WO2025010366A2 - Age-modulating compounds and methods for making age-modulated cells - Google Patents
Age-modulating compounds and methods for making age-modulated cells Download PDFInfo
- Publication number
- WO2025010366A2 WO2025010366A2 PCT/US2024/036791 US2024036791W WO2025010366A2 WO 2025010366 A2 WO2025010366 A2 WO 2025010366A2 US 2024036791 W US2024036791 W US 2024036791W WO 2025010366 A2 WO2025010366 A2 WO 2025010366A2
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- cell
- age
- cells
- inhibitor
- population
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Ceased
Links
Classifications
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
- A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/045—Hydroxy compounds, e.g. alcohols; Salts thereof, e.g. alcoholates
- A61K31/05—Phenols
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/13—Amines
- A61K31/135—Amines having aromatic rings, e.g. ketamine, nortriptyline
- A61K31/136—Amines having aromatic rings, e.g. ketamine, nortriptyline having the amino group directly attached to the aromatic ring, e.g. benzeneamine
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/335—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin
- A61K31/365—Lactones
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
- A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
- A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
- A61K31/445—Non condensed piperidines, e.g. piperocaine
- A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
- A61K31/453—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a six-membered ring with oxygen as a ring hetero atom
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
- A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
- A61K31/47—Quinolines; Isoquinolines
- A61K31/4709—Non-condensed quinolines and containing further heterocyclic rings
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
- A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
- A61K31/47—Quinolines; Isoquinolines
- A61K31/475—Quinolines; Isoquinolines having an indole ring, e.g. yohimbine, reserpine, strychnine, vinblastine
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
- A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
- A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
- A61K31/506—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/70—Carbohydrates; Sugars; Derivatives thereof
- A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
- A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
- A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
- A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/70—Carbohydrates; Sugars; Derivatives thereof
- A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
- A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
- A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
- A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
- A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
- C12N5/06—Animal cells or tissues; Human cells or tissues
- C12N5/0602—Vertebrate cells
- C12N5/0618—Cells of the nervous system
- C12N5/0619—Neurons
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2501/00—Active agents used in cell culture processes, e.g. differentation
- C12N2501/065—Modulators of histone acetylation
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2506/00—Differentiation of animal cells from one lineage to another; Differentiation of pluripotent cells
- C12N2506/13—Differentiation of animal cells from one lineage to another; Differentiation of pluripotent cells from connective tissue cells, from mesenchymal cells
- C12N2506/1307—Differentiation of animal cells from one lineage to another; Differentiation of pluripotent cells from connective tissue cells, from mesenchymal cells from adult fibroblasts
Definitions
- hPSC-derived lineages represent fetal rather than adult or aged states. This poses significant challenges when modelling age-dependent disorders because aging increases the risk of disease across tissue types. This challenge is especially salient to neurons where access to primary tissue is limited, and replicative senescence can’t be used to model cellular aging. Together, these factors have led to a major interest in developing strategies to fast-forward cellular age in hPSC-derived cells.
- induced aging of developmentally specified hPSC-derived neurons versus transdifferentiation of aged fibroblasts directly to neurons.
- Induced aging approaches take advantage of the ability to scale, to direct cell type specificity and to apply the range of cellular engineering technologies inherent to the hPSC disease modelling field, but there is no consensus on the most relevant strategies to trigger aging-like states in hPSC-derive lineages.
- the transdifferentiation of fibroblasts directly to neurons maintains any age-related signature present in the primary fibroblast but this strategy involves several technical challenges including low transdifferentiation efficiency, scalability, and stability of the resulting neurons.
- the present disclosure provides method for inducing cellular aging in a cell or population of cells, comprising contacting the cell or population of cells with one or more age-inducing agent.
- the cell or population of cells comprise fibroblasts.
- the one or more age-inducing agent is selected from the group consisting of one or more cyclin-dependent kinase (CDK) inhibitor, one or more adenosine kinase inhibitor, one or more topoisomerase II inhibitor, one or more protein kinase C (PKC) inhibitor, one or more DNA binding agent, and combinations thereof.
- the one or more CDK inhibitor comprises alvocidib.
- the one or more adenosine kinase inhibitor comprises 5-iodotubercin.
- the one or more topoisomerase II inhibitor comprises mitoxantrone.
- the one or Attorney Docket No.072734.1463PCT PATENT more PKC inhibitor comprises bisindolylmaleimide-ix.
- the one or more DNA binding agent comprises chromomycin-a3.
- the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more age-inducing agent is selected from the group consisting of one or more DNA synthesis inhibitor, one or more microtubule antagonist, one or more Sirtuin-2 (SIRT2) inhibitor, BRD-K25731886, doxercalciferol, and combinations thereof.
- the one or more DNA synthesis inhibitor comprises fludarabine.
- the one or more microtubule antagonist comprises vinorelbine.
- the one or more SIRT2 inhibitor comprises AGK2.
- contacting the cell or population of cells with one or more age-inducing agent increases the expression level or presence in the cell or population of cells of one or more chronological marker signature of an old cell.
- contacting the cell or population of cells with one or more age-inducing agent decreases the expression level or presence in the cell or population of cells of one or more chronological marker signature of a young cell.
- contacting the cell or population of cells with one or more age-inducing agent induces loss of heterochromatin, disrupted nuclear lamina, increased DNA damage, increased cellular senescence, disrupted proteostasis and increased dependence on autophagy, increased caveolin-1 (CAV1) expression, or a combination thereof.
- the cell or population of cells are derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof.
- the cell or population of cells are human.
- the present disclosure further provides a method for rejuvenating cellular age in a cell or population of cells, comprising contacting the cell or population of cells with one or more rejuvenating agent.
- the cell or population of cells comprise fibroblasts.
- the one or more rejuvenating agent is selected from the group consisting of one or more histone deacetylase (HDAC) inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, and combinations thereof.
- the one or more HDAC inhibitor comprises mocetinostat.
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- Attorney Docket No.072734.1463PCT PATENT the one or more adrenergic receptor antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more rejuvenating agent is selected from the group consisting of one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3- related (ATR) signaling inhibitor, and combinations thereof.
- SIRT activator comprises resveratrol.
- HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- contacting the cell or population of cells with one or more rejuvenating agent increases the expression level or presence in the cell or population of cells of one or more chronological marker signature of a young cell. In certain embodiments, contacting the cell or population of cells with one or more rejuvenating agent decreases the expression level or presence in the cell or population of cells of one or more chronological marker signature of an old cell. In certain embodiments, contacting the cell or population of cells with one or more rejuvenating agent reduces loss of heterochromatin, disrupted nuclear lamina, DNA damage, cellular senescence, disrupted proteostasis and dependence on autophagy, caveolin-1 (CAV1) expression, or a combination thereof.
- CAV1 caveolin-1
- the cell or population of cells are derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. In certain embodiments, the cell or population of cells are human.
- the present disclosure further provides an age-induced cell, wherein the age-induced cell is produced by a method comprising contacting a cell with one or more age-inducing agent. In certain embodiments, the age-induced cell is derived from fibroblasts.
- the one or more age-inducing agent is selected from the group consisting of one or more cyclin-dependent kinase (CDK) inhibitor, one or more adenosine kinase inhibitor, one or more topoisomerase II inhibitor, one or more protein kinase C (PKC) inhibitor, one or more DNA binding agent, and combinations thereof.
- CDK cyclin-dependent kinase
- PLC protein kinase C
- the one or more CDK inhibitor comprises alvocidib.
- the one or more adenosine kinase inhibitor comprises 5- Attorney Docket No.072734.1463PCT PATENT iodotubercin.
- the one or more topoisomerase II inhibitor comprises mitoxantrone.
- the one or more PKC inhibitor comprises bisindolylmaleimide-ix.
- the one or more DNA binding agent comprises chromomycin-a3.
- the age-induced cell is derived from neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more age- inducing agent is selected from the group consisting of one or more DNA synthesis inhibitor, one or more microtubule antagonist, one or more Sirtuin-2 (SIRT2) inhibitor, BRD-K25731886, doxercalciferol, and combinations thereof.
- the one or more DNA synthesis inhibitor comprises fludarabine.
- the one or more microtubule antagonist comprises vinorelbine.
- the one or more SIRT2 inhibitor comprises AGK2.
- the age-induced cell is derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. In certain embodiments, the age-induced cell is human.
- the cell with one or more age-inducing agent increases the expression level or presence of one or more chronological marker signature of an old cell. In certain embodiments, contacting the cell with one or more age-inducing agent decreases the expression level or presence of one or more chronological marker signature of a young cell.
- contacting the cell with one or more age-inducing agent induces loss of heterochromatin, disrupted nuclear lamina, increased DNA damage, increased cellular senescence, disrupted proteostasis and increased dependence on autophagy, increased caveolin-1 (CAV1) expression, or a combination thereof.
- the present disclosure further provides a rejuvenated cell, wherein the rejuvenated cell is produced by a method comprising contacting a cell with one or more rejuvenating agent.
- the rejuvenated cell is derived from fibroblasts.
- the one or more rejuvenating agent is selected from the group consisting of one or more histone deacetylase (HDAC) inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, and combinations thereof.
- HDAC histone deacetylase
- HSP heat shock protein
- adrenergic receptor antagonist one or more phosphoinositide 3-kinase
- PI3K phosphoinositide 3-kinase
- the one or more HDAC inhibitor comprises mocetinostat.
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- the one or more adrenergic receptor Attorney Docket No.072734.1463PCT PATENT antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the rejuvenated cell is derived from neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more rejuvenating agent is selected from the group consisting of one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3-related (ATR) signaling inhibitor, and combinations thereof.
- the one or more SIRT activator comprises resveratrol.
- the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- the rejuvenated cell is derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. In certain embodiments, the rejuvenated cell is human. In certain embodiments, contacting the cell with one or more rejuvenating agent increases the expression level or presence of one or more chronological marker signature of a young cell.
- contacting the cell with one or more rejuvenating agent decreases the expression level or presence of one or more chronological marker signature of an old cell. In certain embodiments, contacting the cell with one or more rejuvenating agent reduces loss of heterochromatin, disrupted nuclear lamina, DNA damage, cellular senescence, disrupted proteostasis and dependence on autophagy, caveolin-1 (CAV1) expression, or a combination thereof.
- the present disclosure further provides a composition comprising the age- induced cell disclosed herein or the rejuvenated cell disclosed herein.
- the composition is a pharmaceutical composition.
- the composition further comprises a pharmaceutically acceptable carrier.
- the present disclosure provides a method of modeling neurodegenerative disease, comprising: contacting a cell or population of cells with one or more age- inducing agent to obtain an age-modulated cell or population of age-modulated cells; and contacting the age-modulated cell or population of age-modulated cells with one or more candidate compound.
- the method further comprises detecting an alteration in at least one of the survival, biological activity, structure or morphology of the age-modulated cell or population of age-modulated cells.
- the method further comprises selecting as the drug a candidate one or more compound that alters at least one of the survival, biological activity, structure or morphology of the age-modulated cell or population of age-modulated cells.
- the neurodegenerative disease is Parkinson's disease (PD) or Alzheimer’s Disease (AD).
- the present disclosure further provides a kit for inducing cellular aging in a cell or population of cells, comprising one or more age-inducing agent is selected from the group consisting of one or more DNA synthesis inhibitor, one or more microtubule antagonist, one or more SIRT2 inhibitor, BRD-K25731886, doxercalciferol, one or more CDK inhibitor, one or more adenosine kinase inhibitor, one or more topoisomerase II inhibitor, one or more PKC inhibitor, one or more DNA binding agent, and combinations thereof.
- the one or more DNA synthesis inhibitor comprises fludarabine.
- the one or more microtubule antagonist comprises vinorelbine.
- the one or more SIRT2 inhibitor comprises AGK2.
- the one or more CDK inhibitor comprises alvocidib.
- the one or more adenosine kinase inhibitor comprises 5-iodotubercin.
- the one or more topoisomerase II inhibitor comprises mitoxantrone.
- the one or more PKC inhibitor comprises bisindolylmaleimide-ix.
- the one or more DNA binding agent comprises chromomycin-a3.
- the kit further comprises instructions for contacting a cell or population of cells with the one or more age-inducing agent to induce expression in the cell or population of cells of one or more chronological marker signature of an old cell.
- the present disclosure further provides a kit for rejuvenating a cell or population of cells, comprising one or more rejuvenating agent selected from the group consisting of one or more histone deacetylase (HDAC) inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3-related (ATR) signaling inhibitor, and combinations thereof.
