Patent Application
20230312728
Aspects of this invention relate to at least the fields of molecular biology and medicine.
There is a progressive decline in β-cell function in type-2 diabetes (T2D) that is partly related to the accumulation of the toxic oligomers of islet amyloid pancreatic polypeptide (IAPP) [3-5]. Despite well-documented β-cell stress (altered mitochondrial network and activity, Ca2+ toxicity, oxidative and DNA damage) [6-9] there is a surprisingly slow rate of β-cell attrition, with preservation of β-cell mass between 35% and 76% even decades after onset of T2D [4]. However, relative preservation of β-cell mass contrasts with an early loss of β-cell glucose responsiveness prior to the onset of T2D. This indicates that, although viable, most β-cells in T2D are dysfunctional.
Upon acute injury, in cells of healthy tissue, hypoxia inducible factor-1-alpha (HIF1α) initiates a sequence of steps that are required for successful tissue repair [10, 11]. First, there is a profound metabolic remodeling that is mediated by the HIF1α target 6-pho sphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), from mitochondrial-dependent oxidative phosphorylation to high flux via aerobic glycolysis, generating ATP irrespective of oxygen availability. Energy diversion to aerobic glycolysis permits DNA repair by an increase in nucleotide synthesis via pentose phosphate pathway [12]. High flux glycolysis also enables the mitochondrial network to adopt the defensive fragmented perinuclear posture, which protects mitochondria from Ca2+ toxicity incurred by injury [13]. Second, cells that retain DNA damage are eliminated by apoptosis and those without DNA damage are used to regenerate lost tissue. Tissue regeneration is accomplished either by progenitor stem cell expansion, by replication after dedifferentiation or by trans-differentiation. Third, once tissue regeneration is completed, the injury signals that induced the HIF1α-PFKFB3 pathway abate and the cells readopt their functional metabolic status.
Unlike in healthy tissue, β-cells in humans with T2D remain trapped in the pro-survival phase of the HIF1α injury/repair response with altered metabolism and the mitochondrial network which slow down the rate of cell attrition at the expense of β-cell function [2]. In spite of extensive research it is still not clear why β-cells are unable to undergo successful regeneration. There exists a need for methods and compositions for inducing elimination of damaged cells and regeneration of healthy cells (e.g., β-cells) to improve insulin sensitivity and better treat subjects suffering from diabetes.
Aspects of the present disclosure provide methods for treatment of diabetes and related conditions, including type 2 diabetes, and compositions useful in such methods. Embodiments of the present disclosure fulfill certain needs by providing methods and compositions for facilitating regeneration of healthy β-cells by inhibition of HIF1α activity, in some cases in combination with inhibition of PFKFB3 activity. Certain aspects are directed to methods for treatment of type 2 diabetes comprising providing a HIF1α inhibitor. Such methods may further comprise administration of a PFKFB3 inhibitor. Also disclosed, in some embodiments, are pharmaceutical compositions comprising a HIF1α inhibitor and a PFKFB3 inhibitor.
Embodiments of the present disclosure include methods for treating a subject for disorders associated with protein misfolding, methods for treating a subject for diabetes, methods for treating a subject for type 2 diabetes, methods for treating a subject for type 1 diabetes, methods for diagnosing type 2 diabetes, methods for determining sensitivity of a subject having type 2 diabetes to HIF1α inhibitor treatment, methods for improving insulin sensitivity, methods for targeting a HIF1α inhibitor to β-cells, methods for determining an expression level of PFKFB3, methods for killing damaged β-cells, methods for stimulating regeneration of healthy β-cells, compositions comprising one or more HIF1α inhibitors, compositions comprising one or more PFKFB3 inhibitors, and compositions comprising a HIF1α inhibitor and a PFKFB3 inhibitor. The disclosed methods can include at least 1, 2, 3, 4, 5, or more of the following steps: providing an effective amount of a HIF1α inhibitor, providing an effective amount of a PFKFB3 inhibitor, diagnosing a subject for type 2 diabetes, diagnosing a subject for type 1 diabetes, identifying a subject as having type 2 diabetes, identifying a subject as being at risk for type 2 diabetes, identifying a subject as having prediabetes, measuring an expression level of PFKFB3 in a subject, measuring an expression level of PFKFB3 in β-cells of a subject, determining a subject to have an increased PFKFB3 expression level in β-cells of the subject, and providing a subject with one or more additional treatments for type 2 diabetes. One or more of the foregoing steps may be excluded from embodiments of the present disclosure. A composition of the present disclosure can include 1, 2, 3, 4, or more of the following: a HIF1α inhibitor, a PFKFB3 inhibitor, a targeting molecule, a GLP-1 receptor antibody, metformin, a GLP-1 receptor agonist, a DPP-4 inhibitor, sulfonylurea, and one or more pharmaceutically acceptable excipients. One or more of the foregoing components may be excluded from embodiments of the present disclosure.
Disclosed herein, in some embodiments, is a method of treating a subject for type 2 diabetes, the method comprising administering an effective amount of a HIF1α inhibitor to the subject. Also disclosed herein, in some embodiments, is a method of treating a subject for type 2 diabetes comprising administering an effective amount of a HIF1α inhibitor to a subject determined to have an increased expression level of PFKFB3 in β-cells from the subject relative to an expression level of PFKFB3 in β-cells from a healthy subject who is not suffering from type 2 diabetes. In some embodiments, disclosed is a method of treating a subject for type 2 diabetes, the method comprising (a) determining a subject to have an expression level of PFKFB3 in β-cells from the subject relative to an expression level of PFKFB3 in β-cells from a healthy subject who is not suffering from type 2 diabetes; and (b) administering an effective amount of a HIF1α inhibitor to the subject. In some embodiments, disclosed is a method of stimulating regeneration of healthy β-cells in a subject with type 2 diabetes, where the healthy β-cells do not express PFKFB3, the method comprising administering an effective amount of a HIF1α inhibitor to the subject.
In some embodiments, the HIF1α inhibitor promotes HIF1α degradation. In some embodiments, the HIF1α inhibitor inhibits HIF1α/HIF1β dimer formation. In some embodiments, the HIF1α inhibitor reduces HIF1α transcriptional activity. In some embodiments, the HIF1α inhibitor is KC7F2, IDF-11774, aminoflavone, AJM290, AW464, tanespimycin, alvespimycin, PX-478, or FM19G11. In some embodiments, the HIF1α inhibitor is a nucleic acid inhibitor. In some embodiments, the HIF1α inhibitor is an antisense oligonucleotide. In some embodiments, the HIF1α inhibitor is EZN-2698. In some embodiments, the HIF1α inhibitor is an siRNA or a short hairpin RNA. In some embodiments, the HIF1α inhibitor is resveratrol, rapamycin, everolimus, CCI779, silibinin, digoxin, YC-1, phenethyl isothiocyanite, chetomin, flavopiridol, bortezomib, amphotericin B, Bay 87-2243, PX-478, or ganetasipib. In some embodiments, the HIF1α inhibitor is an anti-HIF1α antibody or antibody-like molecule. In some embodiments, the HIF1α inhibitor is a nanobody. In some embodiments, the HIF1α inhibitor is administered intravenously, intramuscularly, intraperitoneally, subcutaneously, intra-articularly, intrasynovially, intrathecally, orally, topically, through inhalation, or through a combination of two or more routes of administration.
In some embodiments, the method further comprises administering a PFKFB3 inhibitor to the subject. In some embodiments, the PFKFB3 inhibitor is 3-(3-Pyridinyl)-1-(4-pyridinyl)-2-propen-1-one (3-PO) or an analog thereof. In some embodiments, the PFKFB3 inhibitor is an analog of 3-PO, wherein the analog is 1-(4-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one (PFK 15). In some embodiments, the PFKFB3 inhibitor is BrAcNHEtOP, YN1, YZ9, PQP, PFK-158, Compound 26, KAN0436151, or KAN0436067. In some embodiments, the PFKFB3 inhibitor is a nucleic acid inhibitor. In some embodiments, the PFKFB3 inhibitor is an antisense oligonucleotide. In some embodiments, the PFKFB3 inhibitor is an siRNA or a short hairpin RNA. In some embodiments, the PFKFB3 inhibitor is operatively linked to a targeting molecule configured to bind to β-cells of the subject. In some embodiments, the HIF1α inhibitor is operatively linked to a targeting molecule configured to bind to β-cells of the subject. In some embodiments, the targeting molecule is an antibody. In some embodiments, the targeting molecule is an antibody-like molecule. In some embodiments, the targeting molecule is configured to bind to a GLP-1 receptor. In some embodiments, the HIF1α a inhibitor and the PFKFB3 inhibitor are administered to the subject sequentially. In some embodiments, the HIF1α inhibitor and the PFKFB3 inhibitor are administered to the subject substantially simultaneously.
In some embodiments, administering the effective amount of the HIF1α inhibitor increases insulin sensitivity in the subject. In some embodiments, the subject does not have or has not been diagnosed with cancer. In some embodiments, the subject has been diagnosed with type 2 diabetes. In some embodiments, the method further comprises, prior to the administering, diagnosing the subject with the type 2 diabetes. In some embodiments, the subject was previously treated for type 2 diabetes. In some embodiments, the subject was determined to be resistant to the previous treatment. In some embodiments, the subject does not have or has not been diagnosed with diabetic nephropathy or diabetic retinopathy. In some embodiments, the method further comprises measuring an expression level of PFKFB3 in β-cells from the subject. In some embodiments, the expression level of PFKFB3 in the β-cells from the subject is increased relative to an expression level of PFKFB3 in β-cells from a healthy subject who is not suffering from type 2 diabetes.
Embodiments of the disclose also include a method of increasing insulin sensitivity in a subject, the method comprising administering an effective amount of a HIF1α inhibitor to the subject. In some embodiments, the subject suffers from prediabetes. In some embodiments, the subject suffers from insulin resistance. Also disclosed, in some embodiments, is a method for stimulating cell death in damaged β-cells expressing PFKFB3, the method comprising providing a HIF1α inhibitor to the β-cells. In some embodiments, disclosed is a method for stimulating regeneration in β-cells that do not express PFKFB3, the method comprising providing a HIF1α inhibitor to the β-cells. In some embodiments, the HIF1α inhibitor is provided to the β-cells in vitro. In some embodiments, the HIF1α inhibitor is provided to the β-cells in vivo.
In certain aspects, disclosed herein is a method for killing PFKFB3-expressing damaged β-cells in a subject with diabetes, the method comprising administering an effective amount of a HIF1α inhibitor to the subject. Also disclosed, in some embodiments, is a method of treating a subject for diabetes, the method comprising administering an effective amount of a HIF1α inhibitor to the subject. In some embodiments, the diabetes is type 1 diabetes. In some embodiments, the diabetes is type 2 diabetes.
Certain embodiments are directed to methods for diagnosis of a disease or disorder. In some embodiments, disclosed is a method for diagnosing a subject for type 2 diabetes, the method comprising: (a) measuring an expression level of PFKFB3 in β-cells from the subject; (b) comparing the expression level to an expression level of PFKFB3 in β-cells from a healthy subject who is not suffering from type 2 diabetes; and (c) determining the expression level of PFKFB3 in β-cells from the subject to be increased relative to the expression level of PFKFB3 in β-cells from the healthy subject, thereby diagnosing the subject for type 2 diabetes.
Further disclosed herein, in some embodiments, are various pharmaceutical compositions. In some embodiments, disclosed is a pharmaceutical composition comprising (a) a HIF1α inhibitor and (b) a PFKFB3 inhibitor. The HIF1α inhibitor may be any HIF1α inhibitor, examples of which are disclosed herein. The PFKFB3 inhibitor may be any PFKFB3 inhibitor, examples of which are disclosed herein.
Also disclosed, in some embodiments, is a method of eliminating bihormonal cells from a population of cells, the method comprising administering an effective amount of a PFKFB3 inhibitor to the population of cells. In some embodiments, the PFKFB3 inhibitor is administered to the population of cells in vitro. In some embodiments, the PFKFB3 inhibitor is administered to the population of cells in vivo. The PFKFB3 inhibitor may be any PFKFB3 inhibitor, examples of which are disclosed herein. Further disclosed, in some embodiments, is a method of eliminating bihormonal cells from a population of cells, the method comprising administering an effective amount of a HIF1α inhibitor to the population of cells. The HIF1α inhibitor may be any HIF1α inhibitor, examples of which are disclosed herein. some embodiments, the HIF1α inhibitor is administered to the population of cells in vitro. In some embodiments, the HIF1α inhibitor is administered to the population of cells in vivo. In some embodiments, the population of cells is a population of pancreatic islet cells. In some embodiments, the population of cells is a population of differentiated stem cells. In some embodiments, the differentiated stem cells are differentiated induced pluripotent stem cells (iPSCs). In some embodiments, the differentiated stem cells are embryonic stem cells (ESCs).
Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the measurement or quantitation method.
