF10C
tumor necrosis factor receptor
down
−17.69
−4.15



superfamily, member 10c, decoy



without an intracellular domain


ARHGEF7
Rho guanine nucleotide
down
−18.02
−4.17



exchange factor (GEF) 7


OR4C6
olfactory receptor, family 4,
down
−18.80
−4.23



subfamily C, member 6


CCDC158
coiled-coil domain containing
down
−18.86
−4.24



158


RNFT2
ring finger protein,
down
−19.57
−4.29



transmembrane 2


MAPKAPK5-
MAPKAPK5 antisense RNA 1
down
−19.79
−4.31


AS1


MYO15B
myosin XVB pseudogene
down
−20.06
−4.33


ANKRD54
ankyrin repeat domain 54
down
−20.15
−4.33


CLCA4
chloride channel accessory 4
down
−20.19
−4.34


DNAJB1
DnaJ (Hsp40) homolog,
down
−20.40
−4.35



subfamily B, member 1


REEP3
receptor accessory protein 3
down
−21.78
−4.44


PGBD2
piggyBac transposable element
down
−21.84
−4.45



derived 2


CENPV
centromere protein V
down
−22.45
−4.49


CEP83
centrosomal protein 83 kDa
down
−22.45
−4.49


TMEM200C
transmembrane protein 200C
down
−24.02
−4.59


RALBP1
ralA binding protein 1
down
−24.51
−4.62


DHFRL1
dihydrofolate reductase-like 1
down
−24.69
−4.63


TDRKH
tudor and KH domain containing
down
−25.59
−4.68


ALG3
ALG3, alpha-1,3-
down
−26.75
−4.74



mannosyltransferase


CKS1B
CDC28 protein kinase regulatory
down
−27.57
−4.78



subunit 1B


KIAA1841
KIAA1841
down
−27.85
−4.80


BHLHE41
basic helix-loop-helix family,
down
−28.68
−4.84



member e41


DNAJC3
DnaJ (Hsp40) homolog,
down
−29.22
−4.87



subfamily C, member 3


C3orf17
chromosome 3 open reading
down
−29.27
−4.87



frame 17


GTF2H5
general transcription factor IIH,
down
−29.36
−4.88



polypeptide 5


PTGR1
prostaglandin reductase 1
down
−30.46
−4.93


JUN
jun proto-oncogene
down
−31.81
−4.99


TTC28-AS1
TTC28 antisense RNA 1
down
−32.23
−5.01


CHST2
carbohydrate (N-
down
−32.67
−5.03



acetylglucosamine-6-O)



sulfotransferase 2


KIF22
kinesin family member 22
down
−34.17
−5.09


CRHR1-IT1
CRHR1 intronic transcript 1
down
−34.51
−5.11



(non-protein coding)


ZNF746
zinc finger protein 746
down
−34.76
−5.12


ZNF658
zinc finger protein 658
down
−36.25
−5.18


ALS2
amyotrophic lateral sclerosis 2
down
−38.73
−5.28



(juvenile)


MTHFD1L
methylenetetrahydrofolate
down
−39.85
−5.32



dehydrogenase (NADP+



dependent) 1-like


AMACR
alpha-methylacyl-CoA racemase
down
−41.76
−5.38


COMMD7
COMM domain containing 7
down
−45.82
−5.52


FIP1L1
factor interacting with PAPOLA
down
−47.06
−5.56



and CPSF1


PARP9
poly (ADP-ribose) polymerase
down
−50.35
−5.65



family, member 9


HIPK2
homeodomain interacting protein
down
−50.40
−5.66



kinase 2


AFF4
AF4/FMR2 family, member 4
down
−50.87
−5.67


EPB41L4A
erythrocyte membrane protein
down
−52.62
−5.72



band 4.1 like 4A


ZNF658
zinc finger protein 658
down
−54.60
−5.77


EDARADD
EDAR-associated death domain
down
−60.04
−5.91


PHB
prohibitin
down
−62.21
−5.96


ZNF532
zinc finger protein 532
down
−67.26
−6.07


HOXD-AS2
HOXD cluster antisense RNA 2
down
−69.02
−6.11


DSE
dermatan sulfate epimerase
down
−72.55
−6.18


NR2C1
nuclear receptor subfamily 2,
down
−75.82
−6.24



group C, member 1


ACSF3
acyl-CoA synthetase family
down
−76.12
−6.25



member 3


SNORA11C
small nucleolar RNA, H/ACA
down
−76.18
−6.25



box 11C


TMEM144
transmembrane protein 144
down
−77.84
−6.28


CD2AP
CD2-associated protein
down
−83.67
−6.39


CHML
choroideremia-like (Rab escort
down
−90.20
−6.50



protein 2)


