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Konagaya Y, Rosenthal D, Ratnayeke N, Fan Y, Meyer T. An intermediate Rb-E2F activity state safeguards proliferation commitment. Nature 2024:10.1038/s41586-024-07554-2. [PMID: 38926571 DOI: 10.1038/s41586-024-07554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 05/10/2024] [Indexed: 06/28/2024]
Abstract
Tissue repair, immune defence and cancer progression rely on a vital cellular decision between quiescence and proliferation1,2. Mammalian cells proliferate by triggering a positive feedback mechanism3,4. The transcription factor E2F activates cyclin-dependent kinase 2 (CDK2), which in turn phosphorylates and inactivates the E2F inhibitor protein retinoblastoma (Rb). This action further increases E2F activity to express genes needed for proliferation. Given that positive feedback can inadvertently amplify small signals, understanding how cells keep this positive feedback in check remains a puzzle. Here we measured E2F and CDK2 signal changes in single cells and found that the positive feedback mechanism engages only late in G1 phase. Cells spend variable and often extended times in a reversible state of intermediate E2F activity before committing to proliferate. This intermediate E2F activity is proportional to the amount of phosphorylation of a conserved T373 residue in Rb that is mediated by CDK2 or CDK4/CDK6. Such T373-phosphorylated Rb remains bound on chromatin but dissociates from it once Rb is hyperphosphorylated at many sites, which fully activates E2F. The preferential initial phosphorylation of T373 can be explained by its relatively slower rate of dephosphorylation. Together, our study identifies a primed state of intermediate E2F activation whereby cells sense external and internal signals and decide whether to reverse and exit to quiescence or trigger the positive feedback mechanism that initiates cell proliferation.
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Affiliation(s)
- Yumi Konagaya
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Laboratory for Quantitative Biology of Cell Fate Decision, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.
| | - David Rosenthal
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Nalin Ratnayeke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell 2024:S1534-5807(24)00327-7. [PMID: 38823395 DOI: 10.1016/j.devcel.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/14/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.
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Affiliation(s)
- Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA; Rogel Cancer Center and Division of Hematology and Oncology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sidney Y Vermeulen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhishan Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Najihah Aziz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Bjelosevic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha A Nelson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel Block
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jonathan S Weissman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA; Stem Cell Center, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, Riverside, CA 92521, USA
| | - Xiaofeng A Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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3
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Zhang S, Valenzuela LF, Zatulovskiy E, Mangiante L, Curtis C, Skotheim JM. The G1/S transition is promoted by Rb degradation via the E3 ligase UBR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560768. [PMID: 37873473 PMCID: PMC10592979 DOI: 10.1101/2023.10.03.560768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Mammalian cells make the decision to divide at the G1/S transition in response to diverse signals impinging on the retinoblastoma protein Rb, a cell cycle inhibitor and tumor suppressor. Rb is inhibited by two parallel pathways. In the canonical pathway, Cyclin D-Cdk4/6 kinase complexes phosphorylate and inactivate Rb. In the second, recently discovered pathway, Rb's concentration decreases during G1 to promote cells progressing through the G1/S transition. However, the mechanisms underlying this second pathway are unknown. Here, we found that Rb's concentration drop in G1 and recovery in S/G2 is controlled by phosphorylation-dependent protein degradation. In early G1 phase, un- and hypo-phosphorylated Rb is targeted by the E3 ligase UBR5. UBR5 knockout cells have higher Rb concentrations in early G1, exhibit a lower G1/S transition rate, and are more sensitive to Cdk4/6 inhibition. This last observation suggests that UBR5 inhibition can strengthen the efficacy of Cdk4/6 inhibitor-based cancer therapies.
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Affiliation(s)
- Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA 94305
| | | | | | | | | | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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4
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Zhao P, Zhang L, Feng L, Jiang WD, Wu P, Liu Y, Ren HM, Jin XW, Zhou XQ. Novel Perspective on Mechanism in Muscle Growth Inhibited by Ochratoxin A Associated with Ferroptosis: Model of Juvenile Grass Carp ( Ctenopharyngodon idella) In Vivo and In Vitro Trials. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4977-4990. [PMID: 38386875 DOI: 10.1021/acs.jafc.3c08080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ochratoxin A (OTA) is a common mycotoxin in food and feed that seriously harms human and animal health. This study investigated the effect of OTA on the muscle growth of juvenile grass carp (Ctenopharyngodon idella) and its possible mechanism in vitro. Our results have the following innovative findings: (1) Dietary OTA increased the expression of increasing phase I metabolic enzymes and absorbing transporters while reducing the expression of efflux transporters, thereby increasing their residue in muscles; (2) OTA inhibited the expressions of cell cycle and myogenic regulatory factors (MyoD, MyoG, and MyHC) and induced ferroptosis by decreasing the mRNA and protein expressions of FTH, TFR1, GPX4, and Nrf2 both in vivo and in vitro; and (3) the addition of DFO improved OTA-induced ferroptosis of grass carp primary myoblasts and promoted cell proliferation, while the addition of AKT improved OTA-inhibited myoblast differentiation and fusion, thus inhibiting muscle growth. Overall, this study provides a potential research target to further mitigate the myotoxicity of OTA.