- HDAC histone deacetylase
- HSP heat shock protein
- PI3K phosphoinositide 3-kinase
- SIRT Sirtuin
- HDAC inhibitor one or more HDAC inhibitor
- PARP poly ADP ribose polymerase
- ATR Rad3-related
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- Attorney Docket No.072734.1463PCT PATENT the one or more adrenergic receptor antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the one or more SIRT activator comprises resveratrol.
- the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- the kit further comprises instructions for contacting a cell or population of cells with the one or more rejuvenating agent to induce expression in the cell or population of cells of one or more chronological marker signature of a young cell.
- Figures 1A-1F show identification of transcriptional signatures of age in primary fibroblasts, frontal cortex and substantia nigra.
- RNA- seq datasets generated as part of this study were: Total SN (substantia nigra), Total FC (frontal cortex), Total pF (total RNA of primary fibroblast) and PolyA pF (poly-A selection of primary fibroblast). External datasets were PolyA Gage FC (poly-A selection of frontal cortex) and PolyA Gage pF (polyA selection of primary fibroblast).
- Figures 2A-2D show establishment and validation of RNAge score.
- RNAge score refers to the modified t-score for each pairwise comparison. The size of the bubbles indicates the percentage of genes that make up the aging score that change in the expected direction for young vs old.
- Figures 3A-3E show that RNAge score can be used to measure cellular rejuvenation.
- fibroblasts from young and old donors were first reprogrammed to pluripotent stem cells (iPSC) then re-differentiated into iPSC derived fibroblasts (iPSC- FIB). RNA, 5mC and 5hmC was performed at each step.
- iPSC pluripotent stem cells
- RNA, 5mC and 5hmC was performed at each step.
- C) RNA-seq analysis showing that gene expression of fibroblast specific genes in iPSC-FIB closely resembles that of pFIB indicating the re-establishment of fibroblast identity in iPSC-FIB. (N 6 independent cell lines at each stage; 3 derived from young donors and 3 derived from old donors). D) Volcano plots showing DEGs (FDR ⁇ 0.1) between young and old pFibs, iPSCs derived from young and old donors and iPSC-FIB generated from these stem cells. The loss of aged signature (rejuvenation) is indicated by the reduction in the number of significantly differentiated genes in iPSC-FIB compared to pF.
- Figures 4A-4D show RNAge score in accelerated and induced aging models.
- RNA-seq data from primary fibroblasts originating from young, old or individuals with HGPS A) PCA of RNA-seq data from primary fibroblasts originating from young, old or individuals with HGPS.
- FIG. 5A-5E show identification of novel regulators of cellular age using RNAge score.
- RNAge scores were calculated for all L1000 experiments utilizing the candidate drugs by concentration and duration of treatment. RNAge scores were calculated for candidate rejuvenation drugs in fibroblasts (C), candidate aging inducers in fibroblasts (D), and candidate aging inducers in neurons (E).
- FIGS. 6A-6C show experimental validation top scoring modulators of RNAge.
- a larger bubble indicates a greater level of agreement with increased age and a smaller bubble shows smaller agreement with age induction and, consequently, a greater agreement with cellular rejuvenation.
- Resveratrol has a very small bubble size in the fibroblast aging score indicating gene expression changes that are highly correlated with rejuvenation.
- Figures 7A-7C show correlation between RNAge score and cellular hallmarks of age.
- C) Measurement of age associated cellular phenotypes in PSC-derived neurons in response to treatment with DMSO (control), Fludarabine (10 ⁇ M), Vinorelbine (10 ⁇ M) or AGK-2 (0.04 ⁇ M). Absolute values are shown for nuclear area and nuclear roundness. For H3K9me3, LAP2, yH2AX, p21, BAG3 and CAV1 fluorescence intensity is relative to the DMSO control. N 12.
- Figures 8A-8G show functions associated with aging in primary fibroblasts, FC and SN.
- FC frontal cortex
- pF primary fibroblast
- SN substantia nigra.
- C-G Functional enrichment of genes associated with each of our aging signatures from Figure 1E.
- Figures 9A-9F show extended characterization and validation of iPSC reprograming as a model of cellular rejuvenation.
- FIG. 10A-10B show DNA methylation analyses of young, old and HGPS fibroblasts.
- Figures 11A-11B show example immunocytochemistry images for the hallmarks of age assays performed in fibroblasts and PSC-derived neurons.
- Figures 12A-12D show development of RNAge score and application to stem cell-based in vitro models.
- RNAge score is larger when old pFIB are compared to iPSC-FIB than when young donors are used.
- C Application of RNAge scoring to established experimental approaches for age induction including ectopic expression of Progerin, SLO cocktail and SATB1-KO.
- D Application of RNAge to neurons generated by transdifferentiation of primary fibroblasts (pFIB-iN) relative to neurons generated in the same manner from iPSCs (iPSCiN).
- Figures 13A-13E show in silico screening for modulators of RNAge.
- FIG. 14A-14G show experimental validation of age inducing compounds identified In Silico.
- A Schema outlining how validated age inducing hits from the L1000 screen were profiled for changes in the cellular hallmarks of aging.
- A Example immunocytochemistry images of hallmarks of aging assays in PSC-derived neurons after 4 days of treatment with Fludarabine. Scale 100uM.
- Example images shown in (A). Absolute values are shown for nuclear area and nuclear roundness. For H3K9me3, LAP2, yH2AX, p21, BAG3 and CAV1 fluorescence intensity is relative to the DMSO control. N 12; one sample t-test. Experiment repeated 4 times each with 3 replicate wells.
- (C) Presto blue viability assay in WT and APPswe/swe neurons treated with Fludarabine for 4 days relative to DMSO treatment (n 3, paired Student’s t-test).
- RNA-seq datasets generated as part of this study were: Total SN (substantia nigra), Total FC (frontal cortex), Total pF (total RNA of primary fibroblast) and PolyA pF (poly-A selection of primary fibroblast).
- RNA-seq analysis showing that gene expression of fibroblast specific genes in iPSC-FIB closely resembles that of pFIB indicating the re-establishment of fibroblast identity in iPSC-FIB.
- N 6 independent cell lines at each stage; 3 derived from young donors and 3 derived from old donors).
- RNA-seq data from primary fibroblasts originating from young, old or individuals with HGPS.
- D RNAge score of young pFIBs vs. HGPS pFIBs form this study data (top) and similar comparison using RNA-seq data from Fleischer et. al., 2018 (bottom) demonstrating that HGPS fibroblasts do not have an elevated RNAge score.
- Figures 18A-18E show experimental validation of rejuvenating compound identified In Silico.
- A RNAge score distribution for L1000 in silico screen performed in neural progenitor cells (NPC).
- B (B)
- C) Calculation of RNAge for candidate age regulators across all concentrations available within the LINCS 1000 dataset.
- RNAge score was calculated relative to every control sample within the dataset.
- Attorney Docket No.072734.1463PCT PATENT Conditions with the most pronounced effect (yellow) were selected for downstream validation.
- D Experimental validation of mocetinostat as a regulator of RNAge in old primary fibroblasts.
- E ATAC-Seq analyses on primary young and old fibroblasts. Figures 19A-19D show that selecting the optimal concentration candidate age regulators and impact hallmarks of aging.
- A-B Calculation of RNAge for every concentration of our candidate fibroblast (A) and neuron (B) age inducers available within the LINCS 1000 dataset. The RNAge score was calculated relative to every control sample within the dataset.
- C-D Example immunocytochemistry images of hallmarks of aging assays in fibroblasts (C) and neurons (D) after 24h treatment with validated age inducing compounds. Scale 100uM.
- Figure 20 shows incorporation of induced aging into stem cell models of Parkinson’s disease. Quantification of the cellular hallmarks of aging in WT dopaminergic neurons after 4 days of treatment with Fludarabine. Fludarabine induces a subset of senescence associated induced aging hallmarks in dopaminergic neurons. 5.
- the present disclosure relates, in certain embodiments, to methods for modulating cellular aging and/or progression of neurodegenerative diseases (e.g., AD) in hPSC-derived cells.
- the methods described herein induce cellular aging or rejuvenation.
- the methods described herein promote progression of neurodegenerative diseases (e.g., AD).
- the present disclosure also relates, in certain embodiments, to cells, methods, and systems for modeling aging- related neurodegenerative diseases (e.g., AD) in vitro. Transcriptional signatures of cellular age can be determined by comparing RNA expression in distinct tissues.
- the present disclosure relates, in certain embodiments, to methods of determining relative age of a biological sample by comparing RNA expression to one or more reference transcriptional signatures of cellular age.
- a transcriptional score is produced for a biological sample in accordance with the methods described herein.
- the treatment timing and/or concentration of compound is varied.
- the methods comprise quantifying cellular aging or rejuvenation.
- Attorney Docket No.072734.1463PCT PATENT The present disclosure relates, in certain embodiments, to methods of screening for novel regulators of cellular “age.”
- a transcriptional score is produced for a biological sample following contact with one or more compounds or agents.
- the transcriptional score is produced by assessing one or more transcriptional signature of cellular age.
- one or more agent is capable of inducing a change in RNA expression of a treated biological sample is identified as a modulator of cellular age.
- the one or more agent elicits a shift in RNA expression of biological samples towards the transcriptional signature of “old” tissue.
- the one or more agents shifts RNA expression of biological samples towards the transcriptional signature of “young” samples.
- “about” can mean a range of up to 20%, e.g., up to 10%, up to 5%, or up to 1% of a given value.
- Attorney Docket No.072734.1463PCT PATENT particularly with respect to biological systems or processes the term can mean within an order of magnitude, e.g., within 5-fold, or within 2-fold, of a value.
- An “individual” or “subject” or “patient” as described herein is a vertebrate, such as a human or non-human animal, for example, a mammal. Mammals include, but are not limited to, humans, primates, farm animals, sport animals, rodents and pets.
- Non-limiting examples of non-human animal subjects include rodents such as mice, rats, hamsters, and guinea pigs; rabbits; dogs; cats; sheep; pigs; goats; cattle; horses; and non-human primates such as apes and monkeys.
- disease refers to any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ.
- treating or “treatment” refers to clinical intervention in an attempt to alter the disease course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology.
- Therapeutic effects of treatment include, without limitation, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastases, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
- a treatment can prevent deterioration due to a disorder in an affected or diagnosed subject or a subject suspected of having the disorder, but also a treatment may prevent the onset of the disorder or a symptom of the disorder in a subject at risk for the disorder or suspected of having the disorder.
- the term "young" in reference to an individual refers to an early chronological age, which for humans refers to age in years.
- young in reference to a cell refers to a cell displaying a marker signature of cells isolated from young donors for example, a cell state such as an immature cell, such as a young iPSC- derived somatic cell, i.e., a cell displaying a marker signature of cells isolated from young donors regardless of the age of the donor of the original primary cell that gave rise to the iPSC. This is to be contrasted with “old” iPSC-derived or indeed any somatic cell which displays a marker signature of cells isolated from old donors.
- An example of an old iPSC derived somatic cell is that produced when the level of genomic nucleic acid methylation in an iPSC-derived somatic cell is reduced (again, regardless of the age of the donor of the primary cell that gave rise to the iPSC) following Attorney Docket No.072734.1463PCT PATENT reprogramming.
- a young cell may also refer to a population of "young cells” such as young primary cells derived from a donor of young chronological age as in "young primary fibroblasts.”
- the term "old” in reference to an individual refers to chronological age, which for humans refers to age in years.
- old in reference to a cell refers to a cell displaying a marker signature of cells isolated from old donors, for example, a cell state wherein the cell expresses one or more chronological markers associated with aged cells, or primary somatic cells from old donors.
- An old cell may also refer to a population of "old cells” such as old primary cells derived from a donor of old chronological age as in "old primary fibroblasts.”
- donor individual or “donor” refers to any organism, human or non-human, from which cells were obtained to provide a primary cell culture. The donor individual may be of any age, and may be non-diseased or diseased.
- the donor may provide cells for use in the present methods, by providing biological samples, including a biopsy, a skin biopsy, blood cells, and the like.
- Disease refers to any impairment of the normal state of the living animal or plant body or one of its parts that interrupts or modifies the performance of the vital functions. Typically manifested by distinguishing signs and symptoms, it is usually a response to: i) environmental factors (as malnutrition, industrial hazards, or climate); ii) specific infective agents (as worms, bacteria, or viruses); iii) inherent or acquired defects of the organism (as genetic or epigenetic anomalies); and/or iv) combinations of these factors.
- late-onset disease refers to a disease or medical condition of a patient manifesting as a clinical condition in middle age and old age patients.