The use of the word “a” or “an” when used in conjunction with the term “comprising” may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”
The phrase “and/or” means “and” or “or”. To illustrate, A, B, and/or C includes: A alone, B alone, C alone, a combination of A and B, a combination of A and C, a combination of B and C, or a combination of A, B, and C. In other words, “and/or” operates as an inclusive or.
The words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.
The compositions and methods for their use can “comprise,” “consist essentially of,” or “consist of” any of the ingredients or steps disclosed throughout the specification. Compositions and methods “consisting essentially of” any of the ingredients or steps disclosed limits the scope of the claim to the specified materials or steps which do not materially affect the basic and novel characteristic of the claimed invention. As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. It is contemplated that embodiments described herein in the context of the term “comprising” may also be implemented in the context of the term “consisting of” or “consisting essentially of.”
It is specifically contemplated that any limitation discussed with respect to one embodiment of the invention may apply to any other embodiment of the invention. Furthermore, any composition of the invention may be used in any method of the invention, and any method of the invention may be used to produce or to utilize any composition of the invention. Aspects of an embodiment set forth in the Examples are also embodiments that may be implemented in the context of embodiments discussed elsewhere in a different Example or elsewhere in the application, such as in the Summary, Detailed Description, Claims, and Brief Description of the Drawings.
Any method in the context of a therapeutic, diagnostic, or physiologic purpose or effect may also be described in “use” claim language such as “Use of” any compound, composition, or agent discussed herein for achieving or implementing a described therapeutic, diagnostic, or physiologic purpose or effect.
Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.
The present disclosure is based, at least in part, on the identification of β-cell dysfunction in T2D as resulting from a failure of affected β-cells to undergo purifying selection by cell competition with remaining healthy β-cells due to activation of the HIF1α-PFKFB3 injury/repair response. Without wishing to be bound by theory, it is believed that injured β-cells with remodeled metabolism become entrapped via high glycolysis disengaged from the TCA cycle that renders β-cells non-responsive to glucose and that chronic activation of the HIF1α-PFKFB3 pathway prevents homeostatic cell competition necessary for purging damaged β-cells. Given that the survival of injured β-cells in T2D depends on the HIF1α-PFKFB3 pathway, it is believed that that the HIF1α-PFKFB3 injury/repair pathway helps injured β-cells to escape selection by cell competition and that inhibited cell competition by remodeled metabolism impedes β-cell regeneration. Disclosed herein, in some embodiments, are methods and compositions for facilitating β-cell regeneration by inhibition of the HIF1α-PFKFB3 pathway, including HIF1α inhibition, PFKFB3 inhibition, and the combination thereof. Aspects of the disclosure address various needs in the art by providing for treatment of subjects suffering from diabetes, including type-1 diabetes and type-2 diabetes.
Aspects of the present disclosure are directed to methods and compositions for treatment of certain diseases and disorders. In some embodiments, disclosed are methods for treatment of subjects having disorders associated with (e.g., characterized by) protein misfolding. In some embodiments, disorders associated with protein misfolding include diabetes and associated conditions (e.g., prediabetes, type 1 diabetes, type 2 diabetes). Although often described with regards to the treatment or prevention of type 2 diabetes, it is understood that the disclosed methods and compositions may also be used for treating or preventing other disorders associated with protein misfolding, including type 1 diabetes and prediabetes.
In some embodiments, disclosed herein is a method for treating a subject for type 2 diabetes (T2D) and/or preventing a subject from developing T2D, the method comprising providing one or more agents capable of inhibiting the HIF1α-PFKFB3 pathway in cells of the subject. In some embodiments, a subject has been diagnosed for T2D. In some embodiments, a subject is at risk for developing T2D. In some embodiments, a subject has prediabetes. In some embodiments, a subject has T2D subtype 1, subtype 2, or subtype 3. T2D subtypes are known in the art and described in, for example, Li L, Cheng W Y, Glicksberg B S, et al. Sci Transl Med. 2015;7(311):311ra174, incorporated herein by reference in its entirety. In some embodiments, a subject has T2D subtype 1. In some embodiments, a subject has T2D subtype 2. In some embodiments, a subject has T2D subtype 3. In some embodiments, a subject does not have T2D subtype 1. In some embodiments, a subject does not have T2D subtype 2. In some embodiments, a subject does not have T2D subtype 3.
As recognized herein, inhibition of the HIF1α-PFKFB3 pathway enhances killing of unhealthy β-cells and contributes to regeneration of healthy β-cells in T2D. In some embodiments, unhealthy β-cells describe β-cells expressing PFKFB3 (e.g., having a level of expression of PFKFB3 higher than β-cells from a subject that does not have T2D). In some embodiments, healthy β-cells describe β-cells that do not express PFKFB3 or have an expression level of PFKFB3 that is not significantly different from β-cells from a subject that does not have T2D. Treating a subject for T2D may comprise improving symptoms of T2D in the subject, for example increasing insulin sensitivity in the subject.
Methods for treating a subject for T2D may comprise providing an effective amount of a HIF1α inhibitor. In some embodiments, providing a HIF1α inhibitor reduces PFKFB3 levels in β-cells of the subject. Methods for treating a subject for T2D may comprise providing an effective amount of a PFKFB3 inhibitor. In some embodiments, the disclosed methods comprise providing both a HIF1α inhibitor and a PFKFB3 inhibitor to a subject. The HIF1α inhibitor and the PFKFB3 inhibitor may be administered sequentially or substantially simultaneously. The HIF1α inhibitor and the PFKFB3 inhibitor may be provided in the same composition or provided in separate compositions.
In some embodiments, a subject treated as described herein does not have cancer or has not been diagnosed with cancer. In some embodiments, a subject treated as described herein does not have or has not been diagnosed with diabetic nephropathy or diabetic retinopathy.
Aspects of the disclosed methods comprise, in further embodiments, measuring an expression level of PFKFB3 in a subject. In some embodiments, a PFKFB3 expression level is measured in β-cells from a subject. In some embodiments, a PFKFB3 expression level is used to identify a subject as having T2D. In some embodiments, a PFKFB3 expression level is used to determine whether a subject will be sensitive to a treatment comprising a HIF1α and/or PFKFB3 inhibitior. In some embodiments, β-cells from a subject are determined to have a PFKFB3 expression level that is increased relative to a healthy or control subject. In some embodiments, a healthy subject is a subject who does not have diabetes or prediabetes. In some embodiments, a healthy subject is a subject who does not have T2D. In some embodiments, β-cells from a subject are determined to have a PFKFB3 expression level that is increased relative to control cells from the subject.
In some embodiments, a subject is treated with a HIF1α inhibitor and/or a PFKFB3 inhibitor together with one or more additional therapies, e.g., type 2 diabetes therapies. In some embodiments, a subject is treated with a HIF1α inhibitor and/or a PFKFB3 inhibitor together with a GLP-1 receptor agonist. In some embodiments, a subject is treated with a HIF1α inhibitor and/or a PFKFB3 inhibitor together with metformin. In some embodiments, a subject is treated with a HIF1α inhibitor and/or a PFKFB3 inhibitor together with insulin. In some embodiments, a subject is treated with a HIF1α inhibitor and/or a PFKFB3 inhibitor together with a DPP-4 inhibitor.
Hypoxia inducible factor 1-alpha (HIF1α; also HIF1A) is a transcription factor involved in transcriptional regulation of various genes, including those involved in adaptive response to hypoxia.
The following sequence exemplifies the HIF1α mRNA in humans (SEQ ID NO: 1):
The protein sequence is exemplified by the following (SEQ ID NO:2):
A HIF1α inhibitor may refer to any member of the class of compound or agents having an IC50 of 200 μM or lower concentration for a HIF1α activity, for example, at least or at most or about 200, 100, 80, 50, 40, 20, 10, 5, 1 μM, 100, 10, 1 nM or lower concentration (or any range or value derivable therefrom). A HIF1α inhibitor may refer to any compound or agent that inhibits the expression of HIF1α. Examples of inhibitors HIF1α activity or function may include, but are not limited to, agents that prevent HIF1α/HIF1β dimerization, agents that reduce or eliminate protein expression, agents that promote HIF1α degradation (e.g., proteosomal degradation), agents that prevent HIF1α from interacting with DNA, and agents that inhibit HIF1α transcriptional activity. In some embodiments, a HIF1α inhibitor is an agent that binds directly to HIF1α. In some embodiments, a HIF1α inhibitor does not bind directly to HIF1α. Example HIF1α inhibitors are described in, for example, Onnis et al., J. Cell. Mol. Med. 2009 13(9a): 2780-2786, incorporated herein by reference in its entirety. Methods and compositions of the disclosure may comprise one or more HIF1α inhibitors. It is specifically contemplated that one or more of the disclosed HIF1α inhibitors may be excluded from certain embodiments of the disclosure. Also contemplated herein are pharmaceutically acceptable salts and prodrugs of the described HIF1α inhibitors. Although certain example HIF1α inhibitors are described herein, it is contemplated that any HIF1α inhibitor may be implemented in certain embodiments of the disclosure.
In some embodiments, a HIF1α inhibitor is operatively linked (e.g., covalently linked, non-covalently linked, etc.) to a targeting molecule. A targeting molecule describes a molecule designed to bind to a particular biological or cellular target. A targeting molecule may be used to specifically direct or target an agent (e.g., a therapeutic agent such as a HIF1α inhibitor) to a particular biological tissue or cell type (e.g., β-cells). In some embodiments, a targeting molecule is configured to bind to β-cells of a subject. In some embodiments, the targeting molecule is configured to bind to a glucagon-like peptide-1 (GLP-1) receptor, thereby targeting the HIF1α inhibitor to β-cells of the subject. In some embodiments, the targeting molecule is an antibody, antibody fragment, or antibody-like molecule.
Inhibitory nucleic acids or any ways of inhibiting gene expression of HIF1α known in the art are contemplated in certain embodiments. Examples of an inhibitory nucleic acid include but are not limited to antisense nucleic acids such as: siRNA (small interfering RNA), short hairpin RNA (shRNA), double-stranded RNA, and any other antisense oligonucleotide. Also included are ribozymes or nucleic acids encoding any of the inhibitors described herein. An inhibitory nucleic acid may inhibit the transcription of a gene or prevent the translation of a gene transcript in a cell. An inhibitory nucleic acid may be from 16 to 1000 nucleotides long, and in certain embodiments from 18 to 100 nucleotides long. The nucleic acid may have nucleotides of at least or at most 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, 40, 50, 60, 70, 80, 90 or any range derivable therefrom.
As used herein, “isolated” means altered or removed from the natural state through human intervention. For example, an siRNA naturally present in a living animal is not “isolated,” but a synthetic siRNA, or an siRNA partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated siRNA can exist in substantially purified form, or can exist in a non-native environment such as, for example, a cell into which the siRNA has been delivered.
Inhibitory nucleic acids are well known in the art. For example, siRNA and double-stranded RNA have been described in U.S. Pat. Nos. 6,506,559 and 6,573,099, as well as in U.S. Patent Publications 2003/0051263, 2003/0055020, 2004/0265839, 2002/0168707, 2003/0159161, and 2004/0064842, all of which are herein incorporated by reference in their entirety.
Particularly, an inhibitory nucleic acid may be capable of decreasing the expression of HIF1α by at least 10%, 20%, 30%, or 40%, 50%, 60%, 70%, 75%, 80%, 90%, 95% or more or any range or value derivable therein.
In further embodiments, there are synthetic nucleic acids that are HIF1α inhibitors. An inhibitor may be between 17 to 25 nucleotides in length and may comprise a 5′ to 3′ sequence that is at least 90% complementary to any portion of the 5′ to 3′ sequence of a mature HIF1α mRNA. In certain embodiments, an inhibitor molecule is 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, or any range derivable therein. Moreover, an inhibitor molecule has a sequence (from 5′ to 3′) that is or is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or 100% complementary, or any range derivable therein, to any portion of the 5′ to 3′ sequence of a mature HIF1α mRNA, particularly a mature, naturally occurring mRNA. One of skill in the art could use a portion of the probe sequence that is complementary to the sequence of a mature mRNA as the sequence for an mRNA inhibitor. Moreover, that portion of the probe sequence can be altered so that it is still 90% complementary to the sequence of a mature mRNA.
Example HIF1α inhibitory nucleic acids include EZN-2698.