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Affiliation(s)
- Piao Zhao
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lu Zhang
- Key Laboratory of Nutrition and Healthy Culture of Aquatic, Livestock and Poultry, Ministry of Agriculture and Rural Affairs, Healthy Aquaculture Key Laboratory of Sichuan Province, Tongwei Co., Ltd., Chengdu, Sichuan 610041, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Wei-Dan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Hong-Mei Ren
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Xiao-Wan Jin
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Xiao-Qiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
- Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Ministry of Agriculture and Rural Affairs, Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, China
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5
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Zikry TM, Wolff SC, Ranek JS, Davis HM, Naugle A, Luthra N, Whitman AA, Kedziora KM, Stallaert W, Kosorok MR, Spanheimer PM, Purvis JE. Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells. Proc Natl Acad Sci U S A 2024; 121:e2309261121. [PMID: 38324568 PMCID: PMC10873600 DOI: 10.1073/pnas.2309261121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage of tumor cells continues to divide in the presence of palbociclib-a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcomes. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant cells in both cultured and primary breast tumor samples resected from patients. Resistant cells showed premature accumulation of multiple G1 regulators including E2F1, retinoblastoma protein, and CDK2, as well as enhanced sensitivity to pharmacological inhibition of CDK2 activity. Using trajectory inference approaches, we show how plasticity among cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.
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Affiliation(s)
- Tarek M. Zikry
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC27599
| | - Samuel C. Wolff
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jolene S. Ranek
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Harris M. Davis
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Ander Naugle
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Namit Luthra
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Austin A. Whitman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Katarzyna M. Kedziora
- Center for Biologic Imaging, Department of Cell Biology, University of Pittsburg, Pittsburgh, PA15620
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburg, Pittsburgh, PA15620
| | - Michael R. Kosorok
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC27599
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jeremy E. Purvis
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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6
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Singh A, Mishra R, Mazumder A. Breast cancer and its therapeutic targets: A comprehensive review. Chem Biol Drug Des 2024; 103:e14384. [PMID: 37919259 DOI: 10.1111/cbdd.14384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 09/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Breast cancer is a common and deadly disease, so there is a constant need for research to find efficient targets and therapeutic approaches. Breast cancer can be classified on a molecular and histological base. Breast cancer can be divided into ER (estrogen receptor)-positive and ER-negative, HER2 (human epidermal growth factor receptor2)-positive and HER2-negative subtypes based on the presence of specific biomarkers. Targeting hormone receptors, such as the HER2, progesterone receptor (PR), and ER, is very significant and plays a vital role in the onset and progression of breast cancer. Endocrine treatments and HER2-targeted drugs are examples of targeted therapies now being used against these receptors. Emerging immune-based medicines with promising outcomes in the treatment of breast cancer include immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapy. It is also explored how immune cells and the tumor microenvironment affect breast cancer development and treatment response. The major biochemical pathways, signaling cascades, and DNA repair mechanisms that are involved in the development and progression of breast cancer, include the PI3K/AKT/mTOR system, the MAPK pathway, and others. These pathways are intended to be inhibited by a variety of targeted drugs, which are then delivered with the goal of restoring normal cellular function. This review aims to shed light on types of breast cancer with the summarization of different therapeutic approaches which can target different pathways for tailored medicines and better patient outcomes.
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Affiliation(s)
- Ayushi Singh
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Rakhi Mishra
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Avijit Mazumder
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
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7
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Kedziora KM, Stallaert W. Cell Cycle Mapping Using Multiplexed Immunofluorescence. Methods Mol Biol 2024; 2740:243-262. [PMID: 38393480 DOI: 10.1007/978-1-0716-3557-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The development of technologies that allow measurement of the cell cycle at the single-cell level has revealed novel insights into the mechanisms that regulate cell cycle commitment and progression through DNA replication and cell division. These studies have also provided evidence of heterogeneity in cell cycle regulation among individual cells, even within a genetically identical population. Cell cycle mapping combines highly multiplexed imaging with manifold learning to visualize the diversity of "paths" that cells can take through the proliferative cell cycle or into various states of cell cycle arrest. In this chapter, we describe a general protocol of the experimental and computational components of cell cycle mapping. We also provide a comprehensive guide for the design and analysis of experiments, discussing key considerations in detail (e.g., antibody library preparation, analysis strategies, etc.) that may vary depending on the research question being addressed.
