Patent Application
20240325326
The contents of the electronic sequence listing (Name: 041824_Sequence Listing_UKRF 2672US.xml; Size: 4,681 bytes; and Date of Creation: Apr. 18, 2024) is herein incorporated by reference in its entirety.
The presently disclosed subject matter generally relates to treatment of pulmonary fibrosis (PF). In particular, certain embodiments of the presently disclosed subject matter relate to methods of treatment that involve inhibiting glycogen utilization in a subject.
Pulmonary fibrosis (PF) is an incurable disease that impacts hundreds of thousands of patients. For PF patients without the possibility of a lung transplant, the only available treatment options are anti-inflammatory agents, which only modestly delay disease progression.
Accordingly, there remains a need in the art for improved treatments for PF.
The presently disclosed subject matter meets some or all of the above-identified needs, as will become evident to those of ordinary skill in the art after a study of information in this document.
This Summary describes several embodiments of the presently disclosed subject matter and, in many cases, lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently disclosed subject matter, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features or all embodiments disclosed herein.
The presently disclosed subject matter includes a method for treating pulmonary fibrosis (PF) in a subject in need thereof. In some embodiments, the method includes administering to the subject an effective amount of a compound selected from the group consisting of a glycogen phosphatase inhibitor, an acid alpha-glucosidase (GAA) inhibitor, a glycogen synthase (GYS) inhibitor, a glycogen phosphorylase (GP) inhibitor, and combinations thereof, or a pharmaceutically acceptable salt thereof.
In some embodiments, the method includes administering a glycogen phosphatase inhibitor to the subject. In some embodiments, the glycogen phosphatase inhibitor is a laforin inhibitor. In some embodiments, the laforin inhibitor is of the formula selected from the group consisting of
In some embodiments, the laforin inhibitor is of the formula of
In some embodiments the laforin inhibitor is a nanobody comprising the sequence of SEQ ID NO: 1, SEQ ID NO: 2, and SEQ ID NO: 3.
In some embodiments, the method includes administering a GAA inhibitor to the subject. In some embodiments, the GAA inhibitor is selected from the group consisting of acarbose, miglitol, voglibose, castanospermine, miglustat, and 1-deoxynojirimycin.
In some embodiments, the method includes administering a GYS inhibitor to the subject. In some embodiments, the GYS inhibitor is of the formula of:
In some embodiments, the GYS inhibitor is of the formula selected from the group consisting of
In some embodiments, the GYS inhibitor is of the formula of
In some embodiments, the GYS inhibitor is guaiacol.
In some embodiments, the method includes administering a GP inhibitor to the subject. In some embodiments, the GP inhibitor is of the formula selected from the group consisting of
In some embodiments, the subject is identified as being at risk for PF. In some embodiments, the subject is identified as having PF. In some embodiments, the subject has at least one of a history of smoking and a family history of PF.
Further features and advantages of the presently disclosed subject matter will become evident to those of ordinary skill in the art after a study of the description, figures, and non-limiting examples in this document.
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are used, and the accompanying drawings of which:
The details of one or more embodiments of the presently-disclosed subject matter are set forth in this document. Modifications to embodiments described in this document, and other embodiments, will be evident to those of ordinary skill in the art after a study of the information provided in this document. The information provided in this document, and particularly the specific details of the described exemplary embodiments, is provided primarily for clearness of understanding and no unnecessary limitations are to be understood therefrom. In case of conflict, the specification of this document, including definitions, will control.
While the terms used herein are believed to be well understood by those of ordinary skill in the art, certain definitions are set forth to facilitate explanation of the presently-disclosed subject matter. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention(s) belong. All patents, patent applications, published applications and publications, GenBank sequences, databases, websites and other published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety. Where reference is made to a URL or other such identifier or address, it is understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.
As used herein, the abbreviations for any protective groups, amino acids and other compounds, are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (see, Biochem. (1972) 11(9):1726-1732).
Although any methods, devices, and materials similar or equivalent to those described herein can be used in the practice or testing of the presently-disclosed subject matter, representative methods, devices, and materials are described herein.
In certain instances, nucleotides and polypeptides disclosed herein are included in publicly-available databases, such as GENBANK® and SWISSPROT. Information including sequences and other information related to such nucleotides and polypeptides included in such publicly-available databases are expressly incorporated by reference. Unless otherwise indicated or apparent the references to such publicly-available databases are references to the most recent version of the database as of the filing date of this Application.
The present application can “comprise” (open ended) or “consist essentially of” the components of the present invention as well as other ingredients or elements described herein. As used herein, “comprising” is open ended and means the elements recited, or their equivalent in structure or function, plus any other element or elements which are not recited. The terms “having” and “including” are also to be construed as open ended unless the context suggests otherwise.
Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including the claims. Thus, for example, reference to “a cell” includes a plurality of such cells, and so forth.
Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about”. Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently-disclosed subject matter.
As used herein, the term “about,” when referring to a value or to an amount of mass, weight, time, volume, concentration or percentage is meant to encompass variations of in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.5%, in some embodiments ±0.1%, in some embodiments ±0.01%, and in some embodiments ±0.001% from the specified amount, as such variations are appropriate to perform the disclosed method.
As used herein, ranges can be expressed as from “about” one particular value, and/or to “about” another particular value. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
As used herein, “optional” or “optionally” means that the subsequently described event or circumstance does or does not occur and that the description includes instances where said event or circumstance occurs and instances where it does not. For example, an optionally variant portion means that the portion is variant or non-variant.
As used herein, the term “treatment” is inclusive of prophylactic treatment and therapeutic treatment. As would be recognized by one of ordinary skill in the art, treatment that is administered prior to clinical manifestation of a condition is prophylactic (i.e., it protects the subject against or reduces the risk of the subject developing the condition). If the treatment is administered after manifestation of the condition, the treatment is therapeutic (i.e., it is intended to diminish, ameliorate, control, or maintain the existing condition and/or side effects associated with the condition). The terms relate to medical management of a subject with the intent to substantially cure, ameliorate, stabilize, or substantially prevent a condition of interest (e.g., disease, pathological condition, or disorder), including but not limited to prophylactic treatment to preclude, avert, obviate, forestall, stop, or hinder something from happening, or reduce the severity of something happening, especially by advance action. As such, the terms treatment or treating include, but are not limited to: inhibiting the progression of a condition of interest; arresting or preventing the development of a condition of interest; reducing the severity of a condition of interest; ameliorating or relieving symptoms associated with a condition of interest; causing a regression of the condition of interest or one or more of the symptoms associated with the condition of interest; and preventing a condition of interest or the development of a condition of interest. The terms includes active treatment, that is, treatment directed specifically toward the improvement of a condition of interest, and also includes causal treatment, that is, treatment directed toward removal of the cause of the condition of interest.