In certain embodiments, disclosed herein is a HIF1α inhibitor polypeptide. In some embodiments, the HIF1α inhibitor polypeptide is a HIF1α antibody. In some embodiments, the anti-HIF1α antibody is a monoclonal antibody or a polyclonal antibody. In some embodiments, the antibody is a chimeric antibody, an affinity matured antibody, a humanized antibody, or a human antibody. In some embodiments, the inhibitor polypeptide is an antibody-like molecule. In some embodiments, the antibody-like is a nanobody. In some embodiments, the antibody is an antibody fragment. In some embodiments, the antibody fragment comprises a Fab, Fab′, Fab′-SH, F(ab′)2, or scFv. In one embodiment, the antibody is a chimeric antibody, for example, an antibody comprising antigen binding sequences from a non-human donor grafted to a heterologous non-human, human or humanized sequence (e.g., framework and/or constant domain sequences). In one embodiment, the non-human donor is a mouse. In one embodiment, an antigen binding sequence is synthetic, e.g., obtained by mutagenesis (e.g., phage display screening, etc.). In one embodiment, a chimeric antibody has murine V regions and human C region. In one embodiment, the murine light chain V region is fused to a human kappa light chain or a human IgG1 C region.
Examples of antibody fragments include, without limitation: (i) the Fab fragment, consisting of VL, VH, CL and CH1 domains; (ii) the “Fd” fragment consisting of the VH and CH1 domains; (iii) the “Fv” fragment consisting of the VL and VH domains of a single antibody; (iv) the “dAb” fragment, which consists of a VH domain; (v) isolated CDR regions; (vi) F(ab′)2 fragments, a bivalent fragment comprising two linked Fab fragments; (vii) single chain Fv molecules (“scFv”), wherein a VH domain and a VL domain are linked by a peptide linker which allows the two domains to associate to form a binding domain; (viii) bi-specific single chain Fv dimers (see U.S. Pat. No. 5,091,513) and (ix) diabodies, multivalent or multispecific fragments constructed by gene fusion (U.S. Patent Pub. 2005/0214860). Fv, scFv or diabody molecules may be stabilized by the incorporation of disulphide bridges linking the VH and VL domains. Minibodies comprising a scFv joined to a CH3 domain may also be made (Hu et al, 1996).
In some embodiments, disclosed is the use of anti-HIF1α nanobodies, e.g., in treatment of diabetes.
As used herein, a “small molecule” refers to an organic compound that is either synthesized via conventional organic chemistry methods (e.g., in a laboratory) or found in nature. Typically, a small molecule is characterized in that it contains several carbon-carbon bonds, and has a molecular weight of less than about 1500 grams/mole. In certain embodiments, small molecules are less than about 1000 grams/mole. In certain embodiments, small molecules are less than about 550 grams/mole. In certain embodiments, small molecules are between about 200 and about 550 grams/mole. In certain embodiments, small molecules exclude peptides (e.g., compounds comprising 2 or more amino acids joined by a peptidyl bond). In certain embodiments, small molecules exclude nucleic acids.
For example, a small molecule HIF1α inhibitor may be any small molecule that is determined to inhibit HIF1α function or activity. Such small molecules may be determined based on functional assays in vitro or in vivo. Certain HIF1α inhibitory molecules (i.e., HIF1α inhibitors) are known in the art and include, for example, KC7F2, IDF-11774, aminoflavone, AJM290, AW464, tanespimycin, alvespimycin, PX-478, FM19G11, resveratrol, rapamycin, everolimus, CCI779, silibinin, digoxin, YC-1, phenethyl isothiocyanite, chetomin, flavopiridol, bortezomib, amphotericin B, Bay 87-2243, PX-478, and ganetasipib.
One or more of the HIF1α inhibitors described herein may be excluded from certain embodiments of the present disclosure.
PFKFB3 is also referred to as 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3, 6PF-2-K/Fru-2,6-P2ase Brain/Placenta-Type Isozyme, renal carcinoma antigen NY-REN-56, 6PF-2-K/Fru-2,6-P2ase 3, PFK/FBPase 3, IPFK-2, Inducible 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase 3, Fructose-6-Phosphate,2-Kinase/Fructose-2, 6-Bisphosphatase 3, 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase 3, IPFK2, and PFK2.
The following sequence exemplifies the PFKFB3 mRNA in humans (SEQ ID NO:3):
The protein sequence is exemplified by the following (SEQ ID NO:4):
The above protein and mRNA sequence represents one isoform (isoform 2) of the gene, but other isoforms are known in the art. For example, the Genbank numbers below represent additional isoforms. The sequences associated with these Genbank numbers are incorporated by reference for all purposes.
The protein encoded by this gene belongs to a family of bifunctional proteins that are involved in both the synthesis and degradation of fructose-2,6-bisphosphate, a regulatory molecule that controls glycolysis in eukaryotes. The encoded protein has a 6-phosphofructo-2-kinase activity that catalyzes the synthesis of fructose-2,6-bisphosphate (F2,6BP), and a fructose-2,6-biphosphatase activity that catalyzes the degradation of F2,6BP. This protein is required for cell cycle progression and prevention of apoptosis. It functions as a regulator of cyclin-dependent kinase 1, linking glucose metabolism to cell proliferation and survival in tumor cells.
A PFKFB3 inhibitor may refer to any member of the class of compound or agents having an IC50 of 200 μM or lower concentration for a PFKFB3 activity, for example, at least or at most or about 200, 100, 80, 50, 40, 20, 10, 5, 1 μM, 100, 10, 1 nM or lower concentration (or any range or value derivable therefrom) or any compound or agent that inhibits the expression of PFKFB3. Examples of PFKFB3 activity or function may include, but not be limited to, regulation of glycolysis, kinase activity, regulation of CDK1, 6-phosphofructo-2-kinase activity, fructose-2,6-bisphosphate 2-phosphatase activity, ATP binding activity, and enzyme catalysis activity. In some embodiments, the inhibition can be a decrease as compared with a control level or sample. In further embodiments, a functional assay such as MTT assay, cell proliferation assay, Ki67 immunofluoresence, apoptosis assay, or glycolysis assay may be used to test the PFKFB3 inhibitors. Methods and compositions of the disclosure may comprise one or more PFKFB3 inhibitors. It is specifically contemplated that one or more of the disclosed PFKFB3 inhibitors may be excluded from certain embodiments of the disclosure. Also contemplated herein are pharmaceutically acceptable salts and prodrugs of the described PFKFB3 inhibitors. Although certain example PFKFB3 inhibitors are described herein, it is contemplated that any PFKFB3 inhibitor may be implemented in certain embodiments of the disclosure.
In some embodiments, a PFKFB3 inhibitor is operatively linked (e.g., covalently linked, non-covalently linked, etc.) to a targeting molecule. A targeting molecule describes a molecule designed to bind to a particular biological or cellular target. A targeting molecule may be used to specifically direct or target an agent (e.g., a therapeutic agent such as a PFKFB3 inhibitor) to a particular biological tissue or cell type (e.g., β-cells). In some embodiments, a targeting molecule is configured to bind to β-cells of a subject. In some embodiments, the targeting molecule is configured to bind to a glucagon-like peptide-1 (GLP-1) receptor, thereby targeting the PFKFB3 inhibitor to β-cells of the subject. In some embodiments, the targeting molecule is an antibody or antibody-like molecule.
Inhibitory nucleic acids or any ways of inhibiting gene expression of PFKFB3 known in the art are contemplated in certain embodiments. Examples of an inhibitory nucleic acid include but are not limited to antisense nucleic acids such as: siRNA (small interfering RNA), short hairpin RNA (shRNA), double-stranded RNA, an any other antisense oligonucleotide. Also included are ribozymes or nucleic acids encoding any of the inhibitors described herein. An inhibitory nucleic acid may inhibit the transcription of a gene or prevent the translation of a gene transcript in a cell. An inhibitory nucleic acid may be from 16 to 1000 nucleotides long, and in certain embodiments from 18 to 100 nucleotides long. The nucleic acid may have nucleotides of at least or at most 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, 40, 50, 60, 70, 80, 90 or any range derivable therefrom.
As used herein, “isolated” means altered or removed from the natural state through human intervention. For example, an siRNA naturally present in a living animal is not “isolated,” but a synthetic siRNA, or an siRNA partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated siRNA can exist in substantially purified form, or can exist in a non-native environment such as, for example, a cell into which the siRNA has been delivered.
Inhibitory nucleic acids are well known in the art. For example, siRNA and double-stranded RNA have been described in U.S. Pat. Nos. 6,506,559 and 6,573,099, as well as in U.S. Patent Publications 2003/0051263, 2003/0055020, 2004/0265839, 2002/0168707, 2003/0159161, and 2004/0064842, all of which are herein incorporated by reference in their entirety.
Particularly, an inhibitory nucleic acid may be capable of decreasing the expression of PFKFB3 by at least 10%, 20%, 30%, or 40%, 50%, 60%, 70%, 75%, 80%, 90%, 95% or more or any range or value derivable therein.
In further embodiments, there are synthetic nucleic acids that are PFKFB3 inhibitors. An inhibitor may be between 17 to 25 nucleotides in length and comprises a 5′ to 3′ sequence that is at least 90% complementary to any portion of the 5′ to 3′ sequence of a mature PFKFB3 mRNA. In certain embodiments, an inhibitor molecule is 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length, or any range derivable therein. Moreover, an inhibitor molecule has a sequence (from 5′ to 3′) that is or is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or 100% complementary, or any range derivable therein, to any portion of the 5′ to 3′ sequence of a mature PFKFB3 mRNA, particularly a mature, naturally occurring mRNA. One of skill in the art could use a portion of the probe sequence that is complementary to the sequence of a mature mRNA as the sequence for an mRNA inhibitor. Moreover, that portion of the probe sequence can be altered so that it is still 90% complementary to the sequence of a mature mRNA.
Inhibitor nucleic acids for PFKFB3 are also commercially available. For example, the following miRNAs may inhibit PFKFB3: hsa-mir-26b-5p (MIRT028775), hsa-mir-330-3p (MIRT043840), hsa-mir-6779-5p (MIRT454747), hsa-mir-6780a-5p (MIRT454748), hsa-mir-3689c (MIRT454749), hsa-mir-3689b-3p (MIRT454750), hsa-mir-3689a-3p (MIRT454751), hsa-mir-30b-3p (MIRT454752), hsa-mir-1273h-5p (MIRT454753), hsa-mir-6778-5p (MIRT454754), hsa-mir-1233-5p (MIRT454755), hsa-mir-6799-5p (MIRT454756), hsa-mir-7106-5p (MIRT454757), hsa-mir-6775-3p (MIRT454758), hsa-mir-1291 (MIRT454759), hsa-mir-765 (MIRT454760), hsa-mir-423-5p (MIRT454761), hsa-mir-3184-5p (MIRT454762), hsa-mir-6856-5p (MIRT454763), hsa-mir-6758-5p (MIRT454764), hsa-mir-3185 (MIRT527973), hsa-mir-6892-3p (MIRT527974), hsa-mir-6840-5p (MIRT527975), and hsa-mir-6865-3p (MIRT527976).
siRNAs and shRNAs are also commercially available from, for example, Santa Cruz biotechnology (sc-44011 and sc-44011-SH, respectively).
In certain embodiments, disclosed herein is a PFKFB3 inhibitor peptide. In some embodiments, the PFKFB3 inhibitor polypeptide is a PFKFB3 antibody. In some embodiments, the anti- PFKFB3 antibody is a monoclonal antibody or a polyclonal antibody. In some embodiments, the antibody is a chimeric antibody, an affinity matured antibody, a humanized antibody, or a human antibody. In some embodiments, the antibody is an antibody-like molecule. In some embodiments, the antibody is an antibody fragment. In some embodiments, the antibody fragment comprises a Fab, Fab′, Fab′-SH, F(ab′)2, or scFv. In one embodiment, the antibody is a chimeric antibody, for example, an antibody comprising antigen binding sequences from a non-human donor grafted to a heterologous non-human, human or humanized sequence (e.g., framework and/or constant domain sequences). In one embodiment, the non-human donor is a mouse. In one embodiment, an antigen binding sequence is synthetic, e.g., obtained by mutagenesis (e.g., phage display screening, etc.). In one embodiment, a chimeric antibody has murine V regions and human C region. In one embodiment, the murine light chain V region is fused to a human kappa light chain or a human IgG1 C region.
Examples of antibody fragments include, without limitation: (i) the Fab fragment, consisting of VL, VH, CL and CH1 domains; (ii) the “Fd” fragment consisting of the VH and CH1 domains; (iii) the “Fv” fragment consisting of the VL and VH domains of a single antibody; (iv) the “dAb” fragment, which consists of a VH domain; (v) isolated CDR regions; (vi) F(ab')2 fragments, a bivalent fragment comprising two linked Fab fragments; (vii) single chain Fv molecules (“scFv”), wherein a VH domain and a VL domain are linked by a peptide linker which allows the two domains to associate to form a binding domain; (viii) bi-specific single chain Fv dimers (see U.S. Pat. No. 5,091,513) and (ix) diabodies, multivalent or multispecific fragments constructed by gene fusion (U.S. Patent Pub. 2005/0214860). Fv, scFv or diabody molecules may be stabilized by the incorporation of disulphide bridges linking the VH and VL domains. Minibodies comprising a scFv joined to a CH3 domain may also be made (Hu et al, 1996).