- a late-onset disease may include but not limited to degenerative, such as neurodegenerative diseases, such as Parkinson's disease (PD), amyotrophic lateral sclerosis, Alzheimer’s, Huntington’s disease, and diseases of other lineages including cardiac hypertrophy, cardiac fibrosis, Type II diabetes, age-related macular degeneration, cancers, including for example breast cancers, colon cancers, and ovarian cancers, familial adenomatous polyposis (FAP), heart disease, and the like.
- PD Parkinson's disease
- amyotrophic lateral sclerosis Alzheimer’s
- Huntington’s disease Huntington’s disease
- diseases of other lineages including cardiac hypertrophy, cardiac fibrosis, Type II diabetes, age-related macular degeneration, cancers, including for example breast cancers, colon cancers, and ovarian cancers, familial adenomatous polyposi
- the term “cell culture” refers to any in vitro culture of cells in an artificial medium for research or medical treatment. Included within this term are Attorney Docket No.072734.1463PCT PATENT continuous cell lines (e.g., with an immortal phenotype), primary cell cultures, finite cell lines (e.g., non-transformed cells), and any other cell population maintained in vitro, including oocytes and embryos.
- the term “culture medium” refers to a liquid that covers cells in a culture vessel, such as a Petri plate, a multi-well plate, and the like, and contains nutrients to nourish and support the cells.
- Culture medium may also include growth factors added to produce desired changes in the cells.
- the term “deficient” as used herein refers to a cell which either does not express the mRNA of a gene, a protein product of a gene, or both (i.e., devoid of such expressions), or expresses them at a reduced level.
- the term “neuronal maturation medium” or “BAGCT medium” refers to a culture medium comprising N2 medium, further comprising brain- derived neurotrophic factor (BDNF), ascorbic acid (AA), glial cell line-derived neurotrophic factor, dibutyryl cAMP and transforming growth factor type ß3 for differentiating midbrain fate FOXA2/LMX1A+ dopamine (DA) neurons.
- BDNF brain- derived neurotrophic factor
- AA ascorbic acid
- AA glial cell line-derived neurotrophic factor
- dibutyryl cAMP transforming growth factor type ß3 for differentiating midbrain fate FOXA
- the terms “purified,” “to purify,” “purification,” “isolated,” “to isolate,” “isolation,” and grammatical equivalents thereof as used herein, refer to the reduction in the amount of at least one contaminant from a sample.
- a cell type is purified by at least 10%, preferably by at least 30%, more preferably by at least 50%, yet more preferably by at least 75%, and most preferably by at least 90%, reduction in the amount of undesirable cell types.
- purification of a cell type results in “enrichment,” i.e., an increase in the amount, of the cell type in the cell culture.
- the term “differentiation agent” or “differentiation inducing compound” refers to a substance, which can be a biological molecule or a small molecule or a mixture of substances which has the property of causing a stem cell to commit to a cellular pathway leading to a somatic cell.
- inducing compounds may include, but are not limited to, Wnt activators or SMAD inhibitors.
- sonic hedgehog protein or SHH refers to one of three proteins in the mammalian signaling pathway family called hedgehog. SHH is believed to play a role in regulating vertebrate organogenesis, such as the growth of digits on limbs and organization of the brain.
- Sonic hedgehog protein is thus a morphogen that diffuses to form a concentration gradient and has different effects on the cells of the developing embryo depending on its concentration.
- SHH may also Attorney Docket No.072734.1463PCT PATENT control cell division of adult stem cells and has been implicated in development of some cancers.
- Small Mothers against Decapentaplegic or "SMAD” are intracellular proteins that transduce extracellular signals from transforming growth factor beta ligands to the nucleus where they activate downstream gene transcription and are members of a class of signaling molecules capable of modulating directed differentiation of stem cells.
- the term "contacting" refers to exposing the cell to a compound or substance in a manner and/or location that will allow the compound or substance to exert its activity on the cell, for example, by touching the cell. Contacting may be accomplished using any suitable method and may be extracellular or intracellular. For example, in one embodiment, contacting is by introducing the compound/substance intracellularly either as such or by genetically modifying the cell, such that it expresses the compound or substance. Contacting can be achieved by a variety of methods, including exposing cells to a molecule or to a vehicle containing a molecule, delivering a polynucleotide encoding for a polypeptide to the cells through transfection.
- Contacting may also be accomplished by adding the compound or substance to a culture of the cells so that the contacting occurs on the outer cell membrane. Contacting may also be accomplished within a given cell by the production of a recombinant protein within a cell.
- reprogramming refers to the conversion of "primary cells” or “primary differentiated cells” or “primary somatic cells” into undifferentiated cells (i.e., cells that has not yet developed into a specialized cell type), such as induced pluripotent stem (iPS) cells.
- iPS induced pluripotent stem
- a somatic cell culture of primary cells may be reprogrammed into induced pluripotent stem cells. Further, an age-related marker signature appearing in the primary somatic cell culture is then altered in the reprogrammed, undifferentiated cells.
- primary cells e.g., for example, primary fibroblasts isolated from donors of certain ages or primary fibroblasts isolated from patients having a disease, such as Parkinson’s disease (PD), e.g., PD fibroblasts, etc.
- PD Parkinson’s disease
- cell lines including cell lines.
- an age-related marker signature appearing in the primary somatic cell culture is then altered in the reprogrammed, undifferentiated cells.
- disease marker signatures appearing in the differentiated somatic cell cultures may be absent in the converted undifferentiated cells, however the exact signature may differ between iPS cells produced from different primary somatic cell Attorney Docket No.072734.1463PCT PATENT donors.
- Primary cells may be obtained from any source, such as from donors, i.e. a biopsy, a skin biopsy, a blood draw, and the like, cell lines, and the like.
- the term "differentiated” refers to a cell, for example an unspecialized embryonic cell, that has undergone a process whereby the cell acquires the features of a specialized cell such as a heart, liver, or muscle cell.
- a “differentiated” somatic cell refers to a cell having a more committed cell type characteristic, such as a marker signature characteristic of its type.
- a “differentiated" iPSC- derived somatic cell refers to a cell that has at least one marker signature not present in the iPSC, for example, a marker signature of a specialized cell.
- inducing differentiation in reference to a cell refers to changing the default cell type (genotype and/or phenotype) to a non-default cell type (genotype and/or phenotype).
- inducing differentiation in a stem cell refers to inducing the stem cell (e.g., human stem cell) to divide into progeny cells with characteristics that are different from the stem cell, such as genotype (e.g., change in gene expression as determined by genetic analysis such as a microarray) and/or phenotype (e.g., change in expression of a protein).
- “inducing differentiation” refers to a process initiated by compounds that act as differentiation agents, including, but not limited to, Wnt inhibitors and/or activators, sonic hedgehog proteins and/or activators, and/or SMAD inhibitor molecules. Such agents trigger or promote the largely genetically controlled differentiation process which converts an undifferentiated cell (such as an embryonic stem cell, an induced pluripotent stem cell, a primary stem cell etc.), to a committed somatic phenotype, that of a specialized cell having a more distinct form and function, which may or may not admit further differentiation.
- an undifferentiated cell such as an embryonic stem cell, an induced pluripotent stem cell, a primary stem cell etc.
- a committed somatic phenotype that of a specialized cell having a more distinct form and function, which may or may not admit further differentiation.
- induced pluripotent stem cells may be converted into iPSC-derived fibroblasts or iPSC-derived neurons, including without limitation neuron with a specific type of junction, specific range of electrical transmission rate, specific types of neurochemical production and/or secretion, etc.
- aging in reference to a cell or cell population, refers to any stage during the progression from expression of a young marker signature towards an old marker signature.
- aging is the natural aging process in Attorney Docket No.072734.1463PCT PATENT a cell characterized by molecular and morphological markers associated with an aged cell, such as genomic instability, telomere shortening, loss of proteostasis, loss of heterochromatin and altered gene transcription, mitochondrial dysfunction, cellular senescence, and stem cell exhaustion. Aging can also encompass maturation, whereby additional molecular, physical and functional properties of an adult cell are expressed. As used herein, the term “rejuvenation,” in reference to a cell or cell population, refers to the progression from expression of an old marker signature to a young marker signature.
- rejuvenation can be achieved by contacting a cell or cell population with a “rejuvenating compound” or “rejuvenating agent” for inducing the expression of a young marker signature and/or reduces the expression of an old marker signature.
- rejuvenation induces a reduction in one or more molecular and morphological marker associated with an aged cell, such as genomic instability, telomere shortening, loss of proteostasis, loss of heterochromatin and altered gene transcription, mitochondrial dysfunction, cellular senescence, and stem cell exhaustion
- the term “directed differentiation” refers to a manipulation of stem cell culture conditions to induce differentiation into a particular (for example, desired) cell type, such as neuronal precursors.
- the term “directed differentiation” in reference to a stem cell refers to the use of small molecules, growth factor proteins, and other growth conditions to promote the transition of a stem cell from the pluripotent state into a more mature or specialized cell fate (e.g. neuron precursors, neurons, etc.).
- the term “marker” refers to a molecular or morphologic trait characteristic of a state of a cell and therefore useful, alone or in combination with other markers, in indicating that state.
- a “marker” can be a “chronological marker,” which includes “age-related markers” and “maturation-related markers.” “Markers” can also be “disease related markers,” which include “late-onset disease markers.” If a single marker (or combination of markers) is sufficient in indicating the state of a cell, it constitutes a marker signature, as further explained below.
- a “marker” or “cell marker” refers to gene or protein that identifies a particular cell or cell type.
- a marker for a cell may not be limited to one marker, markers may refer to a “pattern” of markers such that a designated group of markers may identity a cell or cell type from another cell or cell type.
- the term "age-related marker signature” refers to any chronological marker signature (comprising one or more markers) that is characteristic of the natural aging process.
- a single age-related marker signature may be sufficient to characterize the age of primary cells from a donor or the phenotypic stage of cells wherein an age phenotype has been induced, or a profile of a plurality of different marker signatures may be evaluated to characterize the age of primary cells from a donor or the phenotypic stage of cells wherein an age phenotype has been induced or the phenotypic age of a cell.
- the term “maturation-related marker signature” refers to any chronological marker signature that is characteristic of the natural maturation process.
- a single maturation-related marker signature may be sufficient to characterize the maturation stage of primary cells or the phenotypic stage of cells wherein an age phenotype has been induced, or a profile of a plurality of different marker signature maybe evaluated to characterize the maturation stage of primary cells or the phenotypic stage of cells wherein an age phenotype has been induced.
- the term “disease-related marker signature” refers to any cellular structure (molecular or morphologic) that is characteristic of a specific disease.
- a single marker signature may be sufficient to characterize a disease, or a profile of a plurality of different marker signatures may need to be evaluated to characterize a disease state.
- the term "cell" refers to a single cell as well as to a population of (i.e., more than one) cells.
- the population may be a homogeneous population comprising one cell type, such as a population of neurons or a population of undifferentiated embryonic stem cells.
- the population may comprise more than one cell type, for example a mixed neural cell population comprising neurons and glial cells. It is not meant to limit the number of cells in a population, for example, a mixed population of cells may comprise at least one differentiated cell.
- a mixed population may comprise at least one differentiated cell and at least one stem cell.
- the terms "primary cell” or “primary somatic cell” refers to any cell in the body other than gametes (egg or sperm), sometimes referred to as “adult” cells, which can be reprogrammed for generating an undifferentiated iPSC in Attorney Docket No.072734.1463PCT PATENT accordance with the methods disclosed herein and/or under the appropriate conditions, i.e. when contacted with a proper growth factor, compound, extracellular signal, intracellular signal, transfected with reprogramming genes (factors), etc.
- a primary cell comprises a fibroblast cell, differentiated primary somatic cell, stem cell lines, and the like.
- primary cells are isolated from patients.
- primary cells are cell lines.
- primary cells are stem cell lines.
- primary cells are embryonic stem cells.
- primary cells are isolated from sources such as from healthy volunteers, from patients, from patients having a particular disease or medical condition, regardless of clinical manifestation, i.e. patients having a certain genotype or phenotype.
- primary cells are isolated from mammals.
- primary cells are isolated from animals.
- a “somatic cell” refers to any cell of an organism, which is a constituent unit of a tissue, skin, bone, blood, or organ, other than a gamete, germ cell, gametocyte, or undifferentiated stem cell.
- Somatic cells include progenitor cells and terminally differentiated cells.
- Such somatic cells include, but are not limited to, neurons, fibroblast cells, cardiomyocyte cells, epithelial cells, neuroendocrine cells, pancreatic cells, astrocytes, hematopoietic cells, midbrain dopamine neurons, motoneurons, and/or cortical neurons.