As used herein, the term “effective amount” refers to an amount that is sufficient to achieve the desired prophylactic or therapeutic result or to have an effect on undesired symptoms, but is generally insufficient to cause adverse side effects. The specific effective amount for any particular subject will depend upon a variety of factors including the particular risk or condition being treated and the severity of the condition; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration; the route of administration; the rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed and like factors well known in the medical arts. For example, it is well within the skill of the art to start doses of a compound at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. If desired, the effective daily dose can be divided into multiple doses for purposes of administration. Consequently, single dose compositions can contain such amounts or submultiples thereof to make up the daily dose. The dosage can be adjusted by the individual medical practitioner in the event of any contraindications. Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days. Guidance can be found in the literature for appropriate dosages for given classes of compounds and products.
As will be recognized by one of ordinary skill in the art, the terms “suppression,” “suppressing,” “suppressor,” “inhibition,” “inhibiting” or “inhibitor” do not refer to a complete elimination of a value in all cases. Rather, the skilled artisan will understand that the term “suppressing” or “inhibiting” refers to a reduction or decrease in a measured value, qualitatively or quantitatively. Such reduction or decrease can be determined relative to a control or a prior status of a subject. In some embodiments, the reduction or decrease relative to a control or the prior status of a subject can be about a 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, or 100% decrease.
As used herein, the term “administering” refers to any method of providing a pharmaceutical preparation to a subject. Such methods are well known to those skilled in the art and include, but are not limited to, oral administration, transdermal administration, administration by inhalation, nasal administration, topical administration, intravaginal administration, ophthalmic administration, intraaural administration, intracerebral administration, rectal administration, and parenteral administration, including injectable such as intravenous administration, intra-arterial administration, intramuscular administration, and subcutaneous administration. Administration can be continuous or intermittent. In various aspects, a preparation can be administered therapeutically; that is, administered to treat an existing disease or condition. In further various aspects, a preparation can be administered prophylactically; that is, administered for prevention of a disease or condition. In some embodiments, oral administration is used. In some embodiments, intravenous (IV) administration is used.
As used herein, the term “subject” when referring to a subject having a particular condition or risk thereof, or when referring to a subject in need of treatment for a particular condition or risk thereof, refers to a target of administration, which optionally displays symptoms and/or has risk factures related to the particular condition or risk thereof, as would be considered relevant to one skilled in the medical art of making a diagnosis of the particular condition or risk thereof. As used herein, the term “subject” can refer to a vertebrate, such as a mammal. The term includes human and veterinary subjects. Thus, the subject can be a human, non-human primate, horse, pig, rabbit, dog, sheep, goat, cow, cat, guinea pig, or rodent. The term does not denote a particular age or sex.
As used herein, the term “derivative” refers to a compound having a structure derived from the structure of a parent compound (e.g., a compound disclosed herein) and whose structure is sufficiently similar to those disclosed herein and based upon that similarity, would be expected by one skilled in the art to exhibit the same or similar activities and utilities as the claimed compounds, or to induce, as a precursor, the same or similar activities and utilities as the claimed compounds. Exemplary derivatives include salts, esters, amides, salts of esters or amides, and N-oxides of a parent compound.
As used herein, the term “pharmaceutically acceptable salt” when made in reference to a compound refers to a salt that is pharmaceutically acceptable and that possesses the desired pharmacological activity of the parent compound.
The presently disclosed subject matter includes a method for treating pulmonary fibrosis (PF). As disclosed herein, it has been surprisingly discovered that lysosomal utilization of glycogen within a subject is required for PF progression and that certain enzymes contributing to such glycogen utilization, namely, laforin, a glycogen phosphatase, and acid alpha-glucosidase (GAA), can prove as useful targets for treating PF. In view of such discoveries and it being known that glycogen synthase (GYS) (as a catalyzer of glycogen chain elongation by incorporating residues from UDP-glucose to growing glycogen strands) and glycogen phosphorylase (GP) (as a catalyzer of the release of glucose monomers from stored glycogen polymers) also contribute to glycogen synthesis and/or utilization, it is thus believed that GYS and GP may also serve as useful targets for inhibiting glycogen utilization and treating PF.
Accordingly, certain embodiments of the method for treating PF involve inhibiting glycogen utilization within a subject. In some embodiments, glycogen utilization is inhibited within a subject by virtue of administering to the subject an effective amount of a compound selected from the group consisting of a glycogen phosphatase inhibitor, a GAA inhibitor, a GYS inhibitor, a GP inhibitor, and combinations thereof, or a pharmaceutically acceptable salt thereof.
In some embodiments, the method includes administering an effective amount of a glycogen phosphatase inhibitor, or a pharmaceutically acceptable salt thereof, to the subject. As further disclosed below, the inhibition of the glycogen phosphatase laforin has been discovered as being useful in reducing glycogen utilization and blunting fibrosis burden in vivo. Accordingly, in some embodiments, the method involves administering a laforin inhibitor to the subject. Certain laforin inhibitors which are known in the art and which may be utilized in the method for treating PF include those described in U.S. Patent Application Publication No. 2018/0170862 and U.S. Pat. No. 10,532,977, the entire disclosure of each of which is incorporated herein in its entirety by reference. For example, in some embodiments, the laforin inhibitor compound administered to the subject can be
In some embodiments, the laforin inhibitor administered to the subject is
In some embodiments, the laforin inhibitor may be in the form of a nanobody. In some embodiments, the nanobody comprises the amino acid sequence of INAMA (SEQ ID NO: 1), the amino acid sequence of HISSDNTNYADSVKG (SEQ ID NO: 2), and the amino acid sequence of VATW (SEQ ID NO: 3). In some embodiments, SEQ ID NO: 1, SEQ ID NO: 2, and SEQ ID NO: 3 correspond to a first complementarity determining region (CDR1), a second complementarity determining region (CDR2), and a third complementarity determining region (CDR3), respectively, of the nanobody. One known laforin-inhibiting nanobody which may be utilized as a laforin inhibitor compound administered to the subject is the Nb72 nanobody disclosed in Simmons, Z. R., Sharma, S., Wayne, J., Li, S., Vander Kooi, C. W., and Gentry, M. S. “Generation and characterization of a laforin nanobody inhibitor,” Clinical Biochemistry 93, 80-89 (2021), the entire disclosure of which is incorporated herein by reference. Accordingly, in some embodiments, the nanobody comprises SEQ ID NO: 4. In some embodiments, a combination of glycogen phosphatase inhibitors may be administered to the subject.
As further disclosed below, PF-induced models lacking GAA have been found to exhibit a multi-fold reduction in fibrosis burden relative to controls. Accordingly, in some embodiments, the method involves administering an effective amount a GAA inhibitor, or a pharmaceutically acceptable salt thereof, to the subject. Certain GAA inhibitors which are known in the art and which may be utilized in the method for treating PF include acarbose, miglitol, voglibose, castanospermine, miglustat, and 1-deoxynojirimycin (DNJ). In some embodiments, a combination of GAA inhibitors may be administered to the subject.