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Affiliation(s)
- Katarzyna M Kedziora
- Department of Cell Biology, Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, PA, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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8
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Zhang M, Kim S, Yang HW. Non-canonical pathway for Rb inactivation and external signaling coordinate cell-cycle entry without CDK4/6 activity. Nat Commun 2023; 14:7847. [PMID: 38030655 PMCID: PMC10687137 DOI: 10.1038/s41467-023-43716-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
Cyclin-dependent kinases 4 and 6 (CDK4/6) are critical for initiating cell proliferation by inactivating the retinoblastoma (Rb) protein. However, mammalian cells can bypass CDK4/6 for Rb inactivation. Here we show a non-canonical pathway for Rb inactivation and its interplay with external signals. We find that the non-phosphorylated Rb protein in quiescent cells is intrinsically unstable, offering an alternative mechanism for initiating E2F activity. Nevertheless, this pathway incompletely induces Rb-protein loss, resulting in minimal E2F activity. To trigger cell proliferation, upregulation of mitogenic signaling is required for stabilizing c-Myc, thereby augmenting E2F activity. Concurrently, stress signaling promotes Cip/Kip levels, competitively regulating cell proliferation with mitogenic signaling. In cancer, driver mutations elevate c-Myc levels, facilitating adaptation to CDK4/6 inhibitors. Differentiated cells, despite Rb-protein loss, maintain quiescence through the modulation of c-Myc and Cip/Kip levels. Our findings provide mechanistic insights into an alternative model of cell-cycle entry and the maintenance of quiescence.
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Affiliation(s)
- Mimi Zhang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Sungsoo Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
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9
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Mouery BL, Baker EM, Mills CA, Herring LE, Fleifel D, Cook JG. APC/C prevents non-canonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566394. [PMID: 37986787 PMCID: PMC10659421 DOI: 10.1101/2023.11.09.566394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase APC/C (anaphase promoting complex/cyclosome), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear if APC/C maintains all types of arrest. Here by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological CDK4/6 inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves cyclin-dependent kinases acting in an atypical order to inactivate RB-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L Mouery
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Eliyambuya M Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christine A Mills
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
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10
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Afifi MM, Crncec A, Cornwell JA, Cataisson C, Paul D, Ghorab LM, Hernandez MO, Wong M, Kedei N, Cappell SD. Irreversible cell cycle exit associated with senescence is mediated by constitutive MYC degradation. Cell Rep 2023; 42:113079. [PMID: 37656618 PMCID: PMC10591853 DOI: 10.1016/j.celrep.2023.113079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 07/21/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023] Open
Abstract
Cells can irreversibly exit the cell cycle and become senescent to safeguard against uncontrolled proliferation. While the p53-p21 and p16-Rb pathways are thought to mediate senescence, they also mediate reversible cell cycle arrest (quiescence), raising the question of whether senescence is actually reversible or whether alternative mechanisms underly the irreversibility associated with senescence. Here, we show that senescence is irreversible and that commitment to and maintenance of senescence are mediated by irreversible MYC degradation. Senescent cells start dividing when a non-degradable MYC mutant is expressed, and quiescent cells convert to senescence when MYC is knocked down. In early oral carcinogenesis, epithelial cells exhibit MYC loss and become senescent as a safeguard against malignant transformation. Later stages of oral premalignant lesions exhibit elevated MYC levels and cellular dysplasia. Thus, irreversible cell cycle exit associated with senescence is mediated by constitutive MYC degradation, but bypassing this degradation may allow tumor cells to escape during cancer initiation.
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Affiliation(s)
- Marwa M Afifi
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Adrijana Crncec
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - James A Cornwell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christophe Cataisson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Laila M Ghorab
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maria O Hernandez
- Collaborative Protein Technology Resource, Office of Science and Technology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Madeline Wong
- Collaborative Protein Technology Resource, Office of Science and Technology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, Office of Science and Technology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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11
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Milletti G, Colicchia V, Cecconi F. Cyclers' kinases in cell division: from molecules to cancer therapy. Cell Death Differ 2023; 30:2035-2052. [PMID: 37516809 PMCID: PMC10482880 DOI: 10.1038/s41418-023-01196-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/31/2023] Open
Abstract
Faithful eucaryotic cell division requires spatio-temporal orchestration of multiple sequential events. To ensure the dynamic nature of these molecular and morphological transitions, a swift modulation of key regulatory pathways is necessary. The molecular process that most certainly fits this description is phosphorylation, the post-translational modification provided by kinases, that is crucial to allowing the progression of the cell cycle and that culminates with the separation of two identical daughter cells. In detail, from the early stages of the interphase to the cytokinesis, each critical step of this process is tightly regulated by multiple families of kinases including the Cyclin-dependent kinases (CDKs), kinases of the Aurora, Polo, Wee1 families, and many others. While cell-cycle-related CDKs control the timing of the different phases, preventing replication machinery errors, the latter modulate the centrosome cycle and the spindle function, avoiding karyotypic abnormalities typical of chromosome instability. Such chromosomal abnormalities may result from replication stress (RS) and chromosome mis-segregation and are considered a hallmark of poor prognosis, therapeutic resistance, and metastasis in cancer patients. Here, we discuss recent advances in the understanding of how different families of kinases concur to govern cell cycle, preventing RS and mitotic infidelity. Additionally, considering the growing number of clinical trials targeting these molecules, we review to what extent and in which tumor context cell-cycle-related kinases inhibitors are worth exploiting as an effective therapeutic strategy.