- neural cell culture refers to a cell culture of neurons and/or glia wherein the cells display characteristics of cells of the central and/or peripheral nervous systems.
- stem cell refers to a cell that is totipotent or pluripotent or multipotent and is capable of differentiating into one or more different cell types, such as embryonic stem cells or stem cells isolated from organs, for example, mesenchymal or skin stem cells or induced pluripotent stem cells.
- embryonic stem cell refers to a primitive (undifferentiated) cell that is derived from preimplantation-stage embryo, embryo, placenta or umbilical cord capable of dividing without differentiating for a prolonged period in culture, and are known to develop into cells and tissues of the three primary germ layers.
- a human embryonic stem cell refers to an embryonic stem cell that is from a human.
- human embryonic stem cell or “hESC” refers to a type of pluripotent stem cells derived from early stage human embryos, up to and including the blastocyst stage, that is capable of dividing without differentiating Attorney Docket No.072734.1463PCT PATENT for a prolonged period in culture, and are known to develop into cells and tissues of the three primary germ layers.
- iPSC induced pluripotent stem cell
- iPSC embryonic stem cell
- progenitor in reference to a cell refers to an intermediate cell stage wherein said cell is no longer a pluripotent stem cell and is also not yet a fully committed cell. Progenitor cells in this disclosure are included within somatic cells. Stem cells according to the present disclosure can be “totipotent” stem cells, “pluripotent” stem cells, and/or “multipotent” stem cells. As used herein, the term “totipotent” refers to an ability of a cell to differentiate into any type of cell in a differentiated organism, as well as into a cell of extra embryonic materials such as placenta.
- the term “pluripotent” refers to a cell or cell line that is capable of differentiating into any differentiated cell type, for example, an ability to develop into the three developmental germ layers of the organism including endoderm, mesoderm, and ectoderm.
- the term “multipotent” refers to a cell or cell line that is capable of differentiating into at least two differentiated cell types.
- Mouse iPSCs were reported in 2006 (Takahashi and Yamanaka, Cell 126:663-676 (2006)), and human iPSCs were reported in late 2007 (Takahashi et al. Cell.2007 Nov 30;131(5):861-72).
- Mouse iPSCs demonstrate important characteristics of pluripotent stem cells, including the expression of stem cell markers. Human and animal iPSCs also express stem cell markers and are capable of generating cells characteristic of all three germ layers. Unlike an embryonic stem cell, an iPSC is formed artificially by the introduction of certain embryonic genes into a somatic cell (such as an OCT4, SOX2, and KLF4 transgenes). See, for example, Takahashi and Yamanaka, Cell 126:663-676 (2006) and Agarwal et al., Nature 292-296 (2010).
- iPSC can be Attorney Docket No.072734.1463PCT PATENT produced from adult human skin cells, or fibroblast cells, which are transfected with one or more genes such as, for example, one or more of OCT4, SOX2, NANOG, LIN28, and/or KLF4. See, Yu et al., Science 324:797-801 (2009). Alternatively, they can be produced from other types of somatic cells, such as blood or keratinocytes.
- the term “derived from” or “established from” or “differentiated from” when made in reference to any cell disclosed herein refers to a cell that was obtained from (e.g., isolated, purified, etc.) a parent cell in a cell line, tissue (such as a dissociated embryo), or fluids using any manipulation, such as, without limitation, single cell isolation, cultured in vitro, treatment and/or mutagenesis using for example proteins, chemicals, radiation, infection with virus, transfection with DNA sequences, such as with a morphogen, etc., selection (such as by serial culture) of any cell that is contained in cultured parent cells.
- a derived cell can be selected from a mixed population by virtue of response to a growth factor, cytokine, selected progression of cytokine treatments, adhesiveness, lack of adhesiveness, sorting procedure, and the like.
- in vitro refers to an artificial environment and to processes or reactions that occur within an artificial environment. In vitro environments include, but are not limited to, test tubes and cell cultures.
- in vivo refers to the natural environment (e.g., in an animal) and to processes or reactions that occur within a natural environment, such as embryonic development, cell differentiation, neural tube formation, etc.
- cultured cells generally refer to cells that are maintained in vitro.
- Cultured cells include “cell lines” and "primary cultured cells.”
- the term “cell culture” refers to any in vitro culture of cells. Included within this term are continuous cell lines (e.g., with an immortal phenotype), primary cell cultures, finite cell lines (e.g., non-transformed cells), and any other cell population (notably neurons) maintained in vitro, including embryos, pluripotent stem cells.
- Preferred small molecules range in size from approximately 10 Da up to about 5000 Da, more preferably up to 2000 Da, and most preferably up to about 1000 Da.
- Attorney Docket No.072734.1463PCT PATENT the term “expressing” in relation to a gene or protein refers to making an mRNA or protein which can be observed using assays such as microarray assays, antibody staining assays, and the like.
- RNAge Transcriptional Aging Signature The present disclosure relates, in certain embodiments, to methods of determining relative age of a biological sample by comparing RNA expression to one or more reference transcriptional signatures of cellular age. Transcriptional signatures of cellular age can be determined by comparing RNA expression in distinct tissues.
- a transcriptional score is produced for a biological sample in accordance with the methods described herein.
- the present disclosure relates, in certain embodiments, to methods of determining relative age of a biological sample by comparing RNA expression to one or more reference transcriptional signatures of cellular age.
- a transcriptional score is produced for a biological sample in accordance with the methods described herein.
- a computational pipeline (“RNAge”) was established to measure changes resulting from cellular age. To establish RNAge, sets of genes whose expression can be used to distinguish different age groups were identified. Gene sets were established by performing total RNA sequencing of young and old primary human tissue samples (fibroblasts, cortex, substantia nigra; Figure 16A-16C).
- pan-aging genes that mark aging across three lineages, fibroblast-specific aging genes, pan- neuronal-specific aging genes, frontal cortex (FC)-specific aging genes and substantia nigra (SN)-specific aging genes (Figure 16D). Markers were ranked based on the combined p-values from all training datasets for each aging gene signature panel (Pan- Aging, Fibroblast, Pan-Neuronal, FC and SN panels) individually.
- the top 100 ranked signatures from each panel were then used to establish scores, named ‘Pan’, ‘pF’, ‘Neuronal’, ‘FC’, and ‘SN’.
- the aging score is based on both the magnitude of the difference in expression between the two datasets and the directionality of the change across the top 100 age-regulated genes (see methods).
- the percent of genes of the age signature that change expression in the expected direction were also included to assess Attorney Docket No.072734.1463PCT PATENT whether the aging score is driven by very large changes in only a small subset of the age-associated genes or by a broader change across most of the genes.
- RNAge performed well when validated on several independent test cases including: transcriptomic datasets from old versus young human primary fibroblasts; in both RNA-seq and microarray-based comparisons of young versus old human frontal cortex; young and old substantia nigra; and young and old mouse brain (Figure 16F). Finally, the ’Pan’ and ‘Neuronal’ aging scores were predictive of cellular age in the cerebellum ( Figure 16G).
- iPSCs induced pluripotent stem cells
- stem cells collected from human subjects and somatic cells derived from such stem cells are also generally devoid of age and often also of disease markers in the case of late-onset diseases.
- methods are disclosed for inducing appropriate chronological marker signatures in stem cell-derived somatic cells, including without limitation human iPSC- derived lineages, and thus generating age-appropriate cell cultures suitable as disease models. 5.3.1 Methods for Inducing Cellular Aging
- the present disclosure relates, in certain embodiments, to methods for modulating cellular aging and/or progression of neurodegenerative diseases (e.g., Alzheimer’s Disease or Parkinson’s Disease).
- the methods described herein induce cellular aging.
- the methods described herein promote progression of neurodegenerative diseases.
- the methods comprise contacting a cell or population of cells with one or more age- inducing agent.
- a transcriptional score is produced for a biological sample in accordance with the methods described herein.
- the one or more age-inducing agent elicits a shift in RNA expression of biological samples towards the transcriptional signature of “old” tissue.
- Methods of the present disclosure can also be applied to methods of quantifying cellular aging.
- a transcriptional score is evaluated Attorney Docket No.072734.1463PCT PATENT for a biological sample that is contacted with one or more age-inducing agent.
- the transcriptional score is compared to one or more reference transcriptional signatures of cellular age.
- contacting the cell or population of cells with one or more age-inducing agent increases the expression level or presence in the cell or population of cells of one or more chronological marker signature of an old cell.
- contacting the cell or population of cells with one or more age- inducing agent reduces the expression level or presence in the cell or population of cells of one or more chronological marker signatures of a young cell.
- the methods of the present invention can be applied for the production of aged cells or mature cells from somatic cells (whether iPSC-derived or primary cells), from stem cells or from fully differentiated or partially differentiated cells.
- the cells are derived from iPSC, stem cells, embryonic stem cells, skin stem cells from adult individuals, mesenchymal stem cells, somatic cells, neurons, and fibroblasts.
- the present disclosure can also be applied to induce aging of a variety of cell lineages. These cells include major cell types found in a variety tissues and organs, including, but not limited to, brain, heart, liver, kidney, spleen, muscle, skin, lung, blood, artery, eye, bone marrow, and lymphatic system.
- the cells are hPSC-derived cells.
- the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the cells are iPS cell-derived fibroblasts.
- one or more the age-inducing agent is selected from the group consisting of one or more cyclin-dependent kinase (CDK) inhibitor, one or more adenosine kinase inhibitor, one or more topoisomerase II inhibitor,
- the one or more CDK inhibitor comprises alvocidib.
- the one or more adenosine kinase inhibitor comprises 5-iodotubercin.
- the one or more topoisomerase II inhibitor comprises mitoxantrone.
- the one or more PKC inhibitor comprises bisindolylmaleimide-ix.
- the one or more DNA binding agent comprises chromomycin-a3.
- the one or more age-inducing agent is selected from the group consisting of one or more DNA synthesis inhibitor, one or more microtubule antagonist, Attorney Docket No.072734.1463PCT PATENT one or more Sirtuin-2 (SIRT2) inhibitor, BRD-K25731886, doxercalciferol, and combinations thereof.
- the one or more DNA synthesis inhibitor comprises fludarabine.
- the one or more microtubule antagonist comprises vinorelbine.
- the one or more SIRT2 inhibitor comprises AGK2.
- the treatment timing and/or concentration of the one or more age-inducing agent is varied.
- the one or more age- inducing agent is administered at a concentration of between about 0.01 and 5 ⁇ M, or any value in between, for example, between about 0.02 and 5 ⁇ M, , or between about 0.03 and 5 ⁇ M, or between about 0.4 and 5 ⁇ M, or between about 0.05 and 5 ⁇ M, or between about 0.1 and 5 ⁇ M, or between about 0.5 and 5 ⁇ M, or between about 1 and 5 ⁇ M, or between about 2 and 5 ⁇ M, or between about 3 and 5 ⁇ M, or between about 4 and 5 ⁇ M, or between about 0.01 and 4 ⁇ M, or between about 0.01 and 3 ⁇ M, or between about 0.01 and 2 ⁇ M, or between about 0.01 and 1 ⁇ M, or between about 0.01 and 0.5 ⁇ M, or between about 0.01 and 0.2 ⁇ M, or between about 0.01 and 0.1 ⁇ M, or
- the one or more age-inducing agent is administered at a concentration of between about 5 and 50 ⁇ M, or any values in between, for example between about 10 and 50 ⁇ M, or between about 15 and 50 ⁇ M, or between about 20 and 50 ⁇ M, or between about 30 and 50 ⁇ M, or between about 40 and 50 ⁇ M, or between about 5 and 40 ⁇ M, or between about 5 and 30 ⁇ M, or between about 5 and 20 ⁇ M, or between about 5 and 15 ⁇ M, or between about 5 and 10 ⁇ M.
- the one or more age-inducing agent is administered at a concentration of about 0.01 ⁇ M, about 0.02 ⁇ M, about 0.03 ⁇ M, about 0.04 ⁇ M, about 0.05 ⁇ M, about 0.06 ⁇ M, about 0.07 ⁇ M, about 0.08 ⁇ M, about 0.09 ⁇ M, about 0.1 ⁇ M, about 0.2 ⁇ M, about 0.3 ⁇ M, about 0.4 ⁇ M, about 0.5 ⁇ M, about 0.6 ⁇ M, about 0.7 ⁇ M, about 0.8 ⁇ M, about 0.9 ⁇ M, about 1 ⁇ M, about 2 ⁇ M, about 3 ⁇ M, about 4 ⁇ M, about 5 ⁇ M, about 6 ⁇ M, about 7 ⁇ M, about 8 ⁇ M, about 9 ⁇ M, about 10 ⁇ M, about 15 ⁇ M, about 20 ⁇ M, about 25 ⁇ M, about 30 ⁇ M, about 35 ⁇ M, about 40 ⁇ M, about 45 ⁇ M, or about 50 ⁇
- the one or more age-inducing agent described herein is contacted to a cell for at least about 1 day, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 7 days, at least about 8 days, at least about 9 days, at least about 10 days.