In some embodiments, the method involves administering an effective amount of a GYS inhibitor, or a pharmaceutically acceptable salt thereof, to the subject. Certain GYS inhibitors which are known in the art and which may be utilized in the method for treating PF include those described in: U.S. Pat. No. 11,712,432 (the “'432 Patent”); Tang, B. et al., “Discovery and Development of Small-Molecule Inhibitors of Glycogen Synthase” Journal of medicinal chemistry 63, 3538-3551 (2020) (“Tang”); and Ullman, et al., “Small-Molecule Inhibition of Glycogen Synthase 1 for the Treatment of Pompe Disease and Other Glycogen Storage Disorders” Science Translational Medicine Vol. 16, Issue 730 (2024) (“Ullman”), the entire disclosure of each of which is incorporated herein in its entirety by reference. For example in some embodiments the GYS inhibitor can be: guaicaol (as disclosed in the '432 Patent);
(as disclosed in Ullman); or a compound of the formula R
(as disclosed in Tang). In some embodiments, a combination of GYS inhibitors may be administered to the subject.
In some embodiments, the method involves administering an effective amount of a GP inhibitor, or a pharmaceutically acceptable salt thereof, to the subject. Certain GP inhibitors which are known in the art and which may be utilized in the method for treating PF include those described in: MedChem Express, CP-91149 Product Data Sheet, available at https://file.medchemexpress.com/batch_PDF/HY-13525/CP-91149-DataSheet-MedChemExpress.pdf (accessed Feb. 14, 2024) (“MedChem”); Huang, et al., “A Novel 5-Chloro-N-phenyl-1H-indole-2-carboxamide Derivative as Brain-Type Glycogen Phosphorylase Inhibitor: Validation of Target PYGB” Molecules 28(4): 1697 (2023) (“Huang”); and Bergans, et al., “Molecular Mode of Inhibition of Glycogenolysis in Rat Liver by the Dihydropyridine Derivative, BAY 3401: Inhibition and Inactivation of Glycgogen Phosphorylase by an Activated Metabolite” Diabetes 40(9): 1419-1426 (2000) (“Bergans”), the entire disclosure of each of which is incorporated herein by reference. For example, in some embodiments, the GP inhibitor can be
(as disclosed in MedChem),
(5-Chloro-N-phenyl-1H-indole-2-carboxamide derivative) (as disclosed in Huang), or
(as disclosed in Bergans). In some embodiments, a combination of GP inhibitors may be administered to the subject.
In some embodiments, the method may involve administering a combination including two or more of a glycogen phosphatase inhibitor, a GAA inhibitor, a GYS inhibitor, and a GP inhibitor, of pharmaceutically acceptable salts thereof, to the subject.
In some embodiments, the compound administered to the subject may comprise a derivative of one or more of the glycogen phosphatase, GAA, GYS, and GP compounds identified above.
In some embodiments, the method further involves identifying a subject as having PF or being at risk for PF. In some embodiments, the subject is identified as having PF. In some embodiments, the subject is identified as being at risk for PF. In some embodiments, the subject has a history of smoking and/or a family history of PF. In some embodiments, the subject has another risk factor associated with PF, such as prolonged exposure to air pollution.
A subject may be identified as having or being at risk of having PF based on one or more of: the subject's medical history; the subject's history of smoking, the subject's familial medial history, particularly with respect to familial history of PF; the results of one or more imaging tests, such as a chest x-ray, a computerized tomography (CT) scan, and an echocardiogram; the results of one or more lung function tests, such as pulmonary function testing, pulse oximetry, exercise stress test, arterial and blood gas test; the results of one or more tissue samples acquired, e.g., by bronchoscopy or surgical biopsy; and the results of one or more blood tests. In some embodiments, a subject may be identified as having or at risk of having PF based on a medical professional's diagnosis of the subject. As used herein, the phrase “at risk of having PF” is inclusive of instances in which a subject is suspected but not yet diagnosed as having PF as well as instances in which a subject is at risk of developing PF as a result of the subject's medical history, the subject's familial medical history, the subject having a history of smoking, the subject having a history of prolonged exposure to air pollution, and/or the subject having another risk factor associated with PF.
The presently-disclosed subject matter is further illustrated by the following specific but non-limiting examples. The following examples may include compilations of data that are representative of data gathered at various times during the course of development and experimentation related to the present invention.
MALDI mass spectrometry imaging (MSI) has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction and spatial clustering (HDR-SC) and histopathological annotation/prediction of MALDI-MSI datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesized that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis using bleomycin in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed blunted N-linked glycan levels and nearly 90% reduction in endpoint fibrosis when compared to WT animals. Collectively, we provide conclusive evidence that lysosomal utilization of glycogen is required for pulmonary fibrosis progression. In summary, our study provides a roadmap to leverage spatial metabolomics to understand foundational biology in pulmonary diseases.
Mapping genotype to phenotype with near single-cell resolution and spatial definition is a major innovation in next-generation life science techniques. Recent improvements in RNA sequencing technologies that allow the detailed analysis of a single isolated cell from host tissues is a major advancement in achieving this goal. The resolution of single-cell RNA sequencing (scRNAseq) technology has impressive resolution that allows interrogation of tissue complexity and interactive networks at a cellular level1-4. The scRNAseq workflow has allowed researchers to study complex cellular heterogeneity from diseased and healthy tissues, revealing complex and rare cell populations, while uncovering regulatory relationships and tracking distinct cell lineages during development5-8. Current single-cell approaches include cell-separation-based methods that are focused on molecular features such as proteins, lipids, and metabolites9-11. To this end, in situ-based spatial technologies are beginning to emerge that can be mapped to anatomical regions, bridging the gap between genotype to phenotype analysis12,13.
Complex carbohydrates such as N-linked glycans and glycogen are dynamic macrometabolites that impact complex and intertwined biochemical pathways14,15. Anabolic pathways for the biosynthesis of glycogen and N-linked glycans span multiple cellular compartments including the nucleus, cytoplasm, endoplasmic reticulum, Golgi, and the plasma membrane14-17. Together, complex carbohydrates modulate a myriad of cellular functions including bioenergetics, epigenetics, protein-ligand binding, membrane transport activity, and protein turnover18. N-linked glycans are especially critical as structural components for anatomical regions, and are vital for immune modulation and organ function19. They are highly concentrated in pulmonary fibrosis and are part of the extracellular collagen, proteoglycan, and N-linked glycan matrix to support fibroblast growth and contribute to remodeled lung architecture, function and hindering gas exchange20,21. Oligomerization of simple sugars to glycogen results in increased polarity and decreased solubility; therefore, quantitative, and spatial analyses of complex carbohydrates has been challenging. To address this limitation, a new technique was recently developed employing enzyme-assisted matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) that can simultaneously perform spatial profiling of both glycogen and N-linked glycans from formalin-fixed paraffin-embedded (FFPE) mammalian tissue sections in situ, preserving important anatomical regionsis15,22.