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Affiliation(s)
- Giacomo Milletti
- DNA Replication and Cancer Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
- Department of Pediatric Hematology and Oncology and of Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy.
| | - Valeria Colicchia
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- IRBM S.p.A., Via Pontina Km 30.60, 00070, Pomezia, Italy
| | - Francesco Cecconi
- Cell Stress and Survival Group, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Institute, Copenhagen, Denmark.
- Università Cattolica del Sacro Cuore and Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
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12
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Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep 2023; 13:7678. [PMID: 37169829 PMCID: PMC10175263 DOI: 10.1038/s41598-023-33329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Cell-cycle control is accomplished by cyclin-dependent kinases (CDKs), motivating extensive research into CDK targeting small-molecule drugs as cancer therapeutics. Here we use combinatorial CRISPR/Cas9 perturbations to uncover an extensive network of functional interdependencies among CDKs and related factors, identifying 43 synthetic-lethal and 12 synergistic interactions. We dissect CDK perturbations using single-cell RNAseq, for which we develop a novel computational framework to precisely quantify cell-cycle effects and diverse cell states orchestrated by specific CDKs. While pairwise disruption of CDK4/6 is synthetic-lethal, only CDK6 is required for normal cell-cycle progression and transcriptional activation. Multiple CDKs (CDK1/7/9/12) are synthetic-lethal in combination with PRMT5, independent of cell-cycle control. In-depth analysis of mRNA expression and splicing patterns provides multiple lines of evidence that the CDK-PRMT5 dependency is due to aberrant transcriptional regulation resulting in premature termination. These inter-dependencies translate to drug-drug synergies, with therapeutic implications in cancer and other diseases.
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Affiliation(s)
- Kyle Ford
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brenton P Munson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Samson H Fong
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wai Keung Chu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Rainaldi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Todd VanArsdale
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Thomas Paul
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Trey Ideker
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Liu C, Kudo T, Ye X, Gascoigne K. Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells. Cell Rep 2023; 42:112401. [PMID: 37060565 DOI: 10.1016/j.celrep.2023.112401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Cell-to-cell heterogeneity is vital for tumor evolution and survival. How cancer cells achieve and exploit this heterogeneity remains an active area of research. Here, we identify c-Myc as a highly heterogeneously expressed transcription factor and an orchestrator of transcriptional and phenotypic diversity in cancer cells. By monitoring endogenous c-Myc protein in individual living cells, we report the surprising pulsatile nature of c-Myc expression and the extensive cell-to-cell variability in its dynamics. We further show that heterogeneity in c-Myc dynamics leads to variable target gene transcription and that timing of c-Myc expression predicts cell-cycle progression rates and drug sensitivities. Together, our data advocate for a model in which cancer cells increase the heterogeneity of functionally diverse transcription factors such as c-Myc to rapidly survey transcriptional landscapes and survive stress.
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Affiliation(s)
- Chad Liu
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Takamasa Kudo
- Department of Cellular and Tissue Genomics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Xin Ye
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Karen Gascoigne
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.
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14
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Zhang ZB, Sinha J, Bahrami-Nejad Z, Teruel MN. The circadian clock mediates daily bursts of cell differentiation by periodically restricting cell-differentiation commitment. Proc Natl Acad Sci U S A 2022; 119:e2204470119. [PMID: 35939672 PMCID: PMC9388110 DOI: 10.1073/pnas.2204470119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
Most mammalian cells have an intrinsic circadian clock that coordinates metabolic activity with the daily rest and wake cycle. The circadian clock is known to regulate cell differentiation, but how continuous daily oscillations of the internal clock can control a much longer, multiday differentiation process is not known. Here, we simultaneously monitor circadian clock and adipocyte-differentiation progression live in single cells. Strikingly, we find a bursting behavior in the cell population whereby individual preadipocytes commit to differentiate primarily during a 12-h window each day, corresponding to the time of rest. Daily gating occurs because cells irreversibly commit to differentiate within only a few hours, which is much faster than the rest phase and the overall multiday differentiation process. The daily bursts in differentiation commitment result from a differentiation-stimulus driven variable and slow increase in expression of PPARG, the master regulator of adipogenesis, overlaid with circadian boosts in PPARG expression driven by fast, clock-driven PPARG regulators such as CEBPA. Our finding of daily bursts in cell differentiation only during the circadian cycle phase corresponding to evening in humans is broadly relevant, given that most differentiating somatic cells are regulated by the circadian clock. Having a restricted time each day when differentiation occurs may open therapeutic strategies to use timed treatment relative to the clock to promote tissue regeneration.