- the one or more age-inducing agent is contacted to the cells for up to about 1 day, up to abut 2 days, up to about 3 days, up to about 4 days, up to about 5 days, up to about 6 days, up to about 7 days, up to about 8 days, up to about 9 days, up to about 10 days.
- the one or more age-inducing agent is contacted to the cells for about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 8 days, about 9 days, or about 10 days.
- the present disclosure provides methods for inducing cellular aging in a cell or population of cells, comprising contacting the cell or population of cells with one or more age-inducing agent.
- the cell or population of cells comprise fibroblasts.
- the one or more age-inducing agent is selected from the group consisting of one or more cyclin-dependent kinase (CDK) inhibitor, one or more adenosine kinase inhibitor, one or more topoisomerase II inhibitor, one or more protein kinase C (PKC) inhibitor, one or more DNA binding agent, and combinations thereof.
- CDK cyclin-dependent kinase
- PKC protein kinase C
- the one or more CDK inhibitor comprises alvocidib.
- the one or more adenosine kinase inhibitor comprises 5-iodotubercin.
- the one or more topoisomerase II inhibitor comprises mitoxantrone.
- the one or more PKC inhibitor comprises bisindolylmaleimide-ix.
- the one or more DNA binding agent comprises chromomycin-a3.
- the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more age-inducing agent is selected from the group consisting of one or more DNA synthesis inhibitor, one or more microtubule antagonist, one or more Sirtuin-2 (SIRT2) inhibitor, BRD-K25731886, doxercalciferol, and combinations thereof.
- the one or more DNA synthesis inhibitor comprises fludarabine.
- the one or more microtubule antagonist comprises vinorelbine.
- the one or more SIRT2 inhibitor comprises AGK2.
- contacting the cell or population of cells with one or more age-inducing agent increases the expression level or presence in the cell or population of cells of one or more chronological marker signature of an old cell.
- contacting the cell or population of cells with one or more age-inducing agent decreases the expression level or presence in the cell or population of cells of one or more chronological marker signature of a young cell.
- contacting the Attorney Docket No.072734.1463PCT PATENT cell or population of cells with one or more age-inducing agent induces loss of heterochromatin, disrupted nuclear lamina, increased DNA damage, increased cellular senescence, disrupted proteostasis and increased dependence on autophagy, increased caveolin-1 (CAV1) expression, or a combination thereof.
- the cell or population of cells are derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof.
- the cell or population of cells are human.
- the present disclosure provides an age-induced cell, wherein the age- induced cell is produced by a method comprising contacting a cell with one or more age-inducing agent.
- the age-induced cell is derived from fibroblasts.
- the one or more age-inducing agent is selected from the group consisting of one or more cyclin-dependent kinase (CDK) inhibitor, one or more adenosine kinase inhibitor, one or more topoisomerase II inhibitor, one or more protein kinase C (PKC) inhibitor, one or more DNA binding agent, and combinations thereof.
- the one or more CDK inhibitor comprises alvocidib.
- the one or more adenosine kinase inhibitor comprises 5- iodotubercin.
- the one or more topoisomerase II inhibitor comprises mitoxantrone.
- the one or more PKC inhibitor comprises bisindolylmaleimide-ix.
- the one or more DNA binding agent comprises chromomycin-a3.
- the age-induced cell is derived from neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more age- inducing agent is selected from the group consisting of one or more DNA synthesis inhibitor, one or more microtubule antagonist, one or more Sirtuin-2 (SIRT2) inhibitor, BRD-K25731886, doxercalciferol, and combinations thereof.
- the one or more DNA synthesis inhibitor comprises fludarabine.
- the one or more microtubule antagonist comprises vinorelbine.
- the one or more SIRT2 inhibitor comprises AGK2.
- the age-induced cell is derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. In certain embodiments, the age-induced cell is human.
- the cell with one or more age-inducing agent increases the expression level or presence of one or more chronological marker signature of an old cell.
- contacting the cell with one or more age-inducing agent decreases the expression level or presence of one or more chronological marker signature of a young cell.
- contacting the cell with one or more age-inducing agent induces loss of heterochromatin, disrupted nuclear lamina, increased DNA damage, increased cellular senescence, disrupted proteostasis and increased dependence on autophagy, increased caveolin-1 (CAV1) expression, or a combination thereof.
- the present disclosure provides methods for rejuvenating or reducing aging of a cell or population of cells, for example, an iPSC-derived cell, such as an iPSC- derived somatic cell (e.g., iPSC-derived fibroblasts and iPS cell-derived neurons).
- an iPSC-derived cell such as an iPSC-derived somatic cell (e.g., iPSC-derived fibroblasts and iPS cell-derived neurons).
- the methods described herein induce cellular rejuvenation.
- the methods include contacting the cell or population of cells with one or more rejuvenating agent.
- a transcriptional score is produced for a biological sample in accordance with the methods described herein.
- the one or more rejuvenating agent elicits a shift in RNA expression of biological samples towards the transcriptional signature of “young” tissue.
- Methods of the present disclosure can also be applied to methods of quantifying cellular rejuvenation.
- a transcriptional score is evaluated for a biological sample that is contacted with one or more rejuvenating agent.
- the transcriptional score is compared to one or more reference transcriptional signatures of cellular age.
- contacting the cell or population of cells with one or more rejuvenating agent increases the expression level or presence in the cell or population of cells of one or more chronological marker signatures of a young cell.
- contacting the cell or population of cells with one or more rejuvenating agent reducing the expression level or presence in the cell or population of cells of one or more chronological marker signature of an old cell.
- the methods of the present invention can be applied for the production of young cells from somatic cells (whether iPSC-derived or primary cells), from stem cells or from fully differentiated or partially differentiated cells.
- the cells are derived from iPSC, stem cells, embryonic stem cells, skin stem cells from adult Attorney Docket No.072734.1463PCT PATENT individuals, mesenchymal stem cells, somatic cells, neurons, and fibroblasts.
- the cells are hPSC-derived cells.
- the one or more rejuvenating agent comprises one or more histone deacetylase (HDAC) inhibitor.
- HDAC histone deacetylase
- HDAC inhibitors function by inhibiting histone deacetylases, which catalyze the removal of acetyl groups from histones.
- HDAC inhibitors include mocetinostat, SB-939, and BRD- A19037878.
- the cell or population of cells comprise fibroblasts.
- the one or more rejuvenating agent is selected from the group consisting of one or more histone deacetylase (HDAC) inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, and combinations thereof.
- HDAC histone deacetylase
- HSP heat shock protein
- PI3K phosphoinositide 3-kinase
- the one or more HDAC inhibitor comprises mocetinostat.
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- the one or more adrenergic receptor antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more rejuvenating agent is selected from the group consisting of one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3-related (ATR) signaling inhibitor, and combinations thereof.
- SIRT activator comprises resveratrol.
- HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- the treatment timing and/or concentration of the one or more rejuvenating agent is varied.
- the one or more rejuvenating agent is administered at a concentration of between about 0.01 and 5 ⁇ M, or any value in between, for example, between about 0.02 and 5 ⁇ M, , or between about 0.03 and 5 ⁇ M, or between about 0.4 and 5 ⁇ M, or between about 0.05 and 5 ⁇ M, or between about 0.1 and 5 ⁇ M, or between about 0.5 and 5 ⁇ M, or between about 1 and Attorney Docket No.072734.1463PCT PATENT 5 ⁇ M, or between about 2 and 5 ⁇ M, or between about 3 and 5 ⁇ M, or between about 4 and 5 ⁇ M, or between about 0.01 and 4 ⁇ M, or between about 0.01 and 3 ⁇ M, or between about 0.01 and 2 ⁇ M, or between about 0.01 and 1 ⁇ M, or between about 0.01 and 0.5 ⁇ M, or between about 0.01 and 0.2 ⁇ M, or between
- the one or more rejuvenating agent is administered at a concentration of between about 5 and 50 ⁇ M, or any values in between, for example between about 10 and 50 ⁇ M, or between about 15 and 50 ⁇ M, or between about 20 and 50 ⁇ M, or between about 30 and 50 ⁇ M, or between about 40 and 50 ⁇ M, or between about 5 and 40 ⁇ M, or between about 5 and 30 ⁇ M, or between about 5 and 20 ⁇ M, or between about 5 and 15 ⁇ M, or between about 5 and 10 ⁇ M.
- the one or more rejuvenating agent is administered at a concentration of about 0.01 ⁇ M, about 0.02 ⁇ M, about 0.03 ⁇ M, about 0.04 ⁇ M, about 0.05 ⁇ M, about 0.06 ⁇ M, about 0.07 ⁇ M, about 0.08 ⁇ M, about 0.09 ⁇ M, about 0.1 ⁇ M, about 0.2 ⁇ M, about 0.3 ⁇ M, about 0.4 ⁇ M, about 0.5 ⁇ M, about 0.6 ⁇ M, about 0.7 ⁇ M, about 0.8 ⁇ M, about 0.9 ⁇ M, about 1 ⁇ M, about 2 ⁇ M, about 3 ⁇ M, about 4 ⁇ M, about 5 ⁇ M, about 6 ⁇ M, about 7 ⁇ M, about 8 ⁇ M, about 9 ⁇ M, about 10 ⁇ M, about 15 ⁇ M, about 20 ⁇ M, about 25 ⁇ M, about 30 ⁇ M, about 35 ⁇ M, about 40 ⁇ M, about 45 ⁇ M, or about 50 ⁇ M.
- the one or more rejuvenating agent described herein is contacted to a cell for at least about 1 day, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 7 days, at least about 8 days, at least about 9 days, at least about 10 days.
- the one or more rejuvenating agent is contacted to the cells for up to about 1 day, up to abut 2 days, up to about 3 days, up to about 4 days, up to about 5 days, up to about 6 days, up to about 7 days, up to about 8 days, up to about 9 days, up to about 10 days.
- the one or more rejuvenating agent is contacted to the cells for about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 8 days, about 9 days, or about 10 days.
- the present disclosure provides a method for rejuvenating cellular age in a cell or population of cells, comprising contacting the cell or population of cells with one or more rejuvenating agent.
- the cell or population of cells comprise fibroblasts.
- the one or more rejuvenating agent is selected from the group consisting of one or more histone deacetylase (HDAC) Attorney Docket No.072734.1463PCT PATENT inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, and combinations thereof.
- HDAC histone deacetylase
- HSP heat shock protein
- adrenergic receptor antagonist one or more phosphoinositide 3-kinase
- PI3K phosphoinositide 3-kinase
- the one or more HDAC inhibitor comprises mocetinostat.
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- the one or more adrenergic receptor antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more rejuvenating agent is selected from the group consisting of one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3- related (ATR) signaling inhibitor, and combinations thereof.
- the one or more SIRT activator comprises resveratrol.
- the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- contacting the cell or population of cells with one or more rejuvenating agent reduces loss of heterochromatin, disrupted nuclear lamina, DNA damage, cellular senescence, disrupted proteostasis and dependence on autophagy, caveolin-1 (CAV1) expression, or a combination thereof.
- the cell or population of cells are derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof.
- the cell or population of cells are human.
- the present disclosure provides a rejuvenated cell, wherein the rejuvenated cell is produced by a method comprising contacting a cell with one or more rejuvenating agent.
- the rejuvenated cell is derived from fibroblasts.
- the one or more rejuvenating agent is selected from the group Attorney Docket No.072734.1463PCT PATENT consisting of one or more histone deacetylase (HDAC) inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, and combinations thereof.
- HDAC histone deacetylase
- HSP heat shock protein
- PI3K phosphoinositide 3-kinase
- the one or more HDAC inhibitor comprises mocetinostat.
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- the one or more adrenergic receptor antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the rejuvenated cell is derived from neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons.
- the one or more rejuvenating agent is selected from the group consisting of one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3-related (ATR) signaling inhibitor, and combinations thereof.
- the one or more SIRT activator comprises resveratrol.
- the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- the rejuvenated cell is derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. In certain embodiments, the rejuvenated cell is human. In certain embodiments, contacting the cell with one or more rejuvenating agent increases the expression level or presence of one or more chronological marker signature of a young cell.