As used herein, a “small molecule” refers to an organic compound that is either synthesized via conventional organic chemistry methods (e.g., in a laboratory) or found in nature. Typically, a small molecule is characterized in that it contains several carbon-carbon bonds, and has a molecular weight of less than about 1500 grams/mole. In certain embodiments, small molecules are less than about 1000 grams/mole. In certain embodiments, small molecules are less than about 550 grams/mole. In certain embodiments, small molecules are between about 200 and about 550 grams/mole. In certain embodiments, small molecules exclude peptides (e.g., compounds comprising 2 or more amino acids joined by a peptidyl bond). In certain embodiments, small molecules exclude nucleic acids.
For example, a small molecule PFKFB3 inhibitor may be any small molecule that is determined to inhibit PFKFB3 function or activity. Such small molecules may be determined based on functional assays in vitro or in vivo. In some embodiments, a PFKFB3 inhibitor of the present disclosure is a PFKFB3 inhibitory molecule. PFKFB3 inhibitory molecules are known in the art and described in, for example, U.S. Patent publications 20130059879, 20120177749, 20100267815, 20100267815, and 20090074884, which are herein incorporated by reference.
Example inhibitory compounds include: (1H-Benzo[g]indol-2-yl)-phenyl-methanone; (3H-Benzo[e]indo1-2-yl)-phenyl-methanone ; (3H-Benzo[e]indo1-2-yl)-(4-methoxy-phenyl)-methanone ; (3H-Benzo[e]indo1-2-yl)-pyridin-4-yl-methanone; HCl salt of (3H-Benzo[e]indo1-2-yl)-pyridin-4-yl-methanone; (3H-Benzo[e]indo1-2-yl)-(3-methoxy-phenyl)-methanone; (3H-Benzo[e]indo1-2-yl)-pyridin-3-yl-methanone ; (3H-Benzo[e]indo1-2-yl)-(2-methoxy-phenyl)-methanone; (3H-Benzo[e]indo1-2-yl)-(2-hydroxy-phenyl)-methanone; (3H-Benzo[e]indo1-2-yl)-(4-hydroxy-phenyl)-methanone; (5-Methyl-3H-benzo[e]indo1-2-yl)-phenyl-methanone; Phenyl-(7H-pyrrolo [2,3-h]quinolin-8-yl)-methanone; (3H-Benzo[e]indo1-2-yl)-(3-hydroxy-phenyl)-methanone; (3H-benzo[e]indo1-2-yl)-(2-chloro-pyridin-4-yl)-methanone; (3H-benzo[e]indo1-2-yl)-(1-oxy-pyridin-4-yl)-methanone; Phenyl-(6,7,8,9-tetrahydro-3H-benzo[e]indo1-2-yl)-methanone ; (3H-Benzo[e]indo1-2-yl)-(4-hydroxy-3-methoxylthenyl)-methanone; (3H-Benzo[e]indo1-2-yl)-(4-benzyloxy-3-methoxy-phenyl)-methanone; 4-(3H-Benzo[e]indole-2-carbonyl)-benzoic acid methyl ester; 4-(3H-Benzo[e]indole-2-carbonyl)-benzoic acid; (4-Amino-phenyl)-(3H-benzo[e]indo1-2-yl)-methanone; 5-(3H-Benzo[e]indole-2-carbonyl)-2-benzyloxy-benzoic acid methyl; 5-(3H-Benzo[e]indole-2-carbonyl)-2-benzyloxy-benzoic Acidmethanone; (3H-Benzo[e]indo1-2-yl)-(2-methoxy-pyridin-4-yl)-methanone; (5-Fluoro-3H-benzo[e]indo1-2-yl)-(3-methoxy-phenyl)-methanone; (5-Fluoro-3H-benzo[e]indo1-2-yl)-pyridin-4-yl-methanone ; (4-Benzyloxy-3-methoxy-phenyl)-(5-fluoro-3H-benzo[e]indo1-2-yl)- methanone; (5-Fluoro-3H-benzo[e]indo1-2-yl)-(4-hydroxy-3-methoxy-phenyl)-methanone; (3H-Benzo[e]indo1-2-yl)-(3-hydroxymethyl-phenyl)-methanone; Cyclohexyl-(5-fluoro-3H-benzo[e]indo1-2-yl)-methanone; (5-Fluoro-3H-benzo[e]indo1-2-yl)-(3-fluoro-4-hydroxy-phenyl)-methanone; (3H-Benzo[e]indo1-2-yl)-p-tolyl-methanone; (3H-B enzo[e]indo1-2-yl)-(3-methoxy-phenyl)-methanol; (3H-Benzo[e]indo1-2-yl)-pyridin-4-yl-methanol; 3H-Benzo[e]indole-2-carboxylic acid phenylamide; 3H-Benzo[e]indole-2-carboxylic acid (3-methoxy-phenyl)-amide; (3H-Benzo[e]indo1-2-yl)-(4-dimethylamino-phenyl)-methanone; (4-Amino-3-methoxy-phenyl)-(3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-3-methoxy-phenyl)-(5-hydroxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-3-methoxy-phenyl)-(5-methoxy-3H-benzo[e]indo1-2-yl)-methanone; N-[4-(3H-Benzo[e]indole-2-carbonyl)-phenyl]-methanesulfonamide; 3H-Benzo[e]indole-2-carboxylic acid (4-amino-phenyl)-amide; (4-Amino-phenyl)-(5-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-2-fluoro-phenyl)-(5-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-3-fluoro-phenyl)-(5-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-2-methoxy-phenyl)-(5-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-phenyl)-(9-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-3-methoxy-phenyl)-(9-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-2-methoxy-phenyl)-(9-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-3-fluoro-phenyl)-(9-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-2-fluoro-phenyl)-(9-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-3-fluoro-phenyl)-(3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-2-fluoro-phenyl)-(3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-phenyl)-(7-methoxy-3H-benzo[e]indo1-2-yl)-methanone; (4-Amino-phenyl)-(5-hydroxy-3-methyl-3H-benzo[e]indol-2-yl)-methanone; (7-Amino-5-fluoro-9-hydroxy-3H-benzo[e]indo1-2-yl)-(3-methyl-pyridin-4-yl)-methanone; (5-Amino-3H-pyrrolo[3,2-f]isoquinolin-2-yl)-(3-methoxy-pyridin-4-yl)-methanone; (4-Amino-2-methyl-phenyl)-(9-hydroxy-3H-pyrrolo[2,3-c]quinolin-2-yl)-methanone; and (4-Amino-phenyl)-(7-methanesulfonyl-3H-benzo[e]indol-2-yl)-methanone.
Further example inhibitory compounds include: 1-Pyridin-4-yl-3-quinolin-4-yl-propenone; 1-Pyridin-4-yl-3-quinolin-3-yl-propenone; 1-Pyridin-3-yl-3-quinolin-2-yl-propenone; 1-Pyridin-3-yl-3-quinolin-4-yl-propenone; 1-Pyridin-3-yl-3-quinolin-3-yl-propenone; 1-Naphthalen-2-yl-3-quinolin-2-yl-propenone; 1-Naphthalen-2-yl-3-quinolin-3-yl-propenone; 1-Pyridin-4-yl-3-quinolin-3-yl-propenone; 3-(4-Hydroxy-quinolin-2-yl)-1-pyridin-4-yl-propenone; 3-(8-Hydroxy-quinolin-2-yl)-1-pyridin-3-yl-propenone; 3-Quinolin-2-yl-1-p-tolyl-propenone; 3-(8-Hydroxy-quinolin-2-yl)-1-pyridin-4-yl-propenone; 3-(8-Hydroxy-quinolin-2-yl)-1-p-tolyl-propenone; 3-(4-Hydroxy-quinolin-2-yl)-1-p-tolyl-propenone; 1-Phenyl-3-quinolin-2-yl-propenone; 1-Pyridin-2-yl-3-quinolin-2-yl-propenone; 1-(2-Hydroxy-phenyl)-3-quinolin-2-yl-propenone; 1-(4-Hydroxy-phenyl)-3-quinolin-2-yl-propenone; 1-(2-Amino-phenyl)-3-quinolin-2-yl-propenone; 1-(4-Amino-phenyl)-3-quinolin-2-yl-prop enone ; 4-(3-Quinolin-2-yl-acryloyl)-benzamide; 4-(3-Quinolin-2-yl-acryloyl)-benzoic acid; 3-(8-Methyl-quinolin-2-yl)-1-pyridin-4-yl-propenone ; 1-(2-Fluoro-pyridin-4-yl)-3-quinolin-2-yl-propenone; 3-(8-Fluoro-quinolin-2-yl)-1-pyridin-4-yl-propenone; 3-(6-Hydroxy-quinolin-2-yl)-1-pyridin-4-yl-propenone; 3-(8-Methylamino-quinolin-2-yl)-1-pyridin-4-yl-propenone; 3-(7-Methyl-quinolin-2-yl)-1-pyridin-4-yl-propenone; and 1-Methyl-4-[3-(8-methyl-quinolin-2-yl)-acrylo yl]-pyridinium.
Further example inhibitory compounds include: PFK15 (1-(4-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one); (2S)-N-[4-[[3-Cyano-1-(2-methylpropyl)-1H-indol-5-yl]oxy]phenyl]-2-pyrrolidinecarboxamide 3PO (3-(3-Pyridinyl)-1-(4-pyridinyl)-2-propen-1-one); (2S)-N-[4-[[3-Cyano-1-[(3,5-dimethyl-4-isoxazolyl)methyl]-1H-indol-5-yl]oxy]phenyl]-2-pyrrolidinecarboxamide; and Ethyl 7-hydroxy-2-oxo-2H-1-benzopyran-3-carboxylate.
Further example inhibitory compounds include: N-bromoacetylethanolamine phosphate (BrAcNHEtOP), 7,8-dihydroxy-3-(4-hydroxyphenyl) chromen-4-one (YN1), ethyl 7-hydroxy-2-oxochromene-3-carboxylate (YZ9), 1-(3-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one (PQP), PFK-158, Compound 26 (Boyd et al. J. Med Chem 2015), KAN0436151, and KAN0436067.
One or more of the PFKFB3 inhibitory molecules described herein may be excluded from certain embodiments of the present disclosure.
Aspects of the present disclosure are directed to methods for elimination of bihormonal cells from a population of cells, as well as compositions for use thereof. As used herein, the term “bihormonal cells” (also “polyhormonal cells”) refers to cells which produce oth insulin (i.e., are “insulin+”) and glucagon (i.e., are “glucacon+”). Such bihormonal cells are recognized in the art and are described in, for example, J E, Erener S. et al., Stem Cell Res. 2014 January;12(1):194-208 and Alvarez-Dominguez J R, et al. Cell Stem Cell. 2020 January 2;26(1):108-122.e10, each of which is incorporated by reference herein.
As disclosed herein, inhibition of PFKFB3 and/or HIF1α can be used to eliminate bihormonal cells from a population of, for example, pancreatic islet cells. Accordingly, aspects of the disclosure are directed to methods for eliminatin of bihormonal cells from a population of cells comprising providing a PFKFB3 inhibitor and/or a HIF1α inhibitor. In some embodiments, the inhibitor is provided to the population of cells in vitro. In some embodiments, the inhibitor is provided to the population of cells in vivo. In some embodiments, the population of cells comprises differentiated stem cells. Such differentiated stem cells include, for example, pancreatic islet cells derived from differentiated stem cells and bihormonal cells derived from differentiated stem cells. In some embodiments, the stem cells are induced pluripotent stem cells (iPSCs). In some embodiments, the stem cells are embryonic stem cells. In some embodiments, the stem cells are obtained from a patient having, at risk of having, or suspected of having Type 1 diabetes or Type 2 diabetes. The disclosed methods may further comprise, after providing the PFKFB3 inhibitor and/or HIF1α inhibitor, administering the population of cells to a subject. In some embodiments, the subject has, is at risk of having, or is suspected of having Type 1 diabetes or Type 2 diabetes. In some embodiments, the population of cells are autologous to the subject. In some embodiments, the population of cells are not autologous to the subject.
Embodiments include methods for treating diabetes with compositions comprising a HIF1α inhibitor and/or a PFKFB3 inhibitor. In some embodiments, a disclosed composition comprises a HIF1α inhibitor. In some embodiments, a disclosed composition comprises a PFKFB3 inhibitor. In some embodiments, a disclosed composition comprises a HIF1α inhibitor and a PFKFB3 inhibitor. Administration of the compositions will typically be via any common route. This includes, but is not limited to oral, parenteral, orthotopic, intradermal, subcutaneous, intramuscular, intraperitoneal, intranasal, intratumoral, or intravenous injection. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain about 10% to about 95% of active ingredient, or about 25% to about 70%. In some embodiments, the compositions are administered orally.
Typically, compositions are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective and immune modifying. The quantity to be administered depends on the subject to be treated. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner.