MALDI-MSI utilizes robotic precision micromovement coupled to a Nd:YAG laser for spatial profiling of both organic and biological matter23-25. It is capable of high sampling aptitude with the ability to record tens of thousands of pixel-mapped spectra from a single tissue section coupled with spatial resolution26-29. The end result is a multidimensional, information-rich dataset containing metabolic features from normal and diseased tissues24,30-32. Recent advances in MALDI-MSI enable the detection of complex carbohydrates such as proteoglycans33, N-linked glycans34, and glycogen architecture15,22 from FFPE tissue sections. The ability to utilize FFPE tissue sections dramatically increases the accessibility to banked clinical specimens with up to decades of patient-matched metadata. These analyses are hypothesis-generating in nature and can illuminate previously unknown regional or cellular-specific metabolic events that can be tested for translational therapeutic interventions.
In these studies, we demonstrate the application of high-dimensionality reduction and spatial clustering (HDR-SC) of MALDI-MSI datasets to map histopathological regions of human FFPE specimens. Further, we identified a set of unique carbohydrate features that predict fibrotic tissue with near 99.6% accuracy in a cohort of human diseased lung tissues. Targeted analysis of enriched features in fibrotic tissues reveal unique sets of complex carbohydrates as previously unidentified metabolic hallmark of human PF tissues. Finally, using both genetically modified mouse models and the bleomycin-induced mouse model of pulmonary fibrosis (PF), we demonstrate that glycogen utilization through the lysosomal salvage pathway and metabolic channeling between glycogen and N-linked glycans are critical for fibrosis development in vivo.
Chemicals, Reagents, and Cell Lines. High-performance liquid chromatography-grade acetonitrile, ethanol, methanol, water, trifluoroacetic acid (TFA), bleomycin (B5507, Lot #SLCG3757), and recombinant isoamylase were purchased from Sigma-Aldrich. α-cyano-4-hydroxycinnamic acid (CHCA) matrix was purchased from Cayman Chemical. Histological-grade xylenes were purchased from Spectrum Chemical. Citraconic anhydride for antigen retrieval was obtained from Thermo Fisher Scientific. Recombinant PNGaseF Prime was obtained from N-Zyme Scientifics (Doylestown, PA, USA). Normal lung fibroblast isolated from adult lung tissue and diseased lung fibroblast isolated from adult idiopathic pulmonary fibrosis lung tissue were purchased from Lonza, USA (Cat #CC-2512 and CC-7231 respectively). 13C6-glucose was purchased from Cambridge Isotope Laboratories, Inc (Cat #CLM-1396-pk).
Mouse Models. Mice were housed in a climate-controlled environment with a 14 (light)/10 (dark) hours light/dark cycle with temperature and humidity control. Water and solid diet provided ad libitum throughout the study. Epm2a−/− mice, referred to as laforin knockout (LKO), were previously described95. In brief, DNA sequence encoding the laforin dual specificity phosphatase domain was replaced with a neomycin domain. Wild-type (WT) C57BL/6J mice were purchased from Jackson Laboratory. Male and female mice between 3- and 6-months of age were anesthetized by i.p. injection of xylazine (AnaSed, Akorn) and ketamine (Ketathesia, Henry Schein) and received intratracheal (IT) instillation of a single dose of 0.3 U/kg of bleomycin sulfate from Streptomyces verticillus (Sigma-Aldrich) dissolved in 50 μL sterile saline. Control mice received saline IT. Mice were monitored and weighed daily throughout the study. At the experimental end point (24 hr after 21 days), mice were sacrificed followed by immediate resection of the lungs. The University of Kentucky Institutional Animal Care and Use Committee has approved all of the animal procedures.
Tissue Procurement. Mice were sedated with ketamine (100 mg/kg) and xylazine (10 mg/kg) followed by exsanguination and immediate resection of the lungs which were fixed in neutral-buffered formalin (NBF) for 24 hr then switched to 70% ethanol and paraffin-embedded for long-term storage. De-identified human patient tissues were obtained from the University of Kentucky Biospecimen Procurement and Translation Pathology Shared Resource Facility. Human tissues were also preserved in NBF and paraffin embedded for long-term storage. All hematoxylin & eosin (H&E) staining was performed by the University of Kentucky Biospecimen Procurement and Translation Pathology Shared Resource Facility using the method previously described96.
Formalin-fixed Paraffin-Embedded Slide Preparation for MALDI-MSI. Tissues were sectioned at 4 μm and mounted on positively charged glass slides for MALDI imaging as previously described97. Slides were heated at 60° C. for 1 hr. After cooling, tissue sections were deparaffinized by washing twice in xylene (3 min each). Tissue sections were then rehydrated by washing slides twice in 100% ethanol (1 min each), once in 95% ethanol (1 min), once in 70% ethanol (1 min), and twice in water (3 min each). Following washes, slides were transferred to a coplin jar containing citraconic anhydride buffer for antigen retrieval and the jar was placed in a vegetable steamer for 25 min. Citraconic anhydride buffer was prepared by adding 25 μL citraconic anhydride in 50 mL water and adjusted to pH 3.0 with HCl. After antigen retrieval, slides were dried in a vacuum desiccator prior to enzymatic digestion.
Glycogen and N-Glycan MALDI-Mass Spectrometry Imaging. An HTX spray station (HTX) was used to coat the slide with a 0.2 ml aqueous solution of isoamylase (3 units/slide) and PNGase F (20 mg total/slide). The spray nozzle was heated to 45° C. with a spray velocity of 900 m/min. Following enzyme application, slides were incubated at 37° C. for 2 hr in a humidified chamber, and dried in a vacuum desiccator prior to matrix application [α-cyano-4-hydroxycinnamic acid matrix (0.021 g CHCA in 3 ml 50% acetonitrile/50% water and 12 μL 25% TFA) applied with HTX sprayer]. For detection and separation of glycogen and N-glycans, a Waters SynaptG2-Si high-definition mass spectrometer equipped with traveling wave ion mobility was used. The laser was operating at 1000 Hz with an energy of 200 AU and spot size of 75 μm, mass range is set at 500-3000 m/z. Ion mobility setting were done according to previously established parameters17,96 with a trap entrance energy of 2V, trap bias of 85V, and DC/exist of 0V. Wave velocity settings were set to: trap 9.6 m/s, IMS 4.6 m/s, transfer 17.4 m/s. Wave height settings were set to: trap 4V, IMS, 42.7, transfer 4V, additional settings are variable wave ramp down of 1400 m/s. MALDI images were produced using the HDI software (Waters Corp) following built in peak integration function to account for mass drift over the MALDI run. All MALDI images were normalized to total ion current (TIC) within each pixel.