- contacting the cell with one or more rejuvenating agent decreases the expression level or presence of one or more chronological marker signature of an old cell. In certain embodiments, contacting the cell with one or more rejuvenating agent reduces loss of heterochromatin, disrupted nuclear lamina, DNA damage, cellular senescence, disrupted proteostasis and dependence on autophagy, caveolin-1 (CAV1) expression, or a combination thereof.
- CAV1 caveolin-1
- Such disease models can be developed by inducing aging chronologic marker Attorney Docket No.072734.1463PCT PATENT signatures in somatic cells (not necessarily derived by induced differentiation of stem cells) that express a “young” marker signature.
- This strategy can be applied to cell cultures derived from a patient with a late-onset disease and/or disorder including, but not limited to, a neurodegenerative disease, such as Alzheimer’s disease (AD) or Parkinson's disease (PD), to derive age-appropriate cell cultures that more accurately represent patient age and thus the disease state.
- Induced cellular aging provides a system to model age-related aspects of late-onset neurodegenerative diseases.
- Such a system can be used to directly test an interaction between genetic susceptibility and age-related vulnerability on disease phenotype.
- Disease phenotypes may, in some instances, be based upon aging and/or genetic susceptibility.
- the present disclosure provides methods for inducing aging to examine late-onset disease and/or disorders in age-appropriate iPSC- based cell culture models, which are characterized by the induction and display of one or more chronological marker signatures, and optionally one or more disease signatures (including for example genetic pre-disposition).
- contacting the cell with one or more age-inducing agent induces loss of heterochromatin, disrupted nuclear lamina, increased DNA damage, increased cellular senescence, disrupted proteostasis and increased dependence on autophagy, increased caveolin-1 (CAV1) expression, or a combination thereof.
- the present disclosure provides a method of modeling neurodegenerative disease, comprising: contacting a cell or population of cells with one or more age- inducing agent to obtain an age-modulated cell or population of age-modulated cells; and contacting the age-modulated cell or population of age-modulated cells with one or more candidate compound.
- the method further comprises detecting an alteration in at least one of the survival, biological activity, structure or morphology of the age-modulated cell or population of age-modulated cells. In certain embodiments, the method further comprises selecting as the drug a candidate one or more compound that alters at least one of the survival, biological activity, structure or morphology of the age-modulated cell or population of age-modulated cells.
- the neurodegenerative disease is Parkinson's disease (PD) or Alzheimer’s Disease (AD).
- Treatment Cells may be isolated from healthy subjects, at risk subjects, and diseased subjects for use in generating undifferentiated iPS cells according to methodology presented herein or as otherwise available in the art.
- Primary somatic cells used for reprogramming may be isolated from a variety of bodily locations, such as circulating cells and/or cells in tissues of patients/subjects, including but not limited to fibroblasts, skin fibroblasts, white blood cells, circulating white blood cells, mucosal cells, and keratinocytes without regard for the "age" of the cell or the "age” of the donor.
- primary somatic cells may be young cells expressing a “young” cell marker signature isolated from young donors, which cells may or may not be expressing a disease signature.
- primary somatic cells may be old cells expressing an “old” marker signature.
- primary somatic cells may be cells expressing a disease marker signature regardless of the chronological age of the donor.
- Generated iPSCs of any origin may be used in differentiation protocols for producing differentiating and differentiated iPSC-derived cells that may find use in hypomethylation aging compositions and methods of the present disclosures.
- Differentiating and differentiated iPSC-derived cells include but are not limited to default and nondefault differentiation lineages, including partially differentiated (i.e., differentiating) cells, so long as they are capable of expressing genetic and cell marker signatures of their particular cell types, i.e., permissive cells.
- iPSC-derived cells including but not limited to neurons (any subtype, such as motoneurons, cortical neurons, peripheral sensory neurons, mid-brain dopamine neurons etc.), and fibroblasts.
- iPSC derived cells at certain stages will find use in induced aging or rejuvenation treatments according to the present disclosure including, but not limited to, iPSC derived cells beginning to undergo differentiation, iPSC derived cells progressing towards committed cells types, iPSC derived cells progressing towards a mature cell type, etc.
- an iPSC-derived midbrain dopamine neuron, or precursor thereof, can be aged according to the Attorney Docket No.072734.1463PCT PATENT present disclosure and can be used in a cell based therapy for introducing into a PD patient. Accordingly, the present disclosure provides for pharmaceutical compositions comprising the aged cells described herein.
- Non-limiting examples of specific iPSC-derived cell types and associated disease(s) which can be used in conjunction with the methods of inducing aging described herein include iPSC derived-neurons for neurodegenerative diseases, iPSC- derived motoneurons for ALS, iPSC-derived cortical neurons for Alzheimer's, iPSC- derived mDA neurons and iPSC-derived cortical neurons for corticobasal degeneration, iPSC-derived astrocytes for neurodegenerative disorders, and the like.
- the presently disclosed cells and the pharmaceutical compositions comprising thereof can be conveniently provided as sterile liquid preparations, e.g., isotonic aqueous solutions, suspensions, emulsions, dispersions, or viscous compositions, which may be buffered to a selected pH.
- sterile liquid preparations e.g., isotonic aqueous solutions, suspensions, emulsions, dispersions, or viscous compositions, which may be buffered to a selected pH.
- Liquid preparations are normally easier to prepare than gels, other viscous compositions, and solid compositions. Additionally, liquid compositions are somewhat more convenient to administer, especially by injection. Viscous compositions, on the other hand, can be formulated within the appropriate viscosity range to provide longer contact periods with specific tissues.
- Liquid or viscous compositions can comprise carriers, which can be a solvent or dispersing medium containing, for example, water, saline, phosphate buffered saline, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like) and suitable mixtures thereof.
- Step injectable solutions can be prepared by incorporating the compositions of the presently disclosed subject matter, e.g., a composition comprising the presently disclosed cells, in the required amount of the appropriate solvent with various amounts of the other ingredients, as desired.
- Such compositions may be in admixture with a suitable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like.
- compositions can also be lyophilized.
- the compositions can contain auxiliary substances such as wetting, dispersing, or emulsifying agents (e.g., methylcellulose), pH buffering agents, gelling or viscosity enhancing additives, preservatives, flavoring agents, colors, and the like, depending upon the route of administration and the preparation desired.
- auxiliary substances such as wetting, dispersing, or emulsifying agents (e.g., methylcellulose), pH buffering agents, gelling or viscosity enhancing additives, preservatives, flavoring agents, colors, and the like, depending upon the route of administration and the preparation desired.
- Standard texts such as “REMINGTON’S PHARMACEUTICAL SCIENCE”, 17th edition, 1985, incorporated herein by reference, may be consulted to prepare suitable preparations, without undue experimentation.
- Viscosity of the compositions can be maintained at the selected level using a pharmaceutically acceptable thickening agent.
- Methylcellulose can be used because it is readily and economically available and is easy to work with.
- suitable thickening agents include, for example, xanthan gum, carboxymethyl cellulose, hydroxypropyl cellulose, carbomer, and the like.
- concentration of the thickener can depend upon the agent selected. The important point is to use an amount that will achieve the selected viscosity.
- suitable carriers and other additives will depend on the exact route of administration and the nature of the particular dosage form, e.g., liquid dosage form (e.g., whether the composition is to be formulated into a solution, a suspension, gel or another liquid form, such as a time release form or liquid-filled form).
- liquid dosage form e.g., whether the composition is to be formulated into a solution, a suspension, gel or another liquid form, such as a time release form or liquid-filled form.
- the components of the compositions should be selected to be chemically inert and will not affect the viability or efficacy of the presently disclosed cells. This will present no problem to those skilled in chemical and pharmaceutical principles, or problems can be readily avoided by reference to standard texts or by simple experiments (not involving undue experimentation), from this disclosure and the documents cited herein.
- An optimal effect include, but are not limited to, repopulation of the CNS of a subject suffering from a neurological disorder (e.g., PD or AD), and/or improved function of the subject’s CNS.
- An “effective amount” is an amount sufficient to affect a beneficial or desired clinical result upon treatment.
- An effective amount can be administered to a subject in one or more doses.
- an effective amount is an amount that is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of the neurological disorder (e.g., PD or AD), or otherwise reduce the pathological consequences of the neurological disorder (e.g., PD or AD).
- the effective amount is generally determined by the physician on a case-by- case basis and is within the skill of one in the art. Several factors are typically taken into account when determining an appropriate dosage to achieve an effective amount. These factors include age, sex and weight of the subject, the condition being treated, the severity of the condition and the form and effective concentration of the cells administered.
- an effective amount of the presently disclosed cells is an amount that is sufficient to repopulate the CNS of a subject suffering from a neurological disorder (e.g., PD or AD). In certain embodiments, an effective amount of the presently disclosed cells is an amount that is sufficient to improve the function of the CNS of a subject suffering from a neurological disorder (e.g., PD or AD), e.g., the improved function can be about 1%, about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 98%, about 99% or about 100% of the function of a normal person’s CNS.
- the quantity of cells to be administered will vary for the subject being treated.
- from about 1 x 10 4 to about 1 x 10 10 from about 1 x 10 4 to about 1 x 10 5 , from about 1 x 10 5 to about 1 x 10 9 , from about 1 x 10 5 to about 1 x 10 6 , from about 1 x 10 5 to about 1 x 10 7 , from about 1 x 10 6 to about 1 x 10 7 , from about 1 x 10 6 to about 1 x 10 8 , from about 1 x 10 7 to about 1 x 10 8 , from about 1 x 10 8 to about 1 x 10 9 , from about 1 x 10 8 to about 1 x 10 10 , or from about 1 x 10 9 to about 1 x 10 10 of the presently disclosed cells are administered to a subject.
- from about 1 x 10 5 to about 1 x 10 7 of the presently disclosed s cells are administered to a subject suffering from a neurological disorder (e.g., PD or AD).
- about 2 x 10 5 of the presently disclosed cells are administered to a subject suffering from a neurological disorder (e.g., PD or AD).
- from about 1 x 10 6 to about 1 x 10 7 the presently disclosed cells are administered to a subject suffering from a neurological disorder (e.g., PD or AD).
- from about 2 x 10 6 to about 4 x 10 6 the presently disclosed cells are administered to a subject suffering from a neurological disorder (e.g., PD or AD).
- the cells that are administered to a subject suffering from a neurological disorder are a population of midbrain dopamine neurons that are differentiated and aged according to the methods described herein.
- the cells that are administered to a subject suffering from a neurological disorder (e.g, PD or AD) for treating a neurological disorder are a population of midbrain dopamine neuron precursors that are differentiated and aged according to the methods described herein.
- a neurological disorder e.g, PD or AD
- the present disclosure provides a composition comprising the age-induced cell disclosed herein or the rejuvenated cell disclosed herein.
- the composition is a pharmaceutical composition.
- the composition further comprises a pharmaceutically acceptable carrier.
- aged iPSC-derived cell types obtained as described herein may find use in disease modeling and for identifying therapeutically relevant cell stages during development, such as identifying aged cellular stages for use in testing new drug compounds for use as therapeutics and for actual use in treatment of patients.
- primary somatic cell donors for iPSC-derived cell types have a disease or a disease phenotype induced in iPSC-derived cell/tissue culture including but are not limited to actual or model neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer’s disease (AD), tauopathies, i.e., a class of neurodegenerative diseases associated with the pathological aggregation of tau protein in the human brain, etc.
- PD Parkinson's disease
- AD Alzheimer’s disease
- tauopathies i.e., a class of neurodegenerative diseases associated with the pathological aggregation of tau protein in the human brain, etc.
- the presently disclosed aged cells can be used to model disorders, for example, a neurological disorder such as Parkinson’s disease (PD) and Alzheimer’s disease (AD), and serve as a platform to screen for candidate compounds that can overcome disease related defects.
- a neurological disorder such as Parkinson’s disease (PD) and Alzheimer’s disease (AD)
- the capacity of a candidate compound to alleviate a disorder can be determined by assaying the candidate compound’s ability to rescue a physiological or cellular defect in a diseased cell, for example, an Attorney Docket No.072734.1463PCT PATENT iPSC-derived midbrain dopamine neuron (mDA), or precursor thereof, wherein the iPSC is prepared from a somatic cell obtained from a PD patient.
- the method comprises identifying a compound that is capable of rescuing at least one cellular disease phenotype.