The manner of application may be varied widely. Any of the conventional methods for administration of a pharmaceutical composition are applicable. These are believed to include oral application on a solid physiologically acceptable base or in a physiologically acceptable dispersion, parenterally, by injection and the like. The dosage of the pharmaceutical composition will depend on the route of administration and will vary according to the size and health of the subject.
In many instances, it will be desirable to have multiple administrations of at most about or at least about 3, 4, 5, 6, 7, 8, 9, 10 or more. The administrations may range from 2 day to twelve week intervals, more usually from one to two week intervals. The course of the administrations may be followed by assays for HIF1α and/or PFKFB3 activity.
The phrases “pharmaceutically acceptable” or “pharmacologically acceptable” refer to molecular entities and compositions that do not produce an adverse, allergic, or other untoward reaction when administered to an animal, or human. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredients, its use in immunogenic and therapeutic compositions is contemplated.
“Pharmaceutically acceptable salts” means salts of compounds (e.g., inihbitors, PFKFB3 inhibitors) of the present invention which are pharmaceutically acceptable, as defined above, and which possess the desired pharmacological activity. Such salts include acid addition salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or with organic acids such as 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, 2-naphthalenesulfonic acid, phenylpropionic acid, 4,4′-methyleriebis(3-hydroxy-2-ene-1-carboxylic acid), 4-methylbicyclo[2,2.2]oct-2-ene-1-carboxylic acid, acetic acid, aliphatic mono- and dicarboxylicacids, aliphatic: sulfuric acids, aromatic sulfuric acids, benzenesulfonic acid, benzoic acid, camphorsulfonic acid, carbonic acid, cinnamic acid, citric acid, cyclopentanepropionic acid, ethanesulfonic acid, fumaric acid, glucoheptonic acid, gluconic acid, glutamic acid, glycolic acid, heptanoic acid, hexanoic acid, hydroxynaphthoic acid, lactic acid, laurylsulfuric acid, maleic acid, make acid, malonic acid, mandelic acid, methanc.sulfonic acid, muconic acid, o-4-hydroxybenzoyl)benzoic acid, oxalic acid, p-chlorobenzenesulfonic acid, phenyl-substituted alkapoic acids, propionic acid, p-toluenesulfonic acid, pyruvic acid, salicylic acid, stearic acid, succinic acid, tartaric acid, tertiarybutylacetic acid, trimethylacetic acid, and the like. Pharmaceutically acceptable salts also include base addition salts which may be formed when acidic protons present are capable of reacting with inorganic or organic bases. Acceptable inorganic bases include sodium hydroxide, sodium carbonate, potassium hydroxide, aluminum hydroxide and calcium hydroxide. Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine and the like. It should be recognized that the particular anion or cation forming a part of any salt of this invention is not critical, so long as the salt, as a whole, is pharmacologically acceptable. Additional examples of pharmace,utically acceptable salts and their methods of preparation and use are presented in Handbook of Pharmaceutical Salts: Properties, and Use (P. H, Stahl & C. G Wermuth eds., Verlag Helvetica Chimica Acta, 2002).
The disclosed compositions may include a prodrug. “Prodrug” means a compound that is convertible in vivo metabolically into an inhibitor according to the present invention. The prodrug itself may or may not also have activity with respect to a given target protein. For example, a compound comprising a hydroxy group may be administered as an ester that is converted by hydrolysis in vivo to the hydroxy compound. Suitable esters that may be converted in vivo into hydroxy compounds include acetates, citrates, lactates, phosphates, tartrates, malonates oxalates, salicylates, propionates, succinates, fumarases, maleates, methylene-bis-β-hydroxynaphthoate, gentisates, isethionates, di-p-toluoyltartrates, methanesulfonates, ethanesulfonates, benzenesuifonates, p-toluenesulfonates, cyclohexylsulfamates, quinates, esters of amino acids, and the like. Similarly, a compound comprising an amine group may be administered as an amide that is converted by hydrolysis in vivo to the amine compound.
The HIF1α inhibitors and/or a PFKFB3 inhibitors can be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intradermal, intramuscular, sub-cutaneous, or even intraperitoneal routes. In some embodiments, the composition is administered by intravenous injection. The preparation of an aqueous composition that contains an active ingredient will be known to those of skill in the art in light of the current disclosure. Typically, such compositions can be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for use to prepare solutions or suspensions upon the addition of a liquid prior to injection can also be prepared; and, the preparations can also be emulsified.
The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil, or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that it may be easily injected. It also should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
The compositions may be formulated into a neutral or salt form. Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions are prepared by incorporating the active ingredients in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques, which yield a powder of the active ingredient, plus any additional desired ingredient from a previously sterile-filtered solution thereof.
An effective amount of therapeutic or prophylactic composition is determined based on the intended goal. The term “unit dose” or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the composition calculated to produce the desired responses discussed above in association with its administration, i.e., the appropriate route and regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the result and/or protection desired. Precise amounts of the composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the subject, route of administration, intended goal of treatment (alleviation of symptoms versus cure), and potency, stability, and toxicity of the particular composition. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically or prophylactically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above.
Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically or prophylactically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above.
As an example, for a human adult (weighing approximately 70 kilograms), from about 0.1 mg to about 3000 mg (including all values and ranges there between), or from about 5 mg to about 1000 mg (including all values and ranges there between), or from about 10 mg to about 100 mg (including all values and ranges there between), of a compound are administered. It is understood that these dosage ranges are by way of example only, and that administration can be adjusted depending on the factors known to the skilled artisan.
In certain embodiments, a subject is administered about, at least about, or at most about 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7. 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5, 15.0, 15.5, 16.0, 16.5, 17.0, 17.5, 18.0, 18.5, 19.0. 19.5, 20.0, 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, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, 230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295, 300, 305, 310, 315, 320, 325, 330, 335, 340, 345, 350, 355, 360, 365, 370, 375, 380, 385, 390, 395, 400, 410, 420, 425, 430, 440, 441, 450, 460, 470, 475, 480, 490, 500, 510, 520, 525, 530, 540, 550, 560, 570, 575, 580, 590, 600, 610, 620, 625, 630, 640, 650, 660, 670, 675, 680, 690, 700, 710, 720, 725, 730, 740, 750, 760, 770, 775, 780, 790, 800, 810, 820, 825, 830, 840, 850, 860, 870, 875, 880, 890, 900, 910, 920, 925, 930, 940, 950, 960, 970, 975, 980, 990, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900, 3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100, 4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 6000, 7000, 8000, 9000, 10000 milligrams (mg) or micrograms (mcg) or μg/kg or micrograms/kg/minute or mg/kg/min or micrograms/kg/hour or mg/kg/hour, or any range derivable therein.
A dose may be administered on an as needed basis or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, or 24 hours (or any range derivable therein) or 1, 2, 3, 4, 5, 6, 7, 8, 9, or times per day (or any range derivable therein). A dose may be first administered before or after signs of a condition. In some embodiments, the patient is administered a first dose of a regimen 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 hours (or any range derivable therein) or 1, 2, 3, 4, or 5 days after the patient experiences or exhibits signs or symptoms of the condition (or any range derivable therein). The patient may be treated for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more days (or any range derivable therein) or until symptoms of an the condition have disappeared or been reduced or after 6, 12, 18, or 24 hours or 1, 2, 3, 4, or 5 days after symptoms of an infection have disappeared or been reduced.
The therapy provided herein may comprise administration of a combination of therapeutic agents, such as a first treatment (e.g., HIF1α inhibitor) and a second treatment (e.g., a PFKFB3 inhibitor). The therapies may be administered in any suitable manner known in the art. For example, the first and second treatment may be administered sequentially (at different times) or concurrently (at the same time). In some embodiments, the first and second treatments are administered in a separate composition. In some embodiments, the first and second treatments are in the same composition.
Embodiments of the disclosure relate to compositions and methods comprising therapeutic compositions. The different therapies may be administered in one composition or in more than one composition, such as 2 compositions, 3 compositions, or 4 compositions. Various combinations of the agents may be employed.
The therapeutic agents of the disclosure may be administered by the same route of administration or by different routes of administration. In some embodiments, the therapy is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. In some embodiments, the antibiotic is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. The appropriate dosage may be determined based on the type of disease to be treated, severity and course of the disease, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician.
The treatments may include various “unit doses.” Unit dose is defined as containing a predetermined-quantity of the therapeutic composition. The quantity to be administered, and the particular route and formulation, is within the skill of determination of those in the clinical arts. A unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time. In some embodiments, a unit dose comprises a single administrable dose.
The quantity to be administered, both according to number of treatments and unit dose, depends on the treatment effect desired. An effective dose is understood to refer to an amount necessary to achieve a particular effect. In the practice in certain embodiments, it is contemplated that doses in the range from 10 mg/kg to 200 mg/kg can affect the protective capability of these agents. Thus, it is contemplated that doses include doses of about 0.1, 0.5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, and 200, 300, 400, 500, 1000 μg/kg, mg/kg, μg/day, or mg/day or any range derivable therein. Furthermore, such doses can be administered at multiple times during a day, and/or on multiple days, weeks, or months.
In certain embodiments, the effective dose of the pharmaceutical composition is one which can provide a blood level of about 1 μM to 150 μM. In another embodiment, the effective dose provides a blood level of about 4 μM to 100 μM.; or about 1 μM to 100 μM; or about 1 μM to 50 μM; or about 1 μM to 40 μM; or about 1 μM to 30 μM; or about 1 μM to 20 μM; or about 1 μM to 10 μM; or about 10 μM to 150 μM; or about 10 μM to 100 μM; or about 10 μM to 50 μM; or about 25 μM to 150 μM; or about 25 μM to 100 μM; or about 25 μM to 50 μM; or about 50 μM to 150 μM; or about 50 μM to 100 μM (or any range derivable therein). In other embodiments, the dose can provide the following blood level of the agent that results from a therapeutic agent being administered to a subject: about, at least about, or at most 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, or 100 μM or any range derivable therein. In certain embodiments, the therapeutic agent that is administered to a subject is metabolized in the body to a metabolized therapeutic agent, in which case the blood levels may refer to the amount of that agent. Alternatively, to the extent the therapeutic agent is not metabolized by a subject, the blood levels discussed herein may refer to the unmetabolized therapeutic agent.
Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the patient, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance or other therapies a subject may be undergoing.
It will be understood by those skilled in the art and made aware that dosage units of μg/kg or mg/kg of body weight can be converted and expressed in comparable concentration units of μg/ml or mM (blood levels), such as 4 μM to 100 μM. It is also understood that uptake is species and organ/tissue dependent. The applicable conversion factors and physiological assumptions to be made concerning uptake and concentration measurement are well-known and would permit those of skill in the art to convert one concentration measurement to another and make reasonable comparisons and conclusions regarding the doses, efficacies and results described herein.
Particular embodiments concern the methods of detecting a genetic signature in an individual. In some embodiments, the method for detecting the genetic signature may include selective oligonucleotide probes, arrays, allele-specific hybridization, molecular beacons, restriction fragment length polymorphism analysis, enzymatic chain reaction, flap endonuclease analysis, primer extension, 5′-nuclease analysis, oligonucleotide ligation assay, single strand conformation polymorphism analysis, temperature gradient gel electrophoresis, denaturing high performance liquid chromatography, high-resolution melting, DNA mismatch binding protein analysis, surveyor nuclease assay, sequencing, or a combination thereof, for example. The method for detecting the genetic signature may include fluorescent in situ hybridization, comparative genomic hybridization, arrays, polymerase chain reaction, sequencing, or a combination thereof, for example. The detection of the genetic signature may involve using a particular method to detect one feature of the genetic signature and additionally use the same method or a different method to detect a different feature of the genetic signature. Multiple different methods independently or in combination may be used to detect the same feature or a plurality of features. In some embodiments, the disclosed methods comprise detecting an expression level of PFKFB3 in cells (e.g., β-cells) from a subject.
In some embodiments, DNA may be analyzed by sequencing. The DNA may be prepared for sequencing by any method known in the art, such as library preparation, hybrid capture, sample quality control, product-utilized ligation-based library preparation, or a combination thereof. The DNA may be prepared for any sequencing technique. In some embodiments, sequencing, may be performed to cover approximately 70%, 75%, 80%, 85%, 90%, 95%, 99%, or greater percentage of targets at more than 20×, 25×, 30×, 35×, 40×, 45×, 50×, or greater than 50× coverage. In some embodiments, DNA sequencing is used to determine an expression level of PFKFB3 in cells (e.g., β-cells) from a subject.
