EP-4739678-A2 - AGE-MODULATING COMPOUNDS AND METHODS FOR MAKING AGE-MODULATED CELLS

Abstract

Provided are age-modulated cells and method for making age-modulated cells. The aging and rejuvenation processes can be induced for young, aged, mature and/or immature cells, such as a somatic cell, a stem cell, a stem cell-derived somatic cell, including an induced pluripotent stem cell-derived cell, by contacting cells with one or more age-inducing or rejuvenating agent. Methods described by the present disclosure can produce age-appropriate cells from a somatic cell or a stem cell, such as an old cell, young cell, immature cell, and/or a mature cell. Such age-modified cells constitute model systems for the study of late-onset diseases and/or disorders.

Inventors

• SAURAT, Nathalie
• STUDER, LORENZ

Assignees

• Memorial Sloan Kettering Cancer Center
• Sloan-Kettering Institute for Cancer Research
• Memorial Hospital for Cancer and Allied Diseases

Dates

Publication Date

20260513

Application Date

20240703

Claims (1)

1. Attorney Docket No.072734.1463PCT PATENT CLAIMS 1. A 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. 2. The method of claim 1, wherein the cell or population of cells comprise fibroblasts. 3. The method of claim 2, wherein 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. 4. The method of claim 3, wherein the one or more CDK inhibitor comprises alvocidib. 5. The method of claim 3, wherein the one or more adenosine kinase inhibitor comprises 5-iodotubercin. 6. The method of claim 3, wherein the one or more topoisomerase II inhibitor comprises mitoxantrone. 7. The method of claim 3, wherein the one or more PKC inhibitor comprises bisindolylmaleimide-ix. 8. The method of claim 3, wherein the one or more DNA binding agent comprises chromomycin-a3. 9. The method of claim 1, wherein the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons. 10. The method of claim 9, wherein 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. 11. The method of claim 10, wherein the one or more DNA synthesis inhibitor comprises fludarabine. 12. The method of claim 10, wherein the one or more microtubule antagonist comprises vinorelbine. 13. The method of claim 10, wherein the one or more SIRT2 inhibitor comprises AGK2. Attorney Docket No.072734.1463PCT PATENT 14. The method of any one of claims 1-13, wherein 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. 15. The method of any one of claims 1-14, wherein the cell or population of cells are human. 16. The method of any one of claims 1-15, wherein 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. 17. The method of any one of claims 1-16, wherein 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. 18. The method of any one of claims 1-17, wherein 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. 19. 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. 20. The method of claim 19, wherein the cell or population of cells comprise fibroblasts. 21. The method of claim 20, wherein 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. 22. The method of claim 21, wherein the one or more HDAC inhibitor comprises mocetinostat. 23. The method of claim 21, wherein the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof. 24. The method of claim 21, wherein the one or more adrenergic receptor antagonist comprises alfuzosin. Attorney Docket No.072734.1463PCT PATENT 25. The method of claim 21, wherein the one or more PI3K inhibitor comprises wortmannin. 26. The method of claim 19, wherein the cell or population of cells comprise neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons. 27. The method of claim 26, wherein 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. 28. The method of claim 27, wherein the one or more SIRT activator comprises resveratrol. 29. The method of claim 27, wherein the one or more HDAC inhibitor comprises SB- 939, BRD-A19037878, or a combination thereof. 30. The method of claim 27, wherein the PARP inhibitor comprises veliparib. 31. The method of claim 27, wherein the ATR signaling inhibitor comprises VE-821. 32. The method of any one of claims 19-31, wherein 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. 33. The method of any one of claims 19-32, wherein the cell or population of cells are human. 34. The method of any one of claims 19-33, wherein 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. 35. The method of any one of claims 19-34, wherein 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. 36. The method of any one of claims 19-35, wherein 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 Attorney Docket No.072734.1463PCT PATENT and dependence on autophagy, caveolin-1 (CAV1) expression, or a combination thereof. 37. 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. 38. The age-induced cell of claim 37, wherein the age-induced cell is derived from fibroblasts. 39. The age-induced cell of claim 38, wherein 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. 40. The age-induced cell of claim 39, wherein the one or more CDK inhibitor comprises alvocidib. 41. The age-induced cell of claim 39, wherein the one or more adenosine kinase inhibitor comprises 5-iodotubercin. 42. The age-induced cell of claim 39, wherein the one or more topoisomerase II inhibitor comprises mitoxantrone. 43. The age-induced cell of claim 39, wherein the one or more PKC inhibitor comprises bisindolylmaleimide-ix. 44. The age-induced cell of claim 39, wherein the one or more DNA binding agent comprises chromomycin-a3. 45. The age-induced cell of claim 37, wherein the age-induced cell is derived from neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons. 46. The age-induced cell of claim 45, wherein 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. 