Quantitative Glycogen MALDI-Mass Spectrometry Imaging. 1, 10, 20, 40, 100, 1000 ng of purified rabbit liver glycogen were directly spotted on the microslide adjacent to the tissue section. An HTX spray station (HTX) was used to coat the slide with a 0.2 ml aqueous solution of isoamylase (3 units/slide). The spray nozzle was heated to 45° C. with a spray velocity of 900 m/min. Following enzyme application, slides were incubated at 37° C. for 2 hr in a humidified chamber, and dried in a vacuum desiccator prior to matrix application [α-cyano-4-hydroxycinnamic acid matrix (0.021 g CHCA in 3 ml 50% acetonitrile/50% water and 12 μL 25% TFA) applied with HTX sprayer]. For detection and separation of glycogen, Bruker timeTOF Flex mass spectrometer was used. The laser was operating at 10,000 Hz and 300 shots/second, mass range is set at 700-3000 m/z. MALDI images were produced using the SCILS software. Pixel information was exported using the SCILS API package in R studio and analysis was performed in prism. The molecular ion of 1175 m/z that corresponds to glucose polymer 6 was used to produce standard curve and absolute quantitation of glycogen levels in situ.
MALDI-MS Dataset Processing as Part of User Input Model. MALDI-MSI data files were processed to adjust for mass drift during the MALDI scan to enhance image quality and improve signal-to-noise ratio that will assist in the machine learning module. Raw MALDI-MSI data files were processed using an algorithm available within the HDI software (Waters Corp). To adjust for mass drift during the MALDI scan, raw files were processed using a carefully curated and established list of 50 MALDI matrix peaks (m/z) and 155 glycogen and N-linked glycan peaks (m/z) listed in Tables 3A and 3B. Files were processed at a sample duration of 10 sec at a frequency rate of 0.5 min, and an m/z window of <1 Da, using an internal lock mass of previously defined N-linked glycan 1257.4296 m/z with a tolerance of lamu and a minimum signal intensity of 100,000 counts. Three to five glycans were spot checked for abundance and known spatial distribution as a positive control97. Post-processed MALDI data files were exported in a tabular format as .CSV for input into the machine learning module.
Data Availability. The MALDI imaging data generated in this study have been deposited in the DRYAD database under https://doi.org/10.5061/dryad.jwstgjqfg. The pool metabolomics data used in this study are available in the Metabolomics Workbench database under accession code/study ID ST002547 [https://doi.org/10.21228/M8QFOW].
Dimensionality Reduction and Clustering as Part of Computer-Based Module. Normalization, high dimensional clustering, and UMAP and spatial plots, were done using the Python® software environment98. First, each complex carbohydrate feature was normalized on total ion count (TIC) within individual pixels. The Leiden algorithm36 automatically performed spatially agnostic clustering of pixels and optimized cluster approximation based on similarities in their carbohydrate features. Uniform Manifold Approximation and Projection (UMAP)37 was applied to embed high dimensional carbohydrate features of pixels in a low dimensional space for data visualization and interpretation. The clustering results were visualized by a pixel-colored UMAP plot in 2D feature space and a pixel-colored spatial plot mapping pixel to the original X-Y coordinates recorded by MALDI-MSI. Both plots are qualified for revealing tissue anatomy, histopathology, and heterogeneity. Leiden clustering algorithm and UMAP plot generation are built-in modules as part of the Scanpy package available within Python®99. Code is available for free at github.com/maldiUKY/HDC-SC. Codes are tested and functional under the MacBook Pro IOS environment.
Discovery of Overrepresented Complex Carbohydrate Features and Pathway Enrichment. Multivariate analyses of all complex carbohydrate features within unique clusters were analyzed using the Metaboanalyst 5.0 software (n=3 technical regions of interest [ROIs] per cluster or biological sample) as previously described100. Log transformation and auto scaling were used for normalization. Heatmaps were generated with the top 50 ranked features and hierarchical clustering was performed using the Euclidean distance measure and Ward linkage. Pathway enrichment analysis based on overrepresented molecular features were done manually based on previously established pathways of N-linked glycosylation and glycogen metabolism101. All MALDI-MSI images of glycogen and N-glycans were generated using the HDI software (Waters Corporation). Representative glycan structures were generated in GlycoWorkbench.
Histopathology Assessments. Histopathology assessments were performed by four board certified clinical pathologists independently to improve rigor and reproducibility. All H&E slides were assessed in a CLIA certified pathology laboratory using an inverted brightfield microscope (Olympus BX43). Image analysis was performed using the HALO image analysis software (Indica labs). Assessments were made based on the spatial clustering produced by HDR-SC and histopathology assessment from an immediate adjacent section 4 μm apart.
Immunohistochemistry. Fixed lung tissues were sectioned at 10 μm and immunohistochemistry was performed at the Biospecimen Procurement and Translation Pathology Shared Resource Facility using the method previously described17. Briefly, tissue was rinsed with 0.01M PBS, incubated for 1 hour in 5% normal goat serum in 0.3% Triton X-100 in PBS. The tissue was then incubated at room temperature in the primary antibody (below) and diluted in 1% normal goat serum, followed by 3×15 minute rinses in 0.05% Tween-20 in PBS. Tissue was then incubated for 1 hour in secondary antibody diluted in 1% normal goat serum in PBS. Antibodies used for other markers are glycogen synthase (LSBio, Cat #LS-B12901), glycogen phosphorylase brain isoform (LSBio, Cat #LS-B4749), and glycogen phosphorylase muscle isoform (Protech, 1Cat #9716-AP). Digital images were acquired through the ZEISS Axio Scan.Z1 high resolution slide scanner. Quantitative image analysis was performed using the Halo software (Indica labs) using the multiplex IHC modules.
Co-Immunofluorescence. Fixed brains were embedded in paraffin and sectioned at 4 μm onto slides by the University of Kentucky Biospecimen Procurement and Translation Pathology Shared Resource Facility. Slides were dewaxed, rehydrated, and heated to 60° C. for 30 minutes in citraconic anhydride buffer (pH 6.5) for antigen retrieval. After cooling, slides were incubated in primary antibody (Table 1A) followed by incubation with a secondary antibody (Table 1B). Slides were then cover slipped using Southern Biotech DAPI Fluoromount-G (Cat. 591 #0100-20). Digital images were acquired as 12 Z-stacks through the Zeiss Axio Scan Z.7 digital slide scanner at 40× magnification and processed using HALO software (v3.3.2541.345, Indica Labs, Albuquerque, NM).