In some embodiments, RNA may be analyzed by sequencing. The RNA may be prepared for sequencing by any method known in the art, such as poly-A selection, cDNA synthesis, stranded or nonstranded library preparation, or a combination thereof. The RNA may be prepared for any type of RNA sequencing technique, including stranded specific RNA sequencing. In some embodiments, sequencing may be performed to generate approximately 10 M, 15 M, 20 M, 25 M, 30 M, 35 M, 40 M or more reads, including paired reads. The sequencing may be performed at a read length of approximately 50 bp, 55 bp, 60 bp, 65 bp, 70 bp, 75 bp, 80 bp, 85 bp, 90 bp, 95 bp, 100 bp, 105 bp, 110 bp, or longer. In some embodiments, raw sequencing data may be converted to estimated read counts (RSEM), fragments per kilobase of transcript per million mapped reads (FPKM), and/or reads per kilobase of transcript per million mapped reads (RPKM). In some embodiments, RNA sequencing is used to determine an expression level of PFKFB3 in cells (e.g., β-cells) from a subject.
In some embodiments, protein may be analyzed by mass spectrometry. The protein may be prepared for mass spectrometry using any method known in the art. Protein, including any isolated protein encompassed herein, may be treated with DTT followed by iodoacetamide. The protein may be incubated with at least one peptidase, including an endopeptidase, proteinase, protease, or any enzyme that cleaves proteins. In some embodiments, protein is incubated with the endopeptidase, LysC and/or trypsin. The protein may be incubated with one or more protein cleaving enzymes at any ratio, including a ratio of μg of enzyme to μg protein at approximately 1:1000, 1:100, 1:90, 1:80, 1:70, 1:60, 1:50, 1:40, 1:30, 1:20, 1:10, 1:1, or any range between. In some embodiments, the cleaved proteins may be purified, such as by column purification. In certain embodiments, purified peptides may be snap-frozen and/or dried, such as dried under vacuum. In some embodiments, the purified peptides may be fractionated, such as by reverse phase chromatography or basic reverse phase chromatography. Fractions may be combined for practice of the methods of the disclosure. In some embodiments, one or more fractions, including the combined fractions, are subject to phosphopeptide enrichment, including phospho-enrichment by affinity chromatography and/or binding, ion exchange chromatography, chemical derivatization, immunoprecipitation, co-precipitation, or a combination thereof. The entirety or a portion of one or more fractions, including the combined fractions and/or phospho-enriched fractions, may be subject to mass spectrometry. In some embodiments, the raw mass spectrometry data may be processed and normalized using at least one relevant bioinformatics tool. In some embodiments, proteomics is used to determine an amount of PFKFB3 in cells (e.g., β-cells) from a subject.
Certain aspects of the present invention also concern kits containing compositions of the disclosure or compositions to implement methods of the disclosure. In some embodiments, kits can be used to evaluate one or more biomarkers. In certain embodiments, a kit contains, contains at least or contains at most 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, 100, 500, 1,000 or more probes, primers or primer sets, synthetic molecules or inhibitors, or any value or range and combination derivable therein. In some embodiments, there are kits for evaluating biomarker activity in a cell. In some embodiments, disclosed are kits for evaluating an expression level of one or more biomarker activities. In some embodiments, disclosed are kits for evaluating an expression level of PFKFB3 in β-cells from a subject.
Kits may comprise components, which may be individually packaged or placed in a container, such as a tube, bottle, vial, syringe, or other suitable container means.
Individual components may also be provided in a kit in concentrated amounts; in some embodiments, a component is provided individually in the same concentration as it would be in a solution with other components. Concentrations of components may be provided as lx, 2×, 5×, 10×, or 20× or more.
Kits for using probes, synthetic nucleic acids, nonsynthetic nucleic acids, and/or inhibitors of the disclosure for prognostic or diagnostic applications are included as part of the disclosure. Specifically contemplated are any such molecules corresponding to any biomarker identified herein, which includes nucleic acid primers/primer sets and probes that are identical to or complementary to all or part of a biomarker, which may include noncoding sequences of the biomarker, as well as coding sequences of the biomarker. In certain aspects, negative and/or positive control nucleic acids, probes, and inhibitors are included in some kit embodiments.
Any embodiment of the disclosure involving specific biomarker by name is contemplated also to cover embodiments involving biomarkers whose sequences are at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% identical to the mature sequence of the specified nucleic acid.
Embodiments of the disclosure include kits for analysis of a pathological sample by assessing biomarker profile for a sample comprising, in suitable container means, two or more biomarker probes, wherein the biomarker probes detect one or more of the biomarkers identified herein. The kit can further comprise reagents for labeling nucleic acids in the sample. The kit may also include labeling reagents, including at least one of amine-modified nucleotide, poly(A) polymerase, and poly(A) polymerase buffer. Labeling reagents can include an amine-reactive dye.
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
After excision of smaller pieces, pancreas was fixed in 4% paraformaldehyde (Electron Microscopy Sciences 19202, Hatfield, PA, USA) overnight in 4° C., paraffin-embedded, and sectioned at 4 μm thickness. For β-cell area, peroxidase- and hematoxylin staining were performed on deparaffinized sections that were sequentially incubated with rabbit anti-insulin antibody (Cell Signaling Technology C27C9, Danvers, MA, USA, 1:400), then with F(ab′)2 conjugates with Biotin-SP (Jackson ImmunoResearch 711-066-152, West Grove, PA, USA, 1:100 for IHC), after which steps the VECTASTAIN ABC Kits (HRP) (Vector Laboratories PK-4000, Burlingame, CA, USA), the DAB substrate Kits (HRP) (Vector Laboratories SK-4100, Burlingame, CA, USA), and Harris Hematoxylin were applied prior mounting the sections with Permount (Fisher SP15-100, Hampton, NH, USA). Morphometric analyses were performed using Image-Pro Plus 5.1 software on the Olympus IX70 inverted tissue culture microscope (Olympus, Center Valley, PA, USA). Imaging and data analysis was performed by two observers in a blinded fashion for the experimental mouse genotype of each section. The islet edges were manually circumscribed using a multichannel image. Insulin- and hematoxylin-positive areas were determined for each islet using pixel thresholding. The β-cell area was then calculated as insulin-positive areas/hematoxylin-positive areas×100%.
Immunofluorescence analysis was performed in Openlab 5.5.0 software on the Leica DM6000 B research microscope. The following antibodies were used: rabbit anti-PFKFB3 (Origene AP15137PU-N, Rockville, MD, USA, 1:100); mouse anti-MCM2 (BD Transduction Laboratories 610700, San Diego, CA, USA, 1:100); rabbit anti-cleaved caspase-3 (Cell Signaling Technology 9664S, Danvers, MA, USA, 1:400); guinea-pig anti-insulin (Abcam ab195956, Cambridge, MA, USA, 1:400); mouse anti-glucagon (Sigma-Aldrich G2654, St.Louis, MO, USA,1:1000 for IF), mouse anti-c-Myc (Santa Cruz Biotechnology Inc 9E10 sc-40, Dallas, Texas, USA, 1:100); mouse anti-HIF1α (Novus Biologicals NB100-105, Centennial, CO, USA, 1:50). Secondary antibodies were: F(ab′)2 conjugates with FITC (Jackson ImmunoResearch 706-096-148, West Grove, PA, USA, 1:200 for IF); F(ab′)2 conjugates with Cy3 (Jackson ImmunoResearch 711-166-152, West Grove, PA, USA, 1:200 for IF) and F(ab′)2 conjugates with Alexa 647 (Jackson ImmunoResearch 715-606-150, West Grove, PA, USA, 1:100 for IF). The In Situ Cell Death Detection Kit (Roche Diagnostics Corporation 12156792910, Indianapolis, IN, USA) was used for determination of cell death by TUNEL assay. Vectashield with DAPI (Vector Laboratories H1200, Burlingame, CA, USA) was used to mount the slides.
There is a progressive decline in β-cell function in T2D that is partly related to the accumulation of the toxic oligomers of hIAPP [3-5]. hIAPP forms membrane-permeable toxic oligomers that are implicated in misfolded protein stress in T2D. In response to misfolded protein stress by hIAPP, mitochondria in β-cells from humans with T2D acquired a defensive posture through mitochondrial network fragmentation (
DNA damage response (p53/p21WAF1 axis and accumulation of γH2A.X) document damage of β-cells in T2D and rodent models of T2D. Stress by protein misfolding and the surge of cytosolic Ca2+ triggered protective metabolic reprogramming of about one third of all β-cells in T2D (
Homozygous hIAPP+/+ mice were a gift from Dr. Peter Butler's laboratory and was previously described [15]. A β-cell-specific inducible PFKFB3 knockout mouse model (RIP-CreERT:PFKFB3m) was developed by crossing mice that carry the floxed PFKFB3 gene (JAX Laboratories) with mice that express Cre recombinase under control of the rat insulin promoter (RIP-CreERT). Mice on a homozygous hIAPP+/+ background were crossed with either PFKFB3fl/fl or RIP-CreERT mice and then crossed PFKFB3fl/fl hIAPP+/− and PFKFB3fl/fl RIP-CreERT mice together to generate the three experimental genotypes: RIP-CreERT PFKFB3wt/wt hIAPP−/−, RIP-CreERT PFKFB3wt/wt hIAPP+/− and RIP-CreERT PFKFB3ft/fl hIAPP+/− hereto referred as PFKFB3WT hIAPP−/−, PFKFB3WT hIAPP+/−, and PFKFB3βKO hIAPP+/−. All experimental groups were subjected to high fat diet. Cre-loxP recombination of the floxed sites in Pfkfb3 was induced by intra-peritoneal tamoxifen injection at the age of 20-27 weeks. The mice were given chow diet for 10 weeks post tamoxifen injection and then all mice were exposed for a high fat diet for another 13 weeks (HFD, Research Diets Inc, New Brunswick, NJ, USA) to induce diabetes in response to hIAPP+/− and HFD, since only male mice homozygous for hIAPP (hIAPP+/+) develop diabetes spontaneously [15]. The mice were maintained on a 12 hours day/night cycle at UCLA Institutional Animal Care and Use Committee (ARC) approved mice colony facility. At 30-37 weeks of age, all mice were assigned to receive diet containing high amounts of fat (35% w/w or 60% calories from fat; number D12492). The fat composition of the high-fat diet was 32.2% saturated, 35.9% monounsaturated, and 31.9% polyunsaturated fats. Mice had ad libitum access to diet and water for the duration of the study. Bodyweight and fasting plasma glucose levels were assessed weekly, with additional measures being made on days that included glucose- and insulin tolerance tests (IP-GTT and ITT, respectively).
An intraperitoneal glucose tolerance test (IP-GTT) was performed at 9 and 12 weeks after HFD (19 and 22 weeks post tamoxifen injection). Tail vein blood glucose was collected prior to and 15, 30, 60, 90, 120 minutes post glucose bolus injection. Retro-orbital bleeding was used to collect the blood for the second IP-GTT prior to and 30 minutes after glucose bolus injection. The mice were anesthetized by brief exposure to isoflurane (10 seconds). The blood was collected in EDTA coated microcentrifuge tube and the plasma was obtained by centrifuging the samples for 10 minutes (5000 RCF, 10 min, 4° C.).
Plasma glucose was determined using the glucose oxidase method and analysed with YSI 2300 STAT PLUS Glucose & L-Lactate Analyzer.
Fasted blood glucose was measured weekly after overnight fasting for 18 hours (after regular change of cages and bedding and withdrawal of food while providing water ad libitum) from a tail drawn blood using a freestyle blood glucose meter (Abbott Diabetes Care Inc, Alameda, CA, USA).
Insulin, c-peptide, and glucagon levels in plasma were determined using Ultrasensitive ELISA for mouse insulin (Mercodia 10-1247-01, Uppsala, Sweden), mouse c-peptide (Crystal Chem 90050, IL, USA), and mouse glucagon (Mercodia 10-1281-01, Uppsala, Sweden).
10 weeks after HFD (19 weeks after tamoxifen injection), intraperitoneal insulin tolerance test (0.75 IU/kg) (Lilly insulin Lispro, LLC, Indianapolis, USA) was performed in conscious mice fasted for 6 hours. Tail vein blood was collected prior to and at 0, 20, 40, 60 minutes post insulin administration for glucose measurement.
One week following IP-GTT and ITT, mice were euthanized by cervical dislocation. Medial cut was used to open the abdomen and chest cavities, while cut of the right ventricle was followed with a poke of the left ventricle with a needle to inject 10 ml cold phosphate buffered saline (PBS) slowly for perfusion of the pancreas. After perfusion, pancreas was placed in a cold PBS and separated it from other tissue including the surrounding fat. Pancreas was then weighed after absorbing the extra PBS with tissue.