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Affiliation(s)
- Zhi-Bo Zhang
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, NY 10065
- The Ira & Gale Drukier Institute of Children’s Health, Weill Cornell Medical College of Cornell University, New York, NY 10065
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Zahra Bahrami-Nejad
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Mary N. Teruel
- Department of Biochemistry, Weill Cornell Medical College of Cornell University, New York, NY 10065
- The Ira & Gale Drukier Institute of Children’s Health, Weill Cornell Medical College of Cornell University, New York, NY 10065
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
- Weill Center for Metabolic Health, Division of Endocrinology, Diabetes, and Metabolism, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College of Cornell University, New York, NY 10065
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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15
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Pandey N, Vinod PK. Model scenarios for cell cycle re-entry in Alzheimer's disease. iScience 2022; 25:104543. [PMID: 35747391 PMCID: PMC9209725 DOI: 10.1016/j.isci.2022.104543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/01/2022] [Accepted: 06/02/2022] [Indexed: 11/30/2022] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease. Aberrant production and aggregation of amyloid beta (Aβ) peptide into plaques is a frequent feature of AD, but therapeutic approaches targeting Aβ accumulation fail to inhibit disease progression. The approved cholinesterase inhibitor drugs are symptomatic treatments. During human brain development, the progenitor cells differentiate into neurons and switch to a postmitotic state. However, cell cycle re-entry often precedes loss of neurons. We developed mathematical models of multiple routes leading to cell cycle re-entry in neurons that incorporate the crosstalk between cell cycle, neuronal, and apoptotic signaling mechanisms. We show that the integration of multiple feedback loops influences disease severity making the switch to pathological state irreversible. We observe that the transcriptional changes associated with this transition are also characteristics of the AD brain. We propose that targeting multiple arms of the feedback loop may bring about disease-modifying effects in AD. Developed mathematical models of cell cycle re-entry in Alzheimer's disease (AD) Integration of multiple feedback loops drives irreversible transition to AD Predicted transcriptional dysregulation is validated using AD gene expression data Inhibition of self-amplifying feedback loops brings about disease-modifying effects
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Affiliation(s)
- Nishtha Pandey
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032 India
| | - P K Vinod
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032 India
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16
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CDK activity sensors: genetically encoded ratiometric biosensors for live analysis of the cell cycle. Biochem Soc Trans 2022; 50:1081-1090. [PMID: 35674434 PMCID: PMC9661961 DOI: 10.1042/bst20211131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 01/04/2023]
Abstract
Cyclin-dependent kinase (CDK) sensors have facilitated investigations of the cell cycle in living cells. These genetically encoded fluorescent biosensors change their subcellular location upon activation of CDKs. Activation is primarily regulated by their association with cyclins, which in turn trigger cell-cycle progression. In the absence of CDK activity, cells exit the cell cycle and become quiescent, a key step in stem cell maintenance and cancer cell dormancy. The evolutionary conservation of CDKs has allowed for the rapid development of CDK activity sensors for cell lines and several research organisms, including nematodes, fish, and flies. CDK activity sensors are utilized for their ability to visualize the exact moment of cell-cycle commitment. This has provided a breakthrough in understanding the proliferation-quiescence decision. Further adoption of these biosensors will usher in new discoveries focused on the cell-cycle regulation of development, ageing, and cancer.
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17
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Zhang Z, Zhu X. MiR-103a-3p Contributes to the Progression of Colorectal Cancer by Regulating GREM2 Expression. Yonsei Med J 2022; 63:520-529. [PMID: 35619575 PMCID: PMC9171664 DOI: 10.3349/ymj.2022.63.6.520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/14/2022] [Accepted: 02/04/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Our research aimed to investigate the influence of miR-103a-3p on the growth and apoptosis of colorectal cancer (CRC) cells. MATERIALS AND METHODS Bioinformatics was employed to analyze differentially expressed microRNAs and predict target genes. qRT-PCR was applied to detect the expression of miR-103a-3p in CRC and normal cells. HCT116 and Caco-2 were chosen, and miR-103a-3p mimics, miR-103a-3p inhibitor, as well as specific siRNAs targeting GREM2, were constructed. We subsequently evaluated alternations in cell proliferation, cell cycle and cell cycle regulators, apoptosis, and related proteins (Bcl-2 and Bax) by CCK-8 testing, Western blotting, luciferase reporter, colony formation, and Annexin V-FITC/PI. Possible binding sites for miR-103a-3p on the 3'UTR of GREM2 were checked with luciferase assay, and the impact of GREM2 on miR-103a-3p activity was also validated with above biological function testing. Additionally, the effect of miR-103a-3p knockdown in CRC cells and the molecular mechanism of miR-103a-3p targeting GREM2 were also studied. RESULTS Bioinformatics analysis revealed that miR-103a-3p expression increased remarkably in CRC, and targeted regulatory correlation existed between miR-103a-3p and GREM2. MiR-103a-3p inhibitor significantly impeded proliferative capacity and caused cell cycle arrest, as well as apoptosis, in HCT116 and Caco-2 cells. Consistent with this finding, overexpression of GREM2 showed similar effects to miR-103a-3p inhibition. Moreover, we demonstrated that miR-103a-3p connected target GREM2 and GREM2 knockdown reversed the effects of miR-103a-3p inhibitor on HCT116 and Caco-2 cell proliferation, cell cycle, and apoptosis. Further study showed that miR-103a-3p targeting GREM2 appeared to affect CRC progression via the transforming growth factor-β pathway. CONCLUSION MiR-103a-3p could augment CRC progression by targeting GREM2 and that miR-103a-3p/GREM2 could be potential novel targets for CRC therapy.