RNF2
ring finger protein 2
down
−106.09
−6.73


HIST1H2BB
histone cluster 1, H2bb
down
−108.05
−6.76


INTS1
integrator complex subunit 1
down
−112.31
−6.81


IFT172
intraflagellar transport 172
down
−118.33
−6.89


PPIA
peptidylprolyl isomerase A
down
−123.27
−6.95



(cyclophilin A)


SLC26A6
solute carrier family 26 (anion
down
−125.10
−6.97



exchanger), member 6


DOPEY1
dopey family member 1
down
−125.80
−6.98


SLC22A23
solute carrier family 22, member
down
−131.70
−7.04



23


SH3BP4
SH3-domain binding protein 4
down
−132.76
−7.05


WDR13
WD repeat domain 13
down
−134.84
−7.08


CSNK1G3
casein kinase 1, gamma 3
down
−141.58
−7.15


ROM1
retinal outer segment membrane
down
−145.30
−7.18



protein 1


MCM4
minichromosome maintenance
down
−148.04
−7.21



complex component 4


HHIP-AS1
HHIP antisense RNA 1
down
−158.31
−7.31


MFAP3L
microfibrillar-associated protein
down
−162.61
−7.35



3-like


ALG1
ALG1,
down
−181.56
−7.50



chitobiosyldiphosphodolichol



beta-mannosyltransferase


TAPT1
transmembrane anterior posterior
down
−183.15
−7.52



transformation 1


AASDHPPT
aminoadipate-semialdehyde
down
−194.22
−7.60



dehydrogenase-



phosphopantetheinyl transferase


RHOU
ras homolog family member U
down
−207.00
−7.69


AP1G2
adaptor-related protein complex
down
−208.91
−7.71



1, gamma 2 subunit


HSPA4
heat shock 70 kDa protein 4
down
−222.32
−7.80


HERC2P2
hect domain and RLD 2
down
−257.78
−8.01



pseudogene 2


PABPC1
poly(A) binding protein,
down
−285.37
−8.16



cytoplasmic 1


ANKRD17
ankyrin repeat domain 17
down
−292.05
−8.19


SERP1
stress-associated endoplasmic
down
−302.29
−8.24



reticulum protein 1


RALGAPB
Ral GTPase activating protein,
down
−322.52
−8.33



beta subunit (non-catalytic)


UBE2Q2P1
ubiquitin-conjugating enzyme
down
−326.90
−8.35



E2Q family member 2



pseudogene 1


PLXNA1
plexin A1
down
−423.72
−8.73


ATXN2
ataxin 2
down
−427.53
−8.74


ANKRD40
ankyrin repeat domain 40
down
−644.04
−9.33


RECK
reversion-inducing-cysteine-rich
down
−655.93
−9.36



protein with kazal motifs


EIF4E2
eukaryotic translation initiation
down
−682.42
−9.41



factor 4E family member 2


CYC1
cytochrome c-1
down
−994.35
−9.96









The above studies, including in vitro experiments and in vivo mouse models of lymphedema, illustrate the potential of therapeutic use of ADSC-EVs for lymphedema treatment. In vitro studies revealed that ADSC-EVs not only have angiogenesis activity, but also lymphangiogeneisis activity. In vivo local injection of ADSC-EVs in lymphedema legs contributed the reduction of enlarged circumference and the induction of capillary vessels and lymphatic vessels. Also, fibrosis of tissue was decreased in ADSC-EVs treatment. Furthermore, the results show that inducing angiogenesis and lymphangiogenesis simultaneously may lead to formation of vessels which expressed both vascular and lymphatic markers and may have function for draining lymphatic system to vascular system, which may work as drainage routes of accumulated fluids and lead to reduction of swelling in lymphedema animal models. Importantly, the results show that lymphedema may be treated with a local application of ADSC-EVs, which also may reduce inflammatory responses, thus decreasing the formation of fibrosis. Results also show that ADSC-EVs contain heterogeneous miRNAs including miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, and miR-29c-3p which target MDM2, and miR-658, miR-493-3p, miR-184, and miR-27a-3p which target PHB, related to lymphangiogenesis and angiogenesis. MDM2 is a cellular oncoprotein encoded by a gene located on chromosome 12q13-14. MDM2 can suppress p53, a cancer suppressor gene (Duffy, et al., Semin Cancer Biol., S1044-579X(20):30160-7 (2020)). The inhibition of MDM2 exerts antiinflammatory effects and may lead to the treatment of autoimmune diseases and cancer (Ebrihim, et al., Histol Histopathol., 30(11):1271-82) (2015). Previous studies have shown that MDM2 negatively regulates the stability of hypoxiainducible factor-1 alpha (HIF1a) at the protein level (Shweta, et al., J Biol Chem., 289(33):22785-97 (2014)). The studies reported herein found that the expression level of HIF1a was elevated in LECs after the addition of ADSC-EVs. HIF1a is a transcription factor that controls the cellular response to hypoxia. HIF1a promotes the transcription of various proteins, such as VEGF, Erythropoietin (EPO) and glucose transporters, and plays a key role in lymphangiogenesis and angiogenesis. Thus, these results are consistent with the conclusions that reduced expression of MDM2 caused by eight lymphangiogenic miRNAs in ADSC-EVs led to increase in HIF1a expression in LECs, which caused angiogenesis and lymphangiogenesis.


Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of skill in the art to which the disclosed invention belongs. Publications cited herein and the materials for which they are cited are specifically incorporated by reference.


Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims
  • 1. A method of promoting generation or regeneration of the lymphatic system in a subject comprising administering the subject a composition comprising an effective amount of extracellular vesicles formed by mesenchymal stem cells (MSCs) to increase generation of the lymphatic system.
  • 2. The method of claim 1, wherein the composition is cell-free.
  • 3. The method of claim 1, wherein the extracellular vesicles are formed by a method comprising culturing MSCs to produce media conditioned with the extracellular vesicles.
  • 4. The method of claim 3, wherein the method further comprises separating extracellular vesicles from the media conditioned by the MSCs.
  • 5. The method of claim 4, wherein the composition does not comprise the media conditioned by the MSCs.
  • 6. The method of claim 1, wherein the MSCs are primary cells or a cell line.
  • 7. The method claim 6, wherein the MSCs are from bone barrow, placenta, umbilical cord blood, adipose tissue, adult muscle, corneal stroma, or the dental pulp of deciduous teeth.
  • 8. The method of claim 7, wherein the MSCs are adipose-derived stem cells.
  • 9. The method of claim 1, wherein the extracellular vesicles comprise or consist of ectosomes, microvesicles (MV), microparticles, exosomes, oncosomes, apoptotic bodies (AB), tunneling nanotubes (TNT), or a combination thereof.
  • 10. The method of claim 9, wherein the extracellular vesicles comprise or consist of exosomes, microvesicles or a combination thereof.
  • 11. The method of claim 10, wherein the extracellular vesicles comprise or consist of a vesicles having a size of between about 20 nm and about 500 nm, or between about 20 nm and about 250 nm, or between about 20 nm and about 200 nm, or between about 20 nm and about 150 nm, or between about 20 nm and about 100 nm.
  • 12. The method of claim 11, wherein the extracellular vesicles comprise CD9, CD36, or a combination thereof
  • 13. The method of claim 11, wherein the extracellular vesicles comprise one or more of miR-199a-3p, miR-145-5p, miR-143-3p, miR-377-3p, miR-100-3p, miR-29a-3p, miR-495-3p, miR-29c-3p, miR-658, miR-493-3p, miR-184, and miR-27a-3p.
  • 14. The method of claim 1 comprising increasing the proliferation, migration, and/or tube formation of lymphatic endothelial cells, increasing expression of one or more lymphatic markers (e.g., hyaluronan receptor-1(LYVE-1), vascular endothelial growth factor receptor-3 (VEGFR-3), prospero homeobox 1 (Prox1), and/or podoplanin) in lymphatic endothelial cells, increasing angiogenesis, increasing lymphangiogeneisis, reducing inflammatory response, decreasing fibrosis formation, enlarging circumference and/or inducing formation of capillary vessels and/or lymphatic vessels, inducing formation of vessels that express both vascular and lymphatic markers, increasing drainage routes (e.g., for accumulated fluids), increasing HIF1-alpha expression and/or activity, reducing Prohibitin (PHB) expression and/or activity, or a combination thereof in the subject.
  • 15. The method of claim 1, wherein the subject has a blockage in the lymphatic system, optionally wherein the blockage prevents lymph fluid from draining well, and wherein the fluid buildup leads to swelling.
  • 16. The method of claim 1, wherein the subject has one or more symptoms selected from swelling of part or all of the arm(s) and/or leg(s), a feeling of heaviness or tightness, restricted range of motion, aching or discomfort, recurring infections, and fibrosis in one or both arms and/or legs.
  • 17. The method of claim 1, wherein the subject has been diagnosed with lymphedema.
  • 18. The method of claim 1, wherein the composition is administered by local injection or infusion at or adjacent to a site of interest.
  • 19. The method of claim 18, wherein the site of interest is in one or both arms and/or legs.
  • 20. The method of claim 18, wherein the site of interest is a site of lymphatic blockage and/or lymphedema.
CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of and priority to U.S. Ser. No. 63/138,969 filed Jan. 19, 2021, and U.S. Ser. No. 63/212,987 filed Jun. 21, 2021, each of which is incorporated by referenced herein in its entirety.

Provisional Applications (2)
Number Date Country
63138969 Jan 2021 US
63212987 Jun 2021 US