After excision of smaller pieces, pancreas was fixed in 4% paraformaldehyde (Electron Microscopy Sciences 19202, Hatfield, PA, USA) overnight in 4° C., paraffin-embedded, and sectioned at 4 μm thickness. For β-cell area, peroxidase- and hematoxylin staining were performed on deparaffinized sections that were sequentially incubated with rabbit anti-insulin antibody (Cell Signaling Technology C27C9, Danvers, MA, USA, 1:400), then with F(ab′)2 conjugates with Biotin-SP (Jackson ImmunoResearch 711-066-152, West Grove, PA, USA, 1:100 for IHC), after which steps the VECTASTAIN ABC Kits (HRP) (Vector Laboratories PK-4000, Burlingame, CA, USA), the DAB substrate Kits (HRP) (Vector Laboratories SK-4100, Burlingame, CA, USA), and Harris Hematoxylin were applied prior mounting the sections with Permount (Fisher SP15-100, Hampton, NH, USA). Morphometric analyses were performed using Image-Pro Plus 5.1 software on the Olympus IX70 inverted tissue culture microscope (Olympus, Center Valley, PA, USA). Imaging and data analysis was performed by two observers in a blinded fashion for the experimental mouse genotype of each section. The islet edges were manually circumscribed using a multichannel image. Insulin- and hematoxylin-positive areas were determined for each islet using pixel thresholding. The β-cell area was then calculated as insulin-positive areas/hematoxylin-positive areas×100%.
Immunofluorescence analysis was performed in Openlab 5.5.0 software on the Leica DM6000 B research microscope. The following antibodies were used: rabbit anti-PFKFB3 (Origene AP15137PU-N, Rockville, MD, USA, 1:100); mouse anti-MCM2 (BD Transduction Laboratories 610700, San Diego, CA, USA, 1:100); rabbit anti-cleaved caspase-3 (Cell Signaling Technology 9664S, Danvers, MA, USA, 1:400); guinea-pig anti-insulin (Abcam ab195956, Cambridge, MA, USA, 1:400); mouse anti-glucagon (Sigma-Aldrich G2654, St.Louis, MO, USA,1:1000 for IF), mouse anti-c-Myc (Santa Cruz Biotechnology Inc 9E10 sc-40, Dallas, Texas, USA, 1:100); mouse anti-HIF1α (Novus Biologicals NB100-105, Centennial, CO, USA, 1:50). Secondary antibodies were: F(ab′)2 conjugates with FITC (Jackson ImmunoResearch 706-096-148, West Grove, PA, USA, 1:200 for IF); F(ab′)2 conjugates with Cy3 (Jackson ImmunoResearch 711-166-152, West Grove, PA, USA, 1:200 for IF) and F(ab′)2 conjugates with Alexa 647 (Jackson ImmunoResearch 715-606-150, West Grove, PA, USA, 1:100 for IF). The In Situ Cell Death Detection Kit (Roche Diagnostics Corporation 12156792910, Indianapolis, IN, USA) was used for determination of cell death by TUNEL assay. Vectashield with DAPI (Vector Laboratories H1200, Burlingame, CA, USA) was used to mount the slides.
Data are presented as an error of the mean (standard error, SEM) for the number of mice indicated. For the IP-GTT and ITT, areas under the curve (AUC) for glucose, insulin, C-peptide and glucagon were calculated using the trapezoidal rule. Mean data were compared between groups by analysis using student's t-test. P values less than 0.05 were considered statistically significant.
To mimic the impact of insulin resistance, misfolded protein stress, and old age as cumulative risk factors in diabetes and study the role of PFKFB3 in the preservation of damaged β-cells under high diabetogenic stress, mice were generated with β-cell-specific conditional disruption of Pfkfb3 gene on a hIAPP+/− background (see Methods section), exposed to a high fat diet for 13 weeks (PFKFB3βKO hIAPP+/−+HFD), and compared to PFKFB3WT hIAPP+/−+HFD and PFKFB3WT hIAPP−/−+HFD controls (experimental timeline presented in
Analysis of the metabolic performance of PFKFB3βKO hIAPP+/−+HFD mice revealed lower fasting glucose levels (
To investigate growth dynamics that ultimately led to comparable β-cell mass between PFKFB3βKO hIAPP+/−+HFD- and PFKFB3WT hIAPP+/−+HFD mice, TUNEL staining was performed to determine β-cell death and MCM2 immunostaining to determine β-cell replication. According to the TUNEL analysis, β-cell death was increased in the PFKFB3βKO hIAPP+/−+HFD mice relative to PFKFB3WT hIAPP−/−+HFD controls while it was comparable to PFKFB3WT hIAPP+/−+HFD mice (
To clarify the failure to recover β-cell function in spite of recovery of β-cell mass, HIF1α immunostaining was performed in the pancreatic sections of PFKFB3βKO hIAPP30 /−+HFD mice and found that about 10% of all β-cells remain positive for HIF1α, indicating a fraction of HIF1α positive- but PFKFB3 negative β-cells that remain after PFKFB3 genetic depletion (
To characterize the potential contribution of HIF1α-positive β-cells to loss of function, published RNA Seq data from human T2D was analyzed [1]. β-cells from healthy and T2D donors were reclustered (umap cluster) and annotated to the specific cell types based on the gene markers such as insulin (INS) for β-cells (umap_celltype,
Homozygous hIAPP+/+ mouse was a gift from Dr. Peter Butler's laboratory and was previously described (Janson et al., 1996). A β-cell-specific inducible PFKFB3 knockout mouse model (RIP-CreERT:PFKFB3fl/fl) was generated by crossing mice that carry the floxed Pfkfb3 gene (JAX Laboratories) with mice that express Cre recombinase under control of the rat insulin promoter (RIP-CreERT). Mice on a homozygous hIAPP+/+ background were crossed with either PFKFB3fl/f or RIP-CreERT mice and then PFKFB3fl/fl hIAPP+/− and PFKFB3fl/fl RIP-CreERT mice were crossed together to generate the three experimental genotypes: RIP-CreERT PFKFB3fl/fl hIAPP−/−, RIP-CreERT PFKFB3wt/wt hIAPP+/− and RIP-CreERT PFKFB3fl/fl hIAPP+/− hereto referred as PFKFB3WT hIAPP−/−, PFKFB3WT hIAPP+/− (PFKFB3WT diabetogenic stress, or PFKFB3WT DS), and PFKFB3βKO hIAPP+/− (PFKFB3βKO DS) respectively. Cre-loxP recombination of the floxed sites in Pfkfb3 was induced by intra-peritoneal tamoxifen injection at the age of 20-27 weeks. The mice were under a chow diet for 10 weeks post tamoxifen injection and then under high fat diet for another 13 weeks (HFD, Research Diets Inc, New Brunswick, NJ, USA) to induce diabetes in response to hIAPP+/− and HFD, since only male mice homozygous for hIAPP (hIAPP+/+) develop diabetes spontaneously (Janson et al., 1996). The mice were maintained on a 12 hours day/night cycle at UCLA Institutional Animal Care and Use Committee (ARC) approved mice colony facility. At 30-37 weeks of age, all mice were assigned to receive a diet containing high fat (35% w/w or 60% calories from fat; D12492). The fat composition of the high-fat diet was 32.2% saturated, 35.9% monounsaturated, and 31.9% polyunsaturated fats. Mice had ad libitum access to diet and water for the duration of the study. Body weight and fasting blood glucose levels were assessed weekly, with additional measures being made on days that included glucose- and insulin tolerance tests (IP-GTT and ITT, respectively).
Intra-peritoneal glucose tolerance test (IP-GTT) was performed at 9 and 12 weeks after HFD (19 and 22 weeks post tamoxifen injection). Tail vein blood glucose was collected prior to and 15, 30, 60, 90, 120 minutes post glucose bolus injection. Retro-orbital bleeding was used to collect the blood for the second IP-GTT prior to and 30 minutes after glucose bolus injection. The mice were anesthetized by brief exposure to isoflurane (10 seconds). The blood was collected in EDTA coated microcentrifuge tube and the plasma was obtained by centrifuging the samples for 10 minutes (5000 RCF, 10 min, 4° C.).
Fasted blood glucose was measured weekly after overnight fasting for 18 hours (after the regular change of cages and bedding and withdrawal of food while providing water ad libitum) from a tail drawn blood using a freestyle blood glucose meter (Abbott Diabetes Care Inc, Alameda, CA, USA). When blood glucose exceeded the detection range of the blood glucose meter, plasma glucose was determined using the glucose oxidase method and analyzed with YSI 2300 STAT PLUS Glucose & L-Lactate Analyzer.
Insulin, C-peptide, and glucagon levels in plasma were determined using Ultrasensitive ELISA for mouse insulin (Mercodia 10-1247-01, Uppsala, Sweden), mouse C-peptide (Crystal Chem 90050, IL, USA), and mouse glucagon (Mercodia 10-1281-01, Uppsala, Sweden).
10 weeks after HFD (19 weeks after tamoxifen injection), intraperitoneal insulin tolerance test (0.75 IU/kg) (Lilly insulin Lispro, LLC, Indianapolis, USA) was performed in conscious mice fasted for 6 hours. Tail vein blood was collected prior to and at 0, 20, 40, 60 minutes post insulin administration for glucose measurement.
One week following IP-GTT and ITT, mice were euthanized by cervical dislocation. Medial cut was used to open the abdomen and chest cavities, while cut of the right ventricle was followed with a poke of the left ventricle with a needle to inject 10 ml cold phosphate buffered saline (PBS) slowly for perfusion of the pancreas. After perfusion, pancreas was placed in a cold PBS and separated from other tissue including the surrounding fat. Pancreas was then weighed after absorbing the extra PBS with tissue.
After excision of smaller pieces, pancreas was fixed in 4% paraformaldehyde (Electron Microscopy Sciences 19202, Hatfield, PA, USA) overnight at 4° C., paraffin-embedded, and sectioned at 41.tm thickness. For β-cell area, peroxidase- and hematoxylin staining were performed on deparaffinized sections that were sequentially incubated with rabbit anti-insulin antibody (Cell Signaling Technology C27C9, Danvers, MA, USA, 1:400), then with F(ab′)2 conjugates with Biotin-SP (Jackson ImmunoResearch 711-066-152, West Grove, PA, USA, 1:100 for IHC), after which steps the VECTASTAIN ABC Kits (HRP) (Vector Laboratories PK-4000, Burlingame, CA, USA), the DAB substrate Kits (HRP) (Vector Laboratories SK-4100, Burlingame, CA, USA), and Harris Hematoxylin were applied prior to mounting the sections with Permount (Fisher SP15-100, Hampton, NH, USA). Morphometric analyses were performed using Image-Pro Plus 5.1 software on the Olympus IX70 inverted tissue culture microscope (Olympus, Center Valley, PA, USA). Imaging and data analysis was performed by two observers in a blinded fashion for the experimental mouse genotype of each section. The islet edges were manually circumscribed using a multichannel image. Insulin- and hematoxylin-positive areas were determined for each islet using pixel thresholding. The β-cell area was then calculated as insulin-positive areas/hematoxylin-positive areas*100%.
Immunofluorescence analysis was performed in Openlab 5.5.0 software on the Leica DM6000 B research microscope. The following antibodies were used: rabbit anti-PFKFB3 (Abcam ab181861, Cambridge, MA, USA, 1:100); mouse anti-MCM2 (BD Transduction Laboratories 610700, San Diego, CA, USA, 1:100); rabbit anti-cleaved caspase-3 (Cell Signaling Technology 9664S, Danvers, MA, USA, 1:400); guinea-pig anti-insulin (Abcam ab195956, Cambridge, MA, USA, 1:400); mouse anti-glucagon (Sigma-Aldrich G2654, St.Louis, MO, USA,1:1000), mouse anti-c-Myc (Santa Cruz Biotechnology Inc 9E10 sc-40, Dallas, Texas, USA, 1:100); mouse anti-HIF1α (Novus Biologicals NB100-105, Centennial, CO, USA, 1:50). Secondary antibodies were: F(ab′)2 conjugates with FITC Donkey Anti-Guinea Pig IgG (H+L) (Jackson ImmunoResearch 706-096-148, West Grove, PA, USA, 1:200 for IF); F(ab′)2 conjugates with Cy3 Donkey Anti-Rabbit IgG (H+L) (Jackson ImmunoResearch 711-166-152, West Grove, PA, USA, 1:200 for IF; F(ab′)2 conjugates with Cy3 Donkey Anti-Mouse IgG (H+L) (Jackson ImmunoResearch 711-165-151, West Grove, PA, USA, 1:200 for IF) and F(ab′)2 conjugates with Alexa 647 Donkey Anti-Mouse IgG (H+L) (Jackson ImmunoResearch 715-606-150, West Grove, PA, USA, 1:100 for IF). The In Situ Cell Death Detection Kit (Roche Diagnostics Corporation 12156792910, Indianapolis, IN, USA) was used for the determination of cell death by TUNEL assay. Vectashield with DAPI (Vector Laboratories H1200, Burlingame, CA, USA) was used to mount the slides.