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Affiliation(s)
- Zongxiang Zhang
- Department of General Surgery, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital/Hangzhou Red Cross Hospital, Hangzhou, China
| | - Xiaolian Zhu
- Department of Medical Oncology, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, China.
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18
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The structure of the human cell cycle. Cell Syst 2022; 13:230-240.e3. [PMID: 34800361 PMCID: PMC8930470 DOI: 10.1016/j.cels.2021.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/16/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023]
Abstract
Understanding the organization of the cell cycle has been a longstanding goal in cell biology. We combined time-lapse microscopy, highly multiplexed single-cell imaging of 48 core cell cycle proteins, and manifold learning to render a visualization of the human cell cycle. This data-driven approach revealed the comprehensive "structure" of the cell cycle: a continuum of molecular states that cells occupy as they transition from one cell division to the next, or as they enter or exit cell cycle arrest. Paradoxically, progression deeper into cell cycle arrest was accompanied by increases in proliferative effectors such as CDKs and cyclins, which can drive cell cycle re-entry by overcoming p21 induction. The structure also revealed the molecular trajectories into senescence and the unique combination of molecular features that define this irreversibly arrested state. This approach will enable the comparison of alternative cell cycles during development, in response to environmental perturbation and in disease. A record of this paper's transparent peer review process is included in the supplemental information.
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19
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Mei L, Kedziora KM, Song EA, Purvis JE, Cook J. The consequences of differential origin licensing dynamics in distinct chromatin environments. Nucleic Acids Res 2022; 50:9601-9620. [PMID: 35079814 PMCID: PMC9508807 DOI: 10.1093/nar/gkac003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
Eukaryotic chromosomes contain regions of varying accessibility, yet DNA replication factors must access all regions. The first replication step is loading MCM complexes to license replication origins during the G1 cell cycle phase. It is not yet known how mammalian MCM complexes are adequately distributed to both accessible euchromatin regions and less accessible heterochromatin regions. To address this question, we combined time-lapse live-cell imaging with immunofluorescence imaging of single human cells to quantify the relative rates of MCM loading in euchromatin and heterochromatin throughout G1. We report here that MCM loading in euchromatin is faster than that in heterochromatin in early G1, but surprisingly, heterochromatin loading accelerates relative to euchromatin loading in middle and late G1. This differential acceleration allows both chromatin types to begin S phase with similar concentrations of loaded MCM. The different loading dynamics require ORCA-dependent differences in origin recognition complex distribution. A consequence of heterochromatin licensing dynamics is that cells experiencing a truncated G1 phase from premature cyclin E expression enter S phase with underlicensed heterochromatin, and DNA damage accumulates preferentially in heterochromatin in the subsequent S/G2 phase. Thus, G1 length is critical for sufficient MCM loading, particularly in heterochromatin, to ensure complete genome duplication and to maintain genome stability.
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Affiliation(s)
- Liu Mei
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eun-Ah Song
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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20
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Kohrman AQ, Kim-Yip RP, Posfai E. Imaging developmental cell cycles. Biophys J 2021; 120:4149-4161. [PMID: 33964274 PMCID: PMC8516676 DOI: 10.1016/j.bpj.2021.04.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 01/05/2023] Open
Abstract
The last decade has seen a major expansion in development of live biosensors, the tools needed to genetically encode them into model organisms, and the microscopic techniques used to visualize them. When combined, these offer us powerful tools with which to make fundamental discoveries about complex biological processes. In this review, we summarize the availability of biosensors to visualize an essential cellular process, the cell cycle, and the techniques for single-cell tracking and quantification of these reporters. We also highlight studies investigating the connection of cellular behavior to the cell cycle, particularly through live imaging, and anticipate exciting discoveries with the combination of these technologies in developmental contexts.
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Affiliation(s)
- Abraham Q Kohrman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Rebecca P Kim-Yip
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey.