47. The age-induced cell of claim 46, wherein the one or more DNA synthesis inhibitor comprises fludarabine. 48. The age-induced cell of claim 47, wherein the one or more microtubule antagonist comprises vinorelbine. Attorney Docket No.072734.1463PCT PATENT 49. The age-induced cell of claim 48, wherein the one or more SIRT2 inhibitor comprises AGK2. 50. The age-induced cell of any one of claims 37-49, wherein the age-induced cell is derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. 51. The age-induced cell of any one of claims 37-50, wherein the age-induced cell is human. 52. The age-induced cell of any one of claims 37-51, wherein contacting 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. 53. The age-induced cell of any one of claims 37-52, wherein 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. 54. The age-induced cell of any one of claims 37-53, wherein 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. 55. A rejuvenated cell, wherein the rejuvenated cell is produced by a method comprising contacting a cell with one or more rejuvenating agent. 56. The rejuvenated cell of claim 55, wherein the rejuvenated cell is derived from fibroblasts. 57. The rejuvenated cell of claim 56, wherein 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. 58. The rejuvenated cell of claim 57, wherein the one or more HDAC inhibitor comprises mocetinostat. 59. The rejuvenated cell of claim 57, wherein the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof. 60. The rejuvenated cell of claim 57, wherein the one or more adrenergic receptor antagonist comprises alfuzosin. Attorney Docket No.072734.1463PCT PATENT 61. The rejuvenated cell of claim 57, wherein the one or more PI3K inhibitor comprises wortmannin. 62. The rejuvenated cell of claim 55, wherein the rejuvenated cell is derived from neurons, motoneurons, cortical neurons, peripheral sensory neurons, or midbrain dopamine neurons. 63. The rejuvenated cell of claim 62, wherein 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. 64. The rejuvenated cell of claim 63, wherein the one or more SIRT activator comprises resveratrol. 65. The rejuvenated cell of claim 63, wherein the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof. 66. The rejuvenated cell of claim 63, wherein the PARP inhibitor comprises veliparib. 67. The rejuvenated cell of claim 63, wherein the ATR signaling inhibitor comprises VE-821. 68. The rejuvenated cell of any one of claims 55-67, wherein the rejuvenated cell is derived from primary cells, fetal cells, pluripotent stem cells, embryonic stem cells, induced pluripotent stem cells, or combinations thereof. 69. The rejuvenated cell of any one of claims 55-68, wherein the rejuvenated cell is human. 70. The rejuvenated cell of any one of claims 55-69, wherein 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. 71. The rejuvenated cell of any one of claims 55-70, wherein 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. 72. The rejuvenated cell of any one of claims 55-71, wherein 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. Attorney Docket No.072734.1463PCT PATENT 73. A composition comprising the age-induced cell of any one of claims 37-55 or the rejuvenated cell of any one of claims 56-72. 74. The composition of claim 73, wherein the composition is a pharmaceutical composition. 75. The composition of claim 74, further comprising a pharmaceutically acceptable carrier. 76. 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. 77. The method of claim 76, further comprising 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. 78. The method of claim 77, further comprising 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. 79. The method of any one of claims 76-78, wherein the neurodegenerative disease is Parkinson's disease (PD) or Alzheimer’s Disease (AD). 80. 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. 81. The kit of claim 80, wherein the one or more DNA synthesis inhibitor comprises fludarabine. 82. The kit of claim 80, wherein the one or more microtubule antagonist comprises vinorelbine. 83. The kit of claim 80, wherein the one or more SIRT2 inhibitor comprises AGK2. 84. The kit of claim 80, wherein the one or more CDK inhibitor comprises alvocidib. Attorney Docket No.072734.1463PCT PATENT 85. The kit of claim 80, wherein the one or more adenosine kinase inhibitor comprises 5-iodotubercin. 86. The kit of claim 80, wherein the one or more topoisomerase II inhibitor comprises mitoxantrone. 87. The kit of claim 80, wherein the one or more PKC inhibitor comprises bisindolylmaleimide-ix. 88. The kit of claim 80, wherein the one or more DNA binding agent comprises chromomycin-a3. 89. The kit of claim 80, further comprising 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. 90. 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. 91. The kit of claim 90, wherein the one or more HDAC inhibitor comprises mocetinostat. 92. The kit of claim 90, wherein the one or more HSP inhibitor comprises radicicol, geldanamycin, or a combination thereof. 93. The kit of claim 90, wherein the one or more adrenergic receptor antagonist comprises alfuzosin. 94. The kit of claim 90, wherein the one or more PI3K inhibitor comprises wortmannin. 95. The kit of claim 90, wherein the one or more SIRT activator comprises resveratrol. 96. The kit of claim 90, wherein the one or more HDAC inhibitor comprises SB-939, BRD-A19037878, or a combination thereof. 97. The kit of claim 90, wherein the PARP inhibitor comprises veliparib. 98. The kit of claim 90, wherein the ATR signaling inhibitor comprises VE-821. Attorney Docket No.072734.1463PCT PATENT 99. The kit of claim 90, further comprising 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.