The single-cell RNA-seq dataset was obtained from GEO accession GSE124742, in which the healthy and type 2 diabetes cells were used. To identify different cell types and find signature genes for each cell type, the R package Seurat (version 3.1.2) was used to analyze the expression matrix. Cells with less than 100 genes and 500 UMIs detected were removed from further analysis. Seurat function NormalizeData was used to normalize the raw counts. Variable genes were identified using the FindVariableGenes function. The Seurat ScaleData function was used to scale and center expression values in the dataset for dimensional reduction. Default parameters were used in the Seurat functions above. Principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) were used to reduce the dimensions of the data, and the first two dimensions were used in plots. The FindClusters function was later used to cluster the cells. The FindAllMarkers function was used to determine the marker genes for each cluster, which were then used to define the cell types. Differential expression analysis between two group of cells was carried out using the FindMarkers function. The Wilcoxon rank sum test was performed in the differential analysis, and the Benjamini-Hochberg procedure was applied to adjust the false discovery rate.
Data are presented as an error of the mean (standard error, SEM) for the number of mice indicated. For the IP-GTT and ITT, areas under the curve (AUC) for glucose, insulin, C-peptide and glucagon were calculated using the trapezoidal rule. Mean data were compared between groups by analysis using student's t-test. P values less than 0.05 were considered significant.
To study and dissect the role of PFKFB3 from HIF1α in the survival of damaged β-cells under diabetogenic stress in vivo, mice were generated with β-cell-specific conditional disruption of Pfkfb3 gene on a hIAPP+/− background and were exposed to a high fat diet for 13 weeks (PFKFB3βKO hIAPP+/−+HFD). Diabetogenic stress was deemed high since it involved insulin resistance (obesity) and exposure to misfolded proteins through hIAPP+/− expression, both impacted through high fat diet as well as old age all together known as cumulative risk factors in diabetes [16-18].
PFKFB3fl/fl hIAPP+/− mice were born at the expected Mendelian ratio. From one week before the monitoring of mice up to the end of the experiment, there was no difference in bodyweight among the different experimental groups (
PFKFB3βKO hIAPP+/−+HFD mice were compared to PFKFB3WT hIAPP+/−+HFD and PFKFB3WT hIAPP−/−+HFD controls. Efficient disruption of PFKFB3 expression was confirmed by PFKFB3 immunostaining of the pancreatic sections of the PFKFB3βKO hIAPP+/−+HFD mice using PFKFB3WT hIAPP+/+ as a positive control (
To establish if PFKFB3 in this model is linked to HIF1α expression, pancreatic sections from all experimental groups were immunostained with HIF1α antibody. HIF1α expression increased to 18.4±4.2% in β-cells from PFKFB3WT hIAPP+/−+HFD mice compared to PFKFB3WT hIAPP−/−+HFD control (*p<0.05). In PFKFB3βKO hIAPP+/−+HFD mice, 14.2±3.8% of all β-cells (
Analysis of the metabolic performance of PFKFB3βKO hIAPP+/−+HFD mice revealed increased glucose intolerance at both 9 (*p<0.05, n=4) and 12 weeks after onset of high fat diet (
Thus, it became imperative to compare β-cell fractional area and mass. β-cell fractional area and mass were unaltered among the experimental groups (
To further elucidate if the increase in β-/α cell ratio relied on the increased generation of β-cells, immunolabeling was performed with an early replication initiation marker, minichromosome maintenance protein 2 (MCM2) [19, 20]. The results showed that β-cells from PFKFB3βKO hIAPP+/−+HFD mice exhibited a three-fold increase in MCM2 labeling (5.3%±0.8%, *p<0.05), indicating increased β-cell replication compared to PFKFB3WT hIAPP+/−+HFD mice (1.9±0.04%) and similar to PFKFB3WT hIAPP−/−+HFD controls (7.0±1.3%,
To clarify whether replicating β-cells possessed any residual injury, the inventors made use of the specific marker of hIAPP-incurred damage in β-cells—the cytoplasmic accumulation of the calpain-mediated truncation of the protein c-Myc, called Myc-nick [14]. The analysis of the c-Myc staining revealed an increase of Myc-nick expression in PFKFB3WT hIAPP+/− (3.3±0.5%, *p<0.05) under diabetogenic stress but reversal to PFKFB3WT hIAPP−/−+HFD control mice levels in PFKFB3βKO hIAPP+/−+HFD mice (0.8±0.4% and 0.7±0.6%, respectively,
HIF1α immunostaining in the pancreatic sections of PFKFB3βKO hIAPP+/−+HFD affected about 14% of all β-cells and although it coincided with reduced misfolding protein stress measured by cytoplasmic c-Myc, this potentially indicated a reason for the non-recovered metabolic function in replicating β-cells (
To find a complement of β-cell population in cluster 7 or LDHA positive cells, the inventors double stained pancreatic sections from the experimental mice groups with specific insulin and glucagon antibodies. Diabetogenic stress increased twice the number of double-positive cells in PFKFB3WT hIAPP+/−+HFD compared to PFKFB3WT hIAPP−/−+HFD controls (5.7±2.8% relative to 2.7±1.8%, respectively). PFKFB3 knockout led to a reduction of cells with concomitant insulin and glucagon immunopositivity when compared to PFKFB3WT DS (0.8±0.3% relative to 5.7±2.8%,
Thus, PFKFB3 knockout led to the disappearance of β-cells with double insulin and glucagon identity, indicating that those are the cells that not only depend on PFKFB3-mediated survival upon hIAPP injury but the ones that accommodate the survival via double identity, probably both contributing to their compromised function.
Interestingly, these data pointed out that the HIF1a-positive cells in PFKFB3βKO hIAPP+/−+HFD do not possess double β- and α-identity indicating that the survival of double β- and α-identity possessing cells depends on PFKFB3 and not HIF1α.
These analyses also indicated that accumulation of HIF1α-positive cells in the mouse model of diabetes may be responsible for the loss of β-cell function in spite of β-cell mass recovery after PFKFB3 gene depletion. PFKFB3 depletion seems to trigger culling of damaged β-cells with both β-cell and α-cell identity that is both sufficient and necessary to replenish healthy β-cells by replication. However, independent immunolabeling by HIF1α further compromises the β-cell insulin secretion.
These studies strongly suggest that targeting (i.e., inhibiting) HIF1α, with or without co-targeting of PFKFB3, will lead to recovery of functionally competent β-cell mass and reversal of diabetes.
In these studies, the inventors demonstrate that the specific β-cell disruption of Pfkfb3 gene in adult mice under high diabetogenic stress leads to a partial islet regeneration.
This is achieved via culling of damaged and bihormonal (insulin and glucagon positive) cells and replication of remnant healthy β-cells.
Culling probably affects a substantial number of β-cells. PFKFB3 implication in remodeled metabolism explains its impact on survival—[13] but also poses a question related to the preservation of β-cell function. So metabolic remodeling by HIF1α-PFKFB3 pathway in misfolded protein stress (hIAPP) recapitulates the consequences of HIF1α expression after conditional inactivation of von Hippel Lindau gene (Vhl) [13, 31]. In presence or absence of diabetogenic stress, HIF1α activation led to diminished glucose-stimulated changes in cytoplasmic Ca2+ concentrations, electric activity and insulin secretion culminating in impaired systemic glucose tolerance in pancreatic β-cells [13, 31].
HIF1α was continuosly expressed in a significant number of β-cells from PFKFB3βKO DS mice (˜14%). This indicated that in this mouse model of diabetes, pertained HIF1α response is independent of PFKFB3. HIF1α expression levels in PFKFB3βKO DS and PFKFB3WT DS mice (14% and 18%, respectively) paralleled the glucose intolerance and the lower plasma insulin- and C-peptide levels in comparison to WT controls (p<0.05).
To investigate the role of HIF1α in the molecular basis for β-cell dysfunction, sc RNA Seq data from humans with obese-T2D and nondiabetics (ND) [27] was analyzed. The inventors made use of the distinction of LDHA positive-versus negative β-cells since LDHA is a bona fide target, serving as a substitute marker for HIF1α. HIF1α is regulated mainly posttranslationally with no changes in the transcript levels. LDHA positive β-cells overlapped with cluster 7 β-cell subpopulation and were represented by HIF1α-(ARNT2, GK, PFKFP, PDK4) and bihormonal signature (a and β-cell identity) (GCG, ARX and INS) and some markers of immaturity (ALDH 1A1). Double insulin- and glucagon positive cells in the mouse model resembled LDHA positive or cluster 7 β-cells and could originate from dedifferentiated or β-cells subjected to transdifferentiation [32].
Ingenuity Pathway Analysis (IPA) used for comparison between LDHA positive (cluster 7) and LDHA negative (cluster 1) β-cells in both health and T2D, indicated an existence of a master upstream regulator, the liver X receptor, a type of retinoid receptor (LXR/RXR) [33], potentially a part of the epistatic HIF1α metabolic pathway. Activation of this receptor may independently increase aerobic glycolysis in response to high fat diet via transcriptional upregulation of hexokinases 1 and 3 (HK1 and 3) and SLC2A1 (GLUT1)) and interplay with HIF1α [34].
Interestingly, the bihormonal β-cell subpopulation was present in the obese nondiabetics and in our WT controls under HFD indicating that formation of bihormonal cells may well be an adaptive response to increased lipogenesis and high fat diet. As such, double insulin and glucagon positive cells were not detected in WT controls or hIAPP+/+ in absence of HFD (used as negative controls), neither at prediabetic or diabetic age. No matter whether in health or in T2D, bihormonal β-cell cluster 7 (LDHA positive β-cells) could be distinguished from cluster 1 by implication of LXR/RXR. Previous reports indicated that unlike acute activation that is adaptive response to increased demand on insulin secretion, the chronic activation of LXR may contribute to β-cell dysfunction by accumulation of free fatty acids and triglycerades [33]. In addition, the STRING analysis indicated that while differences between clusters 1 and 7 as well as LDHA negative and positive β-cells were well preserved in health, these differences were reduced in T2D. Preserved feature of bihormonal cells can be relevant in the context of cell fitness competition, where we propose it could constitute a basis for bihormonal cells' recognition and homeostatic control.
Cell fitness competition is an important extrinsic cell quality control based on the distinction of cell population with inferior- versus cell population with superior fitness (survival) characteristics. This distinction is key in triggering selective culling of the cell population with inferior fitness characteristics (“losers”) and propelling the expansion of the cell population with superior fitness characteristics (“winners”). Replacement of the “losers” with the “winners” allows for maintenance of homeostatic tissue. By implication the reversal of cell competitive tissue makeup such as we see in T2D (clusters 1 and 7 resemblance) may lead to inhibition of cell competition followed by tissue dysfunction over time.
In the mouse model of diabetes, PFKFB3 knockout in adult β-cells led to strong reduction of injured β-cells and bihormonal (insulin and glucagon positive) cells and concomitant increase in healthy β-cell replication. The inventors monitored injured β-cells by measuring the extent of the calpain (hIAPP)-mediated truncation of the cytoplasmic c-Myc [26]. Calpain was previously reported to directly reflect hIAPP misfolded protein toxicity [35, 36]. In PFKFB3βKO DS mice, cytoplasmic c-Myc was reversed to the barely detectable levels as measured in WT controls (0.8±0.4% and 0.7±0.6%, respectively).
These results indicated that the increment in replication was contributed by healthy β-cells and was conceivably facilitated by the excelled loss of β-cells with ongoing calpain activation and thus hIAPP injury. Therefore, the results suggested a cell competition-dependent β-cell regeneration by culling of injured β-cells after PFKFB3 knockout. So, further in PFKFB3βKO DS mice the increase in β-/a ratio and the reduction in glucagon levels in comparison to PFKFB3WT DS may have accounted for the observed trend of higher insulin sensitivity [37-39].
In conclusion, the preservation of the β-cell mass and increase in the β-/a ratio in the PFKFB3βKO DS mice stem cumulatively from β-cell replication that overcomes the initial loss of injured β-cells and reduction in bihormonal cells.
While the regenerative growth in diabetogenic stress was critically dependent on PFKFB3, unmatched metabolic function may be accounted to the fraction of HIF1α-positive cells independent of PFKFB3. Thus, in the mouse model of diabetes, HIF1α may be responsible for the loss of β-cell function in spite of β-cell mass recovery after PFKFB3 gene depletion.
These studies strongly suggest that targeting HIF1α with/without co-targeting PFKFB3 will lead to recovery of functionally competent β-cell mass and reversal of diabetes.
A model for the role of β-cell fitness comparison in β-cell replication under stress was generated based on the studies described in Examples 1-4.
All of the methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.
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This application claims benefit of priority of U.S. Provisional Application No. 63/067,187, filed Aug. 18, 2020, and U.S. Provisional Application No. 63/169,776, filed Apr. 1, 2021, all of which are hereby incorporated by reference in their entirety. The instant application contains a Sequence Listing which has been submitted in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Aug. 16, 2021, is named UCLA_P0116WO_Seq_Listing.txt and is 22,602 bytes in size.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/046267 | 8/17/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63067187 | Aug 2020 | US | |
| 63169776 | Apr 2021 | US |