Lung Fibrosis Assessments. Lung fibrosis was evaluated by Ashcroft score using H&E sections. For analysis, two images from four micrographs of whole lung sections were randomly selected from four mice. These randomly selected images were individually assessed in a blinded manner with an index of 0-8: 0, normal lung; 1, minimal fibrous thickening of alveolar or bronchiolar walls; 2-3, moderate thickening of walls without obvious damage to lung architecture; 4-5, increased fibrosis with definite damage to lung structure and formation of fibrous bands or small fibrous masses; 6-7, severe distortion of structure and large fibrous areas, evidence of “honeycomb lung”; 8, total fibrous obliteration of the field. Soluble collagen content from bronchoalveolar lavage fluid (BALF) was determined using the Sircol assay (Biocolor), according to the manufacturer's instructions. Sircol dye bound to collagen was evaluated by a microplate reader at 555 nm. BALF was collected by performing two washes of 0.7 mL with PBS+EDTA (0.1 mM) on ice.
Collagen Targeted Imaging Proteomics. Samples were prepared as previously described for targeted collagen and extracellular matrix peptide imagingo102-106. Briefly, deglycosylated samples107,108 were antigen retrieved with 10 mM Tris, pH 9, autosprayed (M5, HTX-Technologies) with 0.1 tg/tL collagenase type III (Worthington) dissolved in ammonium bicarbonate pH 7.4, 1 mM CaCl2), and incubated at 38.5° C. with ≥85% humidity for 5 hours. The matrix α-Cyano-4-hydroxycinnamic acid (CHCA, Sigma Aldrich) was dissolved in 1.0% trifluoracetic acid (Sigma), 50% acetonitrile (LC-MS grade, Fisher Chemical) and autosprayed (M5, HTX Technologies) onto tissue. Tissues were imaged on a MALDI-QTOF (timsTOF-flex, Bruker) in positive ion mode over m/z range 7002500. Laser was adjusted to 20 tm2 and each pixel consisted of 300 laser shots. Images were collected with a laser step size of 60 tm. Data was visualized in SCiLS Lab Software (v2022b, Bruker) and processed for image segmentation and principal component analysis. Peak data were exported by mean spectrum processed as peak maximum and further statistical comparisons were done using Metaboanalyst 5.0 and GraphPad Prism 9.0. Exported peak intensities were visualized as heatmaps using the TM4 MultiExperiment Viewer suite109 with clustering by Manhattan metric and single linkage.
Cell Culture and 13C-Glycogen Tracing in Fibroblast Cell Lines. Normal and diseased lung fibroblast were maintained in fibroblast growth medium (Lonza, Cat #CC-3132) supplement with the FGM-2 SingleQuots supplement (Lonza, Cat #CC-4126) in 10 cm dishes. For the 13C-glycogen enrichment experiment, fibroblast cells were allowed to reach ˜50% confluency, followed by the addition of DMEM base media supplemented with 10 mM 13C6-glucose, 2 mM Gln, 10% dialyzed fetal bovine serum in a CO2 incubator maintained at 37° C. At the designated timepoints, cells were washed with cold PBS three times followed by extraction with 50% methanol and separated into polar, insoluble fraction that contains the glycogen. For the 13C-glycogen washout experiment, fibroblast cells were grown in 13C6-glucose enrichment media for 48 hours followed by the replacement of DMEM base media supplement with 12C-glucose. At designated timepoints, cells were washed with cold PBS three times followed by extraction with 50% methanol and separated into polar and the glycogen-containing insoluble fraction.
Gas-Chromatography-Mass Sepctrometry (GCMS) Analysis of 13C-Enriched Glycogen. GCMS assessment of glycogen was done using method previously described58,59. Briefly, insoluble fraction was subject to acid hydrolysis with 2N HCL for 3 hours at 98° C. The reaction was quenched with 2N NaOH for subsequent experiments. For GC-MS analysis, samples were first dried in a SpeedVac (Thermo), followed by sequential addition of 20 mg/ml methoxylamine hydrochloride in pyridine, and then the trimethylsilylating agent N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) was added followed by GCMS analysis. GC-MS protocols were similar to those described previously58,59. The electron ionization (EI) energy was set to 70 eV. Scan (m/z: 50-800) and selected ion monitoring mode were used for qualitative measurement and isotope monitoring, respectively. Ions used for the enrichment of glycogen-derived glucose are 319, (unlabeled) and 320, 321, 322, 323, (labeled). Batch data processing and natural 13C labeling correction were performed using the Data Extraction for Stable Isotope-labeled metabolites (DExSI) software package.
Targeted Analysis of Metabolites by Liquid-Chromatography-Mass Spectrometry. Approximately 20 mg of pulverized, frozen tissue was extracted in 3 ml ice-cold 60% acetonitrile by extensively vortexing. Next, 1 ml chloroform was added to each sample and samples were mixed by manual shaking followed by centrifuging at 3,200 g for 20 minutes at 4° C. The aqueous layer was moved to a new tube and lyophilized. The middle layer containing protein and insoluble material was transferred to a new tube, washed twice with 50% methanol, once with 100% methanol, and briefly dried in a speed-vac. After drying, the insoluble material was hydrolyzed by heating samples in 3N HCl at 95° C. for 2 hours. 100% methanol was added to hydrolysate to achieve a final concentration of 50% methanol, samples mixed, centrifuged at 18,000 g for 10 min at 4° C., then supernatant dried on a speed vac. Polar metabolites were separated by HILIC chromatography using an Agilent InfinityLab Poroshell 120 HILIC-Z column (2.7 m, 2.1×150 mm) with a binary solvent system of 10 mM ammonium acetate in water, pH 9.8 (solvent A) and ACN (solvent B) with a constant flow rate of 0.25 ml/min. The column was equilibrated with 90% solvent B. Polar metabolites were resuspended in a 1:1 mixture of solvents A:B, centrifuged at 18,000 g for 5 minutes at 4° C., then transferred to glass vials. 4 μl of each sample was injected and the gradient proceeded from 0-15 min linear ramp 90% B to 30% B, 15-18 min isocratic flow of 30% B, 18-19 min linear ramp from 30% B to 90% B, and 19-27 min column regeneration with isocratic flow of 90% B. Metabolites were measured using an Agilent 6545 quadrapole-time of flight mass spectrometer (MS) coupled to an Agilent 1290 Infinity II UHPLC. Individual samples and standards were acquired with full scan MS in negative mode. Peaks for the deprotonated [M-H]− ions were extracted and integrated using Agilent Qualitative Analysis software (retention time, formula, and m/z are presented in Table 2). Polar metabolite peaks were normalized to the amino acid content in the hydrolyzed insoluble biomass fraction. Samples were resuspended in 70 μl of 20 mg/ml methoxyamine in pyridine and incubated for 1.5 h at 37° C. Samples were centrifuged at 18,000 g for 5 minutes and 50 μl of each sample was transferred to a glass vial. 80 ul of N-Methyl-N-(trimethylsilyl)trifluoroacetamide+1% chlorotrimethylsilane (Themo Scientific) was added to each sample and incubated at 37° C. for 30 minutes. Samples were then analyzed by gas chromatography mass spectrometry (GCMS) for as described above.