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21
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Jiang Y, Zhang C, Long L, Ge L, Guo J, Fan Z, Yu G. A Comprehensive Analysis of SE-lncRNA/mRNA Differential Expression Profiles During Chondrogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells. Front Cell Dev Biol 2021; 9:721205. [PMID: 34589487 PMCID: PMC8475951 DOI: 10.3389/fcell.2021.721205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/12/2021] [Indexed: 01/22/2023] Open
Abstract
Objective: Articular cartilage injury is common and difficult to treat clinically because of the characteristics of the cartilage. Bone marrow-derived mesenchymal stem cell (BMSC)-mediated cartilage regeneration is a promising therapy for treating articular cartilage injury. BMSC differentiation is controlled by numerous molecules and signaling pathways in the microenvironment at both the transcriptional and post-transcriptional levels. However, the possible function of super enhancer long non-coding RNAs (SE-lncRNAs) in the chondrogenic differentiation of BMSCs is still unclear. Our intention was to explore the expression profile of SE-lncRNAs and potential target genes regulated by SE-lncRNAs during chondrogenic differentiation in BMSCs. Materials and Methods: In this study, we conducted a human Super-Enhancer LncRNA Microarray to investigate the differential expression profile of SE-lncRNAs and mRNAs during chondrogenic differentiation of BMSCs. Subsequent bioinformatic analysis was performed to clarify the important signaling pathways, SE-lncRNAs, and mRNAs associated with SE-lncRNAs regulating the chondrogenic differentiation of BMSCs. Results: A total of 77 SE-lncRNAs were identified, of which 47 were upregulated and 30 were downregulated during chondrogenic differentiation. A total of 308 mRNAs were identified, of which 245 were upregulated and 63 were downregulated. Some pathways, such as focal adhesion, extracellular matrix (ECM)–receptor interaction, transforming growth factor-β (TGF-β) signaling pathway, and PI3K–Akt signaling pathway, were identified as the key pathways that may be implicated in the chondrogenic differentiation of BMSCs. Moreover, five potentially core regulatory mRNAs (PMEPA1, ENC1, TES, CDK6, and ADIRF) and 37 SE-lncRNAs in chondrogenic differentiation were identified by bioinformatic analysis. Conclusion: We assessed the differential expression levels of SE-lncRNAs and mRNAs, along with the chondrogenic differentiation of BMSCs. By analyzing the interactions and co-expression, we identified the core SE-lncRNAs and mRNAs acting as regulators of the chondrogenic differentiation potential of BMSCs. Our study also provided novel insights into the mechanism of BMSC chondrogenic and cartilage regeneration.
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Affiliation(s)
- Yu Jiang
- Department of Stomatology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chen Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Lujue Long
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Hunan, China
| | - Lihua Ge
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Jing Guo
- The Key Laboratory of Oral Biomedicine, The Affiliated Stomatological Hospital of Nanchang University, Nanchang, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China.,Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
| | - Guoxia Yu
- Department of Stomatology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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22
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Adon T, Shanmugarajan D, Kumar HY. CDK4/6 inhibitors: a brief overview and prospective research directions. RSC Adv 2021; 11:29227-29246. [PMID: 35479560 PMCID: PMC9040853 DOI: 10.1039/d1ra03820f] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/22/2021] [Indexed: 11/30/2022] Open
Abstract
The discovery of cyclin-dependent kinases (CDK) and their mechanism in regulating the cell cycle process was considered a game-changer in cancer therapy. Cell cycle arrest and apoptosis were both triggered by their inhibition. The CDK4/6 complex acts as a checkpoint during the cell cycle transition from cell growth (G1) to DNA synthesis (S) phase and its deregulation or overexpression induces abnormal cell proliferation and cancer development. Consequently, targeting CDK4/6 has been proposed as a paradigm shift in the anticancer approach. The design and development of effective CDK4/6 inhibitors are increasingly becoming a promising cancer therapy evident with approved drugs such as palbociclib, ribociclib, and abemaciclib, etc. In this article, we explore the biological importance of CDK4/6 in cancer therapy, the development of resistance to monotherapy, and a short overview of PROTAC (Proteolysis Targeting Chimera), a unique and pioneering technique for degrading CDK4/6 enzymes. Overall, our prime focus is to discuss novel CDK4/6 inhibitors with diverse chemical classes and their correlation with computational studies. The discovery of cyclin-dependent kinases (CDK) and their mechanism in regulating the cell cycle process was considered a game-changer in cancer therapy.![]()
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Affiliation(s)
- Tenzin Adon
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research Sri Shivarathreeshwara Nagar Mysuru-570015 Karnataka India +919726447802
| | - Dhivya Shanmugarajan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research Sri Shivarathreeshwara Nagar Mysuru-570015 Karnataka India +919726447802
| | - Honnavalli Yogish Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research Sri Shivarathreeshwara Nagar Mysuru-570015 Karnataka India +919726447802
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23
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Pack LR, Daigh LH, Chung M, Meyer T. Clinical CDK4/6 inhibitors induce selective and immediate dissociation of p21 from cyclin D-CDK4 to inhibit CDK2. Nat Commun 2021; 12:3356. [PMID: 34099663 PMCID: PMC8184839 DOI: 10.1038/s41467-021-23612-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/06/2021] [Indexed: 12/11/2022] Open
Abstract
Since their discovery as drivers of proliferation, cyclin-dependent kinases (CDKs) have been considered therapeutic targets. Small molecule inhibitors of CDK4/6 are used and tested in clinical trials to treat multiple cancer types. Despite their clinical importance, little is known about how CDK4/6 inhibitors affect the stability of CDK4/6 complexes, which bind cyclins and inhibitory proteins such as p21. We develop an assay to monitor CDK complex stability inside the nucleus. Unexpectedly, treatment with CDK4/6 inhibitors-palbociclib, ribociclib, or abemaciclib-immediately dissociates p21 selectively from CDK4 but not CDK6 complexes. This effect mediates indirect inhibition of CDK2 activity by p21 but not p27 redistribution. Our work shows that CDK4/6 inhibitors have two roles: non-catalytic inhibition of CDK2 via p21 displacement from CDK4 complexes, and catalytic inhibition of CDK4/6 independent of p21. By broadening the non-catalytic displacement to p27 and CDK6 containing complexes, next-generation CDK4/6 inhibitors may have improved efficacy and overcome resistance mechanisms.