Description

Attorney Docket No.072734.1463PCT PATENT AGE-MODULATING COMPOUNDS AND METHODS FOR MAKING AGE- MODULATED CELLS CROSS REFERENCE TO RELATED APPLICATIONS This application claims priority to United States Provisional Application No. 63/524,801 filed July 3, 2023, which is hereby incorporated by reference in its entirety, and to which priority is claimed. 1. TECHNICAL FIELD The present disclosure relates to methods for modulating cellular aging and/or progression of neurodegenerative diseases (e.g., Alzheimers Disease), and age- modulated cells which can be used both clinically as well as in basic research. Furthermore, the present disclosure also relates to methods of reversing cellular aging (i.e., cellular rejuvenation). 2. BACKGROUND OF THE DISCLOSURE hPSC technology offers access to a diverse range of cell types for disease modelling. However, 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. In neurons, these efforts can be grouped into two broad approaches: 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. Furthermore, recent studies indicate that aging may show tissue and Attorney Docket No.072734.1463PCT PATENT cell type specificity raising the question of how relevant fibroblast aging signatures are to neuronal age. To compare, evaluate and expand on any age-modifying interventions it is essential to develop methods that quantitatively measure biological age at the cellular level. A commonly used approach are DNA methylation-based aging clocks that are based on 5mC methylation status at tissue- and age-related CpG sites. In addition, there are transcriptomics-based aging clocks which offer an obvious advantage due to the broad availability of data sets spanning many cell types, disease conditions and cellular states. Transcriptomic clocks may also provide more direct mechanistic insights into the aging process than epigenetic measurements. There have been several efforts to develop both global and cell type specific transcriptional aging clocks. To date, the use of aging clocks has been limited to estimating absolute or relative cellular age. An exciting future application is their use as a direct readout in functional screens aimed at age manipulation to establish improved hPSC-based models of late onset human disease. There is need to identify novel regulators of age that could be incorporated into hPSC-based models of neurodegenerative disease to accelerate the acquisition of late onset phenotypes in vitro, and to develop novel methods to score changes in the relative age of human cells. Furthermore, there is need to develop cellular models that more faithfully recapitulate late-onset disease phenotypes in vitro. 3. SUMMARY OF THE DISCLOSURE 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. In certain embodiments, the cell or population of cells comprise fibroblasts. In certain embodiments, 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. In certain embodiments, the one or more CDK inhibitor comprises alvocidib. In certain embodiments, the one or more adenosine kinase inhibitor comprises 5-iodotubercin. In certain embodiments, the one or more topoisomerase II inhibitor comprises mitoxantrone. In certain embodiments, the one or Attorney Docket No.072734.1463PCT PATENT more PKC inhibitor comprises bisindolylmaleimide-ix. In certain embodiments, the one or more DNA binding agent comprises chromomycin-a3. In certain embodiments, the cell or population of cells comprise neurons, motoneurons, c