Statistical Analysis. All dimensionality reduction and clustering analyses were performed using the Python® software environment. Both clustering and differential analyses were conducted with the Scanpy package by Leiden algorithm and Wilcoxon Rank-Sum test, respectively. For Metaboanalyst multivariate analyses of all glycans, log transformation and auto scaling were used for normalization. Heatmaps were generated based on the Euclidean distance measure and the Ward clustering algorithm. Glycans with variable importance in projection (VIP) scores >1.5 based on partial least squares discriminant analysis (PLS-DA) were selected for further analysis. For biomarker analysis, areas under the curve (AUC) were obtained using multivariate receiver operating characteristic (ROC) analysis based on the linear SVM classification method and SVM feature ranking method. Statistical analysis for discovery of overrepresented complex carbohydrate features in patient samples and in vivo studies were carried out using GraphPad Prism 9.0. All numerical data are represented as mean±S.E.M Column analysis was performed using one-way ANOVA or t-test. A P value less than 0.05 was considered statistically significant. The statistical parameters for each experiment can be found in the figures and figure legends.
HDR-SC of MALDI-MSI Dataset Reveal Tissue Anatomical Regions. Anabolic pathways for complex carbohydrates such as glycogen and N-linked glycans are critical facets of glucose metabolism, and emerging work demonstrates that they are metabolically channeled through common substrates14,15. Comprehensive profiling of both can elucidate compartmentalized glucose metabolism within a cell (
The multidimensional nature of MALDI-MSI datasets is highlighted by the fact that each pixel from a MALDI-MSI experiment contains a full ion spectrum of detectable molecular features (
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To test whether unique pixel clusters match known liver anatomical regions and structures, we performed detailed histology analysis using a liver section stained with hematoxylin and eosin (H&E) followed by annotation by expert clinical surgical pathologists (
HDR-SC Reveals Major Histopathology of Human Lung Disease. To test whether HDR-SC analysis can identify pathological changes in human diseased tissue, we performed MALDI-MSI on lung tissue sections from multiple human idiopathic pulmonary fibrosis (IPF) patients and a single COVID-19 patient (
Glycogen as a Clinical Hallmark of PF from Different Disease Origins. Pulmonary fibrosis (PF) is a severe and terminal disease that currently lacks a cure. There is a critical need to identify therapeutic vulnerabilities within PF for the future development of small molecule inhibitors. Based on HDR-SC, we performed metabolite enrichment analysis among each pixel within different annotated clusters and examined overrepresented carbohydrate features specific to fibrotic regions (
To further establish that glycogen is a metabolic hallmark of lung fibrosis, we purchased a commercial tissue microarray (TMA) comprised of both human fibrotic tissue cores (n=26) and normal adjacent lung resected at surgery (n=7) (
Bleomycin-Induced Pulmonary Fibrosis display Increased Glycogen. Based on human specimens, we identified extensive changes in N-linked glycan and glycogen accumulation in PF (
Interestingly, amino acids such as alanine, glutamic acid, and glutamine remain unchanged between the two groups (
Inability to Utilize Glycogen blunts Fibrosis Development In Vivo. To test whether glycogen utilization is necessary for fibrosis disease progression, we employed a mouse model of glycogen storage disease lacking the glycogen phosphatase laforin (Epm2a−/−). Glycogen dephosphorylation is required for efficient glycogenolysis and the release of glucose-6-phosphate by glycogen phosphorylase48,49. Laforin deficiency results in hyperphosphorylated glycogen aggregates that are inaccessible to glycogen degradation enzymes15,50-52. Thus, the mice accumulate glycogen that they are unable to degrade. We administered bleomycin to both WT and Epm2a−/− mice (LKO) and collected lungs 24 hours after day 21 post-treatment similar to the previous experiment (
Fibrosis progression relies on remodeling of the lung extracellular matrix proteins53. Primarily, extensive collagen deposition within the alveolar airways provides the necessary structural and mechanical support for the chronic proliferation of diseased fibroblasts54. While mechanisms behind increased collagen synthesis during PF remain to be elucidated, it is known that the degree of collagen lattice correlates with disease severity55. In our study, we performed total collagen quantitation from the bronchoalveolar lavage fluid (BALF) and observed similar trends between LKO and WT bleomycin treated cohorts (
Acid Alpha-Glucosidase (GAA) Drives Glycogen Utilization in PF. Elucidating the route of glycogen utilization is needed to improve our understanding of PF biology and future translational opportunities. First, we performed immunohistochemical staining to assess the levels of glycogen synthase (GYS) and glycogen phosphorylase muscle and brain isoform (PYGM and PYGB respectively) at the protein level17. We observed increased GYS protein expression within the fibrotic regions when compared with the non-diseased regions from the same tissue section (
Increased rate of glycogen utilization without increases in GP protein expression, a key glycogen degradation enzyme, suggested an alternative route of glycogen degradation in the diseased fibroblasts. In our IF analysis using the anti-glycogen antibody, we observed round/puncta glycogen within the cytoplasm of myofibroblasts (
The lysosome participates in the intracellular salvage pathways providing substrates for complex carbohydrate production (
To confirm that the lysosomal salvage pathway is compromised in GKO and LKO mice, we performed MALDI MSI to assess the N-linked glycome of the lung in both GKO and LKO cohorts of bleomycin and saline treated animals. We observed broad spectrum reduction in a wide variety of N-linked glycans in both GKO and LKO bleomycin treated lungs when compared to the WT bleomycin treated cohort (
In this study, we applied multidimensional spatial metabolomics analyses to demonstrate application for histopathology prediction and biomarker identification in human and mouse diseased tissues. We chose spatial metabolomics analysis of complex carbohydrates for a number of reasons: First, the ability to utilize stored FFPE tissue samples significantly increases accessibility to a variety of human disease clinical specimens34,65. Second, complex carbohydrate metabolism is intimately connected to glucose utilization and spans multiple cellular compartments14. Third, complex carbohydrates are critical structural metabolites for cell-cell adhesion, signaling, and extracellular matrix remodeling14,66. Fourth, aberrant complex carbohydrate metabolism drives pathogenesis in multiple human diseases including neurodegeneration67,68, type II diabetes69, cardiovascular disease70, and several types of cancer71,72. In this study, we demonstrate HDR-SC and biomarker prediction using spatial metabolomics datasets. HDR-SC accurately captured fibrotic regions in multiple tissue sections analyzed when matched to histopathology annotation. Further, differential feature analysis identified biomarkers that highlight a potential role for glycogen utilization during fibrosis disease progression. Using two separate mouse model of fibrosis, we demonstrate that the inability to utilize glycogen leads to significantly blunted N-linked glycan and collagen content and fibrosis development in vivo.