- the method comprises: (a) providing (i) a population of the presently disclosed aged cells (e.g., iPSC-derived PD neurons or progenitors thereof), and (ii) a test compound; (b) contacting the cells with the test compound; and (c) measuring the level or presence of one or more disease phenotype, for example, wherein a test compound that reduces the level of presence of the one or more disease phenotype is selected as a candidate therapeutic compound.
- a test compound that reduces the level of presence of the one or more disease phenotype is selected as a candidate therapeutic compound.
- kits for inducing aging and/or maturation of a cell for example, an iPSC-derived cell, such as an iPSC-derived somatic cell (e.g., iPSC-derived fibroblasts and iPSC-derived neurons), wherein the expression of one or more chronological markers of an aged cell is increased following contact of the cell with one or more age-inducing agent.
- the kit comprises one or more age-inducing agent that induces or increases expression of one or more chronological markers of an aged cell.
- the kit comprises instructions for inducing age in the cell, such that the expression of one or more chronological markers of an aged cell is increased in the cell following treatment of the cell according to the instructions.
- one or more chronological markers of a young cell is decreased in the cell following treatment of the cell according to the instructions.
- kits for reducing aging and/or maturation of a cell for example, an iPSC-derived cell, such as an iPSC-derived somatic cell (e.g., iPSC-derived fibroblasts and iPSC-derived neurons), wherein the expression of one or more chronological markers of a young cell is increased following contact of the cell with one or more rejuvenating agent.
- the kit comprises one or more rejuvenating agent that induces or increases expression of one or more chronological markers of a young cell.
- the kit Attorney Docket No.072734.1463PCT PATENT comprises instructions for reducing age in the cell, such that the expression of one or more chronological markers of a young cell is increased in the cell following treatment of the cell according to the instructions. In certain embodiments, one or more chronological markers of an aged cell is decreased in the cell following treatment of the cell according to the instructions.
- the kit comprises instructions for administering a population of the presently disclosed cells, for example, stem-cell-derived neurons, such as midbrain dopamine neurons, or precursors thereof, or a composition comprising said cells, to a subject suffering from a disorder, such as a neurological disorder, for example, Parkinson’s disease or Alzheimer’s disease.
- the instructions can comprise information about the use of the cells or composition for treating or preventing the disorder.
- the instructions comprise at least one of the following: description of the therapeutic agent; dosage schedule and administration for treating or preventing the disorder, or symptoms thereof; precautions; warnings; indications; counter-indications; over dosage information; adverse reactions; animal pharmacology; clinical studies; and/or references.
- the instructions can be printed directly on a container (when present) comprising the cells, or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
- the present disclosure further provides a kit for rejuvenating a cell or population of cells, comprising one or more rejuvenating agent selected from the group consisting of one or more histone deacetylase (HDAC) inhibitor, one or more heat shock protein (HSP) inhibitor, one or more adrenergic receptor antagonist, one or more phosphoinositide 3-kinase (PI3K) inhibitor, one or more Sirtuin (SIRT) activator, one or more HDAC inhibitor, one or more poly ADP ribose polymerase (PARP) inhibitor, one or more ataxia telangiectasia and Rad3-related (ATR) signaling inhibitor, and combinations thereof.
- HDAC histone deacetylase
- HSP heat shock protein
- PI3K phosphoinositide 3-kinase
- SIRT Sirtuin
- HDAC inhibitor one or more HDAC inhibitor
- PARP poly ADP ribose polymerase
- ATR Rad3-related
- the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof.
- the one or more adrenergic receptor antagonist comprises alfuzosin.
- the one or more PI3K inhibitor comprises wortmannin.
- the one or more SIRT activator comprises resveratrol.
- the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, Attorney Docket No.072734.1463PCT PATENT or a combination thereof.
- the PARP inhibitor comprises veliparib.
- the ATR signaling inhibitor comprises VE-821.
- the kit further comprises instructions for contacting a cell or population of cells with the one or more rejuvenating agent to induce expression in the cell or population of cells of one or more chronological marker signature of a young cell.
- RNAge a transcriptome-based computational platform, enables the evaluation of induced aging or rejuvenated states. This approach is validated across independent datasets spanning different tissues and species. RNAge can be used to evaluate the effectiveness of existing age modulating interventions. RNAge is used to perform an in silico compound screen using the LINCS L1000 dataset. This approach led to the identification and experimental confirmation of several novel compounds capable of inducing aging or rejuvenation in primary fibroblasts or hPSC-derived neurons. In addition, applying such compounds to hPSC-models of Alzheimer’s disease neurodegeneration in a genotype specific manner.
- RNAge offers a robust method for quantifying age-related manipulations and unveils compounds that significantly broaden the toolkit for age-modifying strategies in hPSC-derived lineages.
- Methods Reprogramming of primary fibroblasts to iPSCs. Young and old primary fibroblasts were obtained from Coriell and maintained in ⁇ -MEM + 15% FBS. Fibroblasts were reprogrammed to iPSCs using CytoTune Sendai viruses expressing Attorney Docket No.072734.1463PCT PATENT SOX2, OCT4, KLF4 and c-MYC. After the formation of iPSC colonies (aprox.30 days after transduction), individual colonies were manually isolated, replated onto MEFs and maintained in KSR media.
- iPSCs Differentiation of iPSCs into fibroblasts. Differentiation of iPSCs into fibroblasts was performed. In brief, pluripotent stem cells were cultured on MEFs in KSR based media supplemented with 10 ng/ml FGF2. For differentiation, colonies were dissociated from the feeder layer using dispase and replated onto gelatin coated plates. Cells were maintained in DMEM + 20% heat-inactivated fibroblasts for 25 days with passaging ever 5-6 days. Fibroblasts were isolated by flow cytometry (CD-13 high and HLA-CD44 high ) after 25 days of culture and cultured for an additional 7 days before harvest. Fibroblast maintenance and culture.
- Fibroblasts were maintained in DMEM-F12 containing GlutaMAX,15% heat inactivated FBS and 1X Pen/Strep and passaged using Trypsin.
- RNA-seq old (GM04204; Coriell) or young (HDF-f; ScienCell #2300) fibroblasts were plated at a density of 4000 cm 2 , test compounds were applied when cultures reached 70% confluence.
- Generation of human cortical neurons Cortical neurons were generated by directed differentiation of human embryonic stem cells (H9; WA-09) maintained in E8 on vitronectin coated plates.
- Differentiation was performed by seeding pluripotent stem cells onto Matrigel coated dishes at a density of 300,000/cm 2 in the presence of Y27632 (10 ⁇ M). After 24h the E8 medium was replaced with E6 containing SB431542 (10 ⁇ M), LDN193189 (100 nM) and XAV939 (2 ⁇ M). After three days the XAV939 was removed from the differentiation media and cells were cultured for an additional seven days in E6 containing SB431542 (10 ⁇ M), LDN193189 (100 nM). The neuroepithelium was maintained for an additional 10 days in neurobasal supplemented with N2 and B27. Media was changed daily throughout the differentiation.
- DIV 20 the cultures were dissociated using Accutase to generate a single cell suspension and plated out for subsequent experiments in Neurobasal medium supplemented with B27, L-glutamine, BDNF, cAMP, ascorbic acid and GDNF (neural maintenance media).
- DAPT was also added to the culture medium from DIV20 to DIV30.
- Age induction experiments in young fibroblasts were performed with 5-Iodotubercin (10 ⁇ M; Selleck S8314), Alvocidib (10 ⁇ M; Selleck S1230) and Mitoxantrone (1.1 ⁇ M; Selleck S2485) with DMSO (1:1000) used as a control.
- Compounds used for age induction experiments in PSC-derived neurons were: Fludarabine (10 ⁇ M; Selleck S1491) Vinorelbine (10 ⁇ M; sc-205885) and AGK-2 (0.04 ⁇ M; Selleck S7577) with DMSO (1:1000) used as a control. Assaying Hallmarks of Age by high content microscopy.
- HDF fibroblasts were plated at a density of 4500/cm 2 and cultured for 48h before drug treatment. Neurons were plated at a density of 100,000/cm 2 and cultured for 12 days before the application of candidate age inducers. After 24h of treatment culture wells were washed 2x in PBS then fixed with 4% paraformaldehyde. For immunocytochemistry cells were permeabilized in PBS+0.3% Triton and blocked in 5% normal goat serum. All antibody primary incubations were performed overnight at 4 degrees and secondary antibodies at RT for 1h.
- BAG3 (abcam; ab47124), CAV1 (Thermo; MA3-600), H3K9me3 (abcam; ab176916), LAP2 (BD Bioscience; 611000), p21 (CST; 2947), yH2AX (EMD Millipore; 05 ⁇ 636).
- RNA Extraction Cell were harvested, lysed, and stored in Trizol (Life Technologies) until further processing. For primary frontal cortex or substantia nigra a total of 10 mg of brain tissue from was lysed in Trizol aided by a tissue dounce.
- RNAge Training datasets Primary fibroblast samples from 9 young (7-14 years old) and 9 old (70-96 years old) profiled by total-RNA-seq protocol.
- PolyA pF Randomly picked 4 young (10-11 years old) and 4 old (71-96 years old) out of above 18 primary fibroblast samples. These samples were profiled by polyA RNA- seq kit.
- PolyA Gage pF Primary fibroblast RNA-seq data from 6 young ( ⁇ 15-year- old) and 4 old (> 70-year-old) were downloaded from E-MTAB-3037 dataset. All raw data were processed by our RNA-seq analysis protocol.
- PolyA Gage FC frontal cortex RNA-seq data from 4 young ( ⁇ 15-year-old) and 4 old (> 70-year-old) were downloaded from E-MTAB-3037 dataset. All raw data were processed by our RNA- seq analysis protocol.
- Total FC Primary frontal cortex samples from 9 young (13-14 years old) and 9 old (70-91 years old) profiled by total-RNA-seq protocol.
- Total SN Primary substantia nigra samples from 10 young (13-14 years old) and 9 old (70-91 years old) profiled by total-RNA-seq protocol. Other datasets.
- GSE113957 Fleischer et al. collected fibroblast samples from 133 healthy individuals. The FPKM of gene expression were downloaded from GEO database. Out of 133 samples, 10 young (8-13 years old), 10 old (> 89-year-old) and 10 HGPS (2–8 years old) samples were used in this study.
- GSE36192 Microarray data of the cerebellum and frontal cortex from 396 subjects (total 911 tissue samples) were generated by North American Brain Expression Consortium. The normalized gene expression matrix was downloaded from GEO database.
- GSE52431 The raw RNA-seq data from 4 iPSC-derived Attorney Docket No.072734.1463PCT PATENT dopamine neurons with overexpressing progerin and 4 corresponding control samples were downloaded and processed with proposed pipeline.
- GSE132040 Bulk RNA-seq data from Tabula Muris Consortium study were downloaded and processed. The whole brain data from young ( ⁇ 3-month) and old (>24-month) mice were used in this study.
- GSE141028 Fathi et al. presented a study of inducing senescence by treating human embryonic stem cells with compounds.
- E-MTAB-5965 Genetic ablation of SATB1 induces a senescence phenotype in human embryonic stem cell (hESC)-derived DA neurons.
- the raw RNA-seq data from 3 STAB1-KO and 3 WT cell lines were downloaded, processed, and used in this study.
- E-MTAB-10352 The raw RNA-seq data from 42 samples were downloaded, processed, and used in this study, including 17 samples from iPSC derived induced neurons and 25 samples from direct conversion of human fibroblasts into induced neurons.
- GTEx The FPKM data of four tissues was downloaded from GTEx Portal, including frontal cortex, cortex, substantia nigra and stomach. Aging markers identification.
- ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ _ ⁇ ⁇ .
- Differential gene expression analysis was performed using DESeq2 between young and old samples in each of the RNA-seq datasets, resulting in log fold change values and p- value from each of the six datasets.
- the log2 based fold change between young and old groups for each gene i in each dataset j is denoted as ⁇ ⁇ , ⁇ , where ⁇ ⁇ ⁇ , ⁇ ⁇ ⁇ .
- the p- value between young and old groups for each gene in each dataset is denoted as ⁇ ⁇ , ⁇ , where ⁇ ⁇ ⁇ , ⁇ ⁇ ⁇ .
- the simplified ⁇ ⁇ , ⁇ of above signatures is consistent across multiple datasets from the corresponding tissue type and it excludes genes that do not exhibit any change between the young and old groups.
- ⁇ ⁇ ⁇ ⁇ , ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇
- the aging score is applied on a gene expression test data where two conditions are compared for expression changes in the aging signature, group1 has n samples and group2 has m samples.
- group1 has n samples
- group2 has m samples.