MALDI-MSI is a high-dimensional dataset, similar to the scRNAseq format73 wherein complex carbohydrates are biological features stored within each pixel, similar to gene expression levels within each cell. However, there are several important differences. First, each pixel from MALDI-MSI is recorded with precise X-Y coordinates to allow true spatial mapping of anatomical regions. Second, multiplexed glycogen and N-linked glycan MALDI-MSI takes advantage of a large collection of well-annotated human clinical specimens with decades of clinical metadata in the form of FFPE. The ability to utilize FFPE tissue also bypasses the need to collect fresh tissue from surgery for human clinical studies. The in situ nature of MALDI-MSI also avoids lengthy and potentially destructive cell isolation steps, thus preserving anatomical regions. Of note, many histopathological features such as end-stage fibrosis and mucin patches contain large fractions of non-cellular features. For example, the presence of mucin within airways and in regions of honeycomb change contain abundant glycoproteins. These features are often lost in single-cell analyses but are preserved by the MALDI-MSI workflow. To this end, what MALDI-MSI lacks in cellular information could be complimented with scRNAseq, multiplexed ion beam imaging by time of flight (MIBI-TOF), or co-detection by indexing (CODEX) analyses74. Co-analysis or vertical integration with single-cell techniques would enhance cellular metabolic origins that are related to the etiologies of diseases.
Pulmonary fibrosis (PF) is the long-term consequence of genetic mutations or acute damage to the lung from environmental exposures, including radiation/chemotherapy75,76, acute respiratory distress syndrome (ARDS)77, cancer78, and, more recently, severe lung disease caused by the SARS CoV-2 virus (COVID-19)79. In some cases, PF arises from undefined causes and is classified as IPF80. The pathology of PF includes remodeling of the alveolar regions with excessive matrix production such as N-glycans and collagen by fibroblasts, myofibroblasts, and mucin aggregation that lead to severe thickening of the alveolar septa of the lung81,82. PF patients suffer from poor gas exchange and subsequently low tissue oxygenation that leads to other comorbidities and death83. Our pipeline identified unique subclasses of complex carbohydrates enriched in myofibroblasts of PF patient samples. In our analyses, core fucosylated N-glycans and glucose polymers from glycogen are differentially enriched in the myofibroblasts of PF. Using a separate TMA containing fibrosis and normal tissues, we demonstrate exceptional binary predictability of N-glycans and glycogen for the diagnosis of fibrosis. Future studies should focus on the predictability in multivariant pathologies such as acute fibrinous and organizing pneumonia (AFOP), DAD, and mucinous lesions. We anticipate that artificial intelligence (AI) would aid in the development process of implementing spatial metabolomics to digital pathology.
Current PF treatment relies on steroids that only temporarily delay fibrosis progression84, and there are no effective treatments to reverse the clinical course of the disease, resulting in permanent loss of lung function80. MALDI-MSI analyses of human pulmonary disease specimens revealed a glycogen-rich phenotype within the fibrotic regions. Interestingly, mouse models of PF through bleomycin-induction also displayed a similar glycogen-rich phenotype.
Through a series of molecular, cellular, and animal modeling experiments, we concluded that there is an increased metabolic demand for glycogen metabolism in diseased fibroblasts and highlighted that glycogen utilization by GAA through the lysosomal pathway is a critical metabolic process that occurs during pulmonary fibrosis. Mice deficient in GAA did not form PF after bleomycin treatment. The lysosomal salvage pathway provides substrates for the synthesis of proteoglycans85 and N-linked glycans86 that are critical component of the extracellular matrix. Coincidentally, myofibroblasts drive extracellular remodeling of PF44, and increased glycogen utilization through the lysosomal salvage pathway would support the metabolic demand for extracellular matrix remodeling. This hypothesis is supported by the result demonstrating that Gaa−/− mice blunted the increase in N-linked glycans after bleomycin treatment. We propose that this phenotype is shared between PF from different disease origins. These results are particularly exciting, as recent developments of glycogen targeting therapeutics demonstrate efficacy in preclinical models of glycogen storage diseases87-90, these include multiple modalities that targeting GYS through small molecule inhibition or anti-sense oligonucleotides with some already being tested in patients91. Repurposing these compounds could offer an additional treatment avenue for patients suffering from PF.
Normal human lung fibroblasts (NHLF) or diseased human lung fibroblasts (DHLF) derived from idiopathic pulmonary fibrosis patients were treated for two days with a laforin inhibitor (or vehicle control). The laforin inhibitor used in this Example was compound “L319-21-M50,” as described in U.S. Patent Application Publication No. 2018/0170862. Following treatment, mRNA was harvested from the cells and gene expression was assessed. As shown in
In view of the above-discussed findings and results in Examples 1 and 2 and the known roles of glycogen phosphatase, GAA, GYS, and GP in glycogen synthesis and/or utilization, the efficacy of certain glycogen phosphatase inhibitors, GAA inhibitors, GYS inhibitors, and GP inhibitors with respect to treating pulmonary fibrosis (PF) in a subject having or at risk of having PF will be examined.
In future studies the efficacy of other glycogen phosphatase inhibitors besides L319-21-M50 examined in Example 2 with respect to treating PF in a subject having or at risk of having PF will be examined. Glycogen phosphatase inhibitor compounds to be tested include:
(as disclosed in U.S. Patent Application Publication No. 2018/0170862). The efficacy of the Nb72 nanobody disclosed in Simmons, et al. (2021)110 will also be examined. Further testing of the L319-21-M50 compound utilized in Example 2 may also be examined.
In future studies, the efficacy of the GAA inhibitors of acarbose, miglitol, voglibose, castanospermine, miglustat, and 1-deoxynojirimycin with respect to treating PF in a subject having or at risk of having PF will be examined.
In future studies, the efficacy of the GYS inhibitors will be examined. GYS inhibitors to be examined include, guaiacol,
(as disclosed in Ullman et al. (2024)117), and compounds of the formula
In future studies, the efficacy of the GP inhibitors will be examined. GP inhibitors to be examined include
(as disclosed in MedChem119)
(5-Chloro-N-phenyl-1H-indole-2-carboxamide derivative) (as disclosed in Huang, et al. (2023)120), and
(as disclosed in Bergens, et al. (2000)121).
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference, including the references set forth in the following list:
It will be understood that various details of the presently disclosed subject matter can be changed without departing from the scope of the subject matter disclosed herein. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation.
The present application claims priority to U.S. Patent Application Ser. No. 63/486,086, filed on Feb. 21, 2023, the entire disclosure of which is incorporated herein by reference.
This invention was made with government support under grant number R35NS116824 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63486086 | Feb 2023 | US |