- This score is calculated using the tissue-specific aging marker set ⁇ ⁇ . It indicates the aging difference between the two groups as well as distinguishes which group is older.
- ⁇ ⁇ indicates a consistent expression change of gene ⁇ in both the aging signature and in the comparison between group1 and group2 in the test dataset. Conversely, a negative ⁇ ⁇ indicates an opposite expression trend. Therefore, the "Percentage score" is defined as: ⁇ ⁇ ⁇ Results Measuring cellular rejuvenation in stem cell models. Transcriptional reprogramming of primary fibroblasts to pluripotent stem cells is one of the best described methods of resetting cellular age. As a positive control for RNAge, a subset of fibroblast lines were reprogrammed to pluripotent stem cells then differentiated them back into iPSC-derived fibroblasts ( Figure 12B).
- RNA-seq was performed, and RNAge was applied.
- Reprogramming fibroblasts to iPSCs resulted in the loss of age- related differential expressed genes (DEGs) that were not re-established once iPSCs were differentiated back into iPSC-derived fibroblasts ( Figure 17B). This matched the RNAge score where young and old primary fibroblasts show an increased aging score relative to iPSC derived fibroblasts.
- DEGs age- related differential expressed genes
- iNs generated from old fibroblasts were tested to determine whether they had a higher aging score compared to iNs generated from PSCs where cellular age is reset during reprogramming (Figure 12D).
- the aging score showed that forebrain-like neurons generated from old fibroblasts displayed an increase in the ‘Pan’, ‘Neuronal’, and ‘FC’-specific aging scores but not the ‘SN’ aging score.
- RNAge score is tractable and can be used to identify age-regulating compounds. RNAge can be used to compare the relative age of primary tissues and hPSC-derived cells in response to different aging and rejuvenating paradigms. RNAge can also be used as a drug discovery tool to identify tissue-specific drivers of cellular age. An in silico screen was designed (outlined in Figure 13A) using the LINCS L1000 dataset.
- the L1000 dataset included a total of 348 and 3968 perturbations for 1HAE and NEU respectively.
- the aging scores were calculated for each of those perturbations relative to matched control samples in the dataset, and averaged to get a single value for each perturbation. Aging scores fell on a normal distribution for all cell types and sub-scores ( Figures 13B and 13C) indicating that most drug treatments did not induce changes in the aging score. However, there were several compounds that rejuvenated or induced transcriptional age (> 3 std from mean RNAage score). HDAC inhibitors induce rejuvenation. The screening strategy can identify candidate rejuvenating drugs.
- HDAC-i HDAC inhibitors
- Validation experiments were performed in fibroblasts due to the availability of primary fibroblasts isolated from aged individuals which is not readily feasible for primary human neurons. Mocetinostat treatment was able to reverse cellular aging in old primary fibroblasts across all RNAge sub scores ( Figure 18D). To further validate this finding, ATAC-seq was performed on primary young and old fibroblasts and results were overlayed with the DEGs identified by RNAseq to identify the top candidate regulators of age in primary fibroblasts ( Figure 18E).
- RNAage is suitable to identify candidate rejuvenating factors and provides further impetus to study HDAC-i as potential compounds to promote transcriptional features of cellular rejuvenation. Identification of candidate age inducers using the L1000 dataset. Certain compounds induced an increase in RNAage in fibroblast and in neurons for the L1000 dataset ( Figure 13B-13E).
- fibroblast top scoring compounds were selected including Alvocidib (CDK inhibitor), 5-iodotubercin (adenosine kinase inhibitor) and Mitoxantrone (Topoisomerase II inhibitor), as these three drugs were among the top four age inducers for both the ‘Pan’ and ‘pF’ aging scores.
- Fludarabine (STAT1 and DNA synthesis inhibitor), Vinorelbine (microtubule antagonist) and AGK-2 (SIRT2 inhibitor) were selected for further validation in neurons, as these were the top three candidate regulators of the pan-neuronal score. Fludarabine was also the top candidate as measured by the ‘Pan’ aging score.
- the L1000 dataset was first analyzed, which included data sets across multiple independent perturbations with varying drug concentrations and treatment lengths for many candidate age regulators (Figure 19A- 19B).
- Principal component analysis ( Figure 14B) of the RNA-seq data indicated that all the fibroblast aging inducers segregated from the control, with Alvocidib and 5-iodotubercin clustering closely together.
- the RNA-seq data were used to calculate the RNAge score for each of the perturbations relative to DMSO ( Figure 14C).
- the age modifying drug treatments were assessed to determine whether they also trigger the well described cellular hallmarks of age (Figure 14A) including loss of heterochromatin (H3K9me3 and LAP2), disrupted nuclear lamina (decreased nuclear roundness and loss of LAP2), increased DNA damage ( ⁇ H2AX), increased cellular senescence (p21 and nuclear area), disrupted proteostasis and increased dependence on autophagy (BAG3) and increased CAV1 (multiple functions, broadly increased with age).
- Alvocidib, 5-iodotubercin and Mitoxantrone (24h) all increased the relative transcriptional age of fetal fibroblasts ( Figure 14C).
- AD-genetic susceptibility can synergize with Fludarabine-mediated induction of cellular age to trigger genotype- specific neuronal loss, a phenotype that that cannot be captured in most hPSC-based in vitro models of AD (Figure 15E).
- a novel transcriptomic measure of relative age is developed, demonstrated in benchmarking published age inducing strategies, and used for identifying novel age modifying strategies.
- aging scores showed tissue specificity showing that Attorney Docket No.072734.1463PCT PATENT transcriptional aging, and perhaps the aging process more generally can be tissue dependent.
- HDAC-i are one of the compounds incorporated into chemical based partial reprogramming strategies and has been shown to improve age and late onset disease phenotypes in mouse models.
- This Attorney Docket No.072734.1463PCT PATENT acts as a proof of principle that RNAge could also be used to identify and optimize cellular rejuvenation strategies and potentially to identify new ways to increase human health span.
- RNAge score can be particularly useful in tracking the dynamics of cell fate rejuvenation versus fate reprogramming when optimizing partial reprogramming strategies and assessing therapeutic strategies for age associated diseases.
- This study demonstrates the use of aging scores to perform an in silico screen for novel age-inducing perturbations.
- RNAge the performance of novel age inducers can be directly compared using the RNAge score and tested in conjunction with previously published strategies to establish an optimal strategy to induce aging in PSC-derived neurons.
- RNAge could allow the aging field to explore which of the hallmarks of age act as drivers of cellular age in different cell types and conditions and lead to a deeper understanding of the mechanistic underpinngs of the aging process.
- induction of transcriptional age in fibroblasts can be associated with two distinct patterns of cellular hallmarks of age. Mitoxantrone showed a strong cellular senescence phenotype with increased p21 expression, increased DNA damage and loss of H3K9me3 in contrast to Alvocidib and 5-Iodotubercin. This indicates that the RNAge score can capture aging triggered by distinct cellular mechanisms.
Landscapes
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Chemical & Material Sciences (AREA)
- General Health & Medical Sciences (AREA)
- Public Health (AREA)
- Veterinary Medicine (AREA)
- Animal Behavior & Ethology (AREA)
- Pharmacology & Pharmacy (AREA)
- Medicinal Chemistry (AREA)
- Epidemiology (AREA)
- Engineering & Computer Science (AREA)
- Biomedical Technology (AREA)
- Organic Chemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Wood Science & Technology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Zoology (AREA)
- Genetics & Genomics (AREA)
- Neurology (AREA)
- Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
- General Chemical & Material Sciences (AREA)
- Microbiology (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Neurosurgery (AREA)
- Cell Biology (AREA)
- General Engineering & Computer Science (AREA)
- Biochemistry (AREA)
- Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
- Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
- Medicines Containing Material From Animals Or Micro-Organisms (AREA)
- Micro-Organisms Or Cultivation Processes Thereof (AREA)
Abstract
Description
Claims
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202363524801P | 2023-07-03 | 2023-07-03 | |
| US63/524,801 | 2023-07-03 |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| US19/438,959 Continuation US20260125647A1 (en) | 2026-01-02 | Age-modulating compounds and methods for making age-modulated cells |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO2025010366A2 true WO2025010366A2 (en) | 2025-01-09 |
| WO2025010366A3 WO2025010366A3 (en) | 2025-05-15 |
Family
ID=94172538
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US2024/036791 Ceased WO2025010366A2 (en) | 2023-07-03 | 2024-07-03 | Age-modulating compounds and methods for making age-modulated cells |
Country Status (1)
| Country | Link |
|---|---|
| WO (1) | WO2025010366A2 (en) |
Family Cites Families (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20250213608A1 (en) * | 2022-05-19 | 2025-07-03 | The University Of Chicago | Vanadyl sulfate compositions and methods of use therefor for the treatement and prevention of aging-related diseases and cancer |
-
2024
- 2024-07-03 WO PCT/US2024/036791 patent/WO2025010366A2/en not_active Ceased
Also Published As
| Publication number | Publication date |
|---|---|
| WO2025010366A3 (en) | 2025-05-15 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| Vadodaria et al. | Altered serotonergic circuitry in SSRI-resistant major depressive disorder patient-derived neurons | |
| Akkouh et al. | Decreased IL-1β-induced CCL20 response in human iPSC-astrocytes in schizophrenia: Potential attenuating effects on recruitment of regulatory T cells | |
| Vadodaria et al. | Serotonin-induced hyperactivity in SSRI-resistant major depressive disorder patient-derived neurons | |
| Shah et al. | Single-cell transcriptomics and fate mapping of ependymal cells reveals an absence of neural stem cell function | |
| Kang et al. | Characteristic analyses of a neural differentiation model from iPSC-derived neuron according to morphology, physiology, and global gene expression pattern | |
| Chen et al. | Transcripts involved in calcium signaling and telencephalic neuronal fate are altered in induced pluripotent stem cells from bipolar disorder patients | |
| Sheng et al. | A stably self-renewing adult blood-derived induced neural stem cell exhibiting patternability and epigenetic rejuvenation | |
| Zhao et al. | A high-throughput screen for Wnt/β-catenin signaling pathway modulators in human iPSC-derived neural progenitors | |
| Mishra et al. | Circadian rhythms in bipolar disorder patient-derived neurons predict lithium response: preliminary studies | |
| Park et al. | Small molecule-based lineage switch of human adipose-derived stem cells into neural stem cells and functional GABAergic neurons | |
| Gao et al. | Suppression of glioblastoma by a drug cocktail reprogramming tumor cells into neuronal like cells | |
| Paul et al. | Lithium response in bipolar disorder correlates with improved cell viability of patient derived cell lines | |
| Lischka et al. | N eonatal mouse cortical but not isogenic human astrocyte feeder layers enhance the functional maturation of induced pluripotent stem cell‐derived neurons in culture | |
| Boza-Morán et al. | Decay in survival motor neuron and plastin 3 levels during differentiation of iPSC-derived human motor neurons | |
| Boshans et al. | Direct reprogramming of oligodendrocyte precursor cells into GABAergic inhibitory neurons by a single homeodomain transcription factor Dlx2 | |
| Li et al. | Asynchronous excitatory neuron development in an isogenic cortical spheroid model of Down syndrome | |
| Yelamanchili et al. | The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins | |
| Grazioli et al. | Lithium as a possible therapeutic strategy for Cornelia de Lange syndrome | |
| Brady et al. | Mispatterning and interneuron deficit in Tourette Syndrome basal ganglia organoids | |
| Yang et al. | Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder | |
| Freitag et al. | Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development | |
| Salas-Lucia et al. | Thyroid hormone promotes fetal neurogenesis | |
| Halder et al. | PCDHB14-and GABRB1-like nervous system developmental genes are altered during early neuronal differentiation of NCCIT cells treated with ethanol | |
| Colleoni et al. | Characterisation of a neural teratogenicity assay based on human ESCs differentiation following exposure to valproic acid | |
| Liu et al. | Canonical microRNAs enable differentiation, protect against DNA damage, and promote cholesterol biosynthesis in neural stem cells |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| 121 | Ep: the epo has been informed by wipo that ep was designated in this application |
Ref document number: 24836587 Country of ref document: EP Kind code of ref document: A2 |
|
| WWE | Wipo information: entry into national phase |
Ref document number: 2024836587 Country of ref document: EP |
|
| NENP | Non-entry into the national phase |
Ref country code: DE |
|
| ENP | Entry into the national phase |
Ref document number: 2024836587 Country of ref document: EP Effective date: 20260203 |
|
| 121 | Ep: the epo has been informed by wipo that ep was designated in this application |
Ref document number: 24836587 Country of ref document: EP Kind code of ref document: A2 |