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Affiliation(s)
- Lindsey R Pack
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Leighton H Daigh
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
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24
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Fan Y, Köberlin MS, Ratnayeke N, Liu C, Deshpande M, Gerhardt J, Meyer T. LRR1-mediated replisome disassembly promotes DNA replication by recycling replisome components. J Cell Biol 2021; 220:212186. [PMID: 34037657 PMCID: PMC8160578 DOI: 10.1083/jcb.202009147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022] Open
Abstract
After two converging DNA replication forks meet, active replisomes are disassembled and unloaded from chromatin. A key process in replisome disassembly is the unloading of CMG helicases (CDC45–MCM–GINS), which is initiated in Caenorhabditis elegans and Xenopus laevis by the E3 ubiquitin ligase CRL2LRR1. Here, we show that human cells lacking LRR1 fail to unload CMG helicases and accumulate increasing amounts of chromatin-bound replisome components as cells progress through S phase. Markedly, we demonstrate that the failure to disassemble replisomes reduces the rate of DNA replication increasingly throughout S phase by sequestering rate-limiting replisome components on chromatin and blocking their recycling. Continued binding of CMG helicases to chromatin during G2 phase blocks mitosis by activating an ATR-mediated G2/M checkpoint. Finally, we provide evidence that LRR1 is an essential gene for human cell division, suggesting that CRL2LRR1 enzyme activity is required for the proliferation of cancer cells and is thus a potential target for cancer therapy.
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Affiliation(s)
- Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Nalin Ratnayeke
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Madhura Deshpande
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Jeannine Gerhardt
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
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25
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Hurtado A. Targeting CDK4/6 reorganizes chromatin. NATURE CANCER 2021; 2:16-17. [PMID: 35121894 DOI: 10.1038/s43018-020-00164-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Antoni Hurtado
- Cancer Genomics and Proteomics Group, Department of Biomedical Sciences, University of Barcelona, Casanova, Barcelona, Spain.
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26
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Sood AK, Nemeth M, Wang J, Wu Y, Gandhi S. Opportunities for Antigen Discovery in Metastatic Breast Cancer. Front Immunol 2020; 11:570049. [PMID: 33193348 PMCID: PMC7661635 DOI: 10.3389/fimmu.2020.570049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
Immune checkpoint inhibitor-based immunotherapy (ICI) of breast cancer is currently efficacious in a fraction of triple negative breast cancers (TNBC) as these cancers generally carry high tumor mutation burden (TMB) and show increased tumor infiltration by CD8+ T cells. However, most estrogen receptor positive breast cancers (ERBC) have low TMB and/or are infiltrated with immunosuppressive regulatory T cells (Tregs) and thus fail to induce a significant anti-tumor immune response. Our understanding of the immune underpinning of the anti-tumor effects of CDK4/6 inhibitor (CDKi) treatment coupled with new knowledge about the mechanisms of tolerance to self-antigens suggests a way forward, specifically via characterizing and exploiting the repertoire of tumor antigens expressed by metastatic ERBC. These treatment-associated tumor antigens (TATA) may include the conventional tumor neoantigens (TNA) encoded by single nucleotide mutations, TNA encoded by tumor specific aberrant RNA transcription, splicing and DNA replication induced frameshift (FS) events as well as the shared tumor antigens. The latter may include the conventional tumor associated antigens (TAA), cancer-testis antigens (CTA) and antigens encoded by the endogenous retroviral (ERV) like sequences and repetitive DNA sequences induced by ET and CDKi treatment. An approach to identifying these antigens is outlined as this will support the development of a multi-antigen-based immunotherapy strategy for improved targeting of metastatic disease with potential for minimal autoimmune toxicity against normal tissues.
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Affiliation(s)
- Ashwani K Sood
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Michael Nemeth
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States.,Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Yun Wu
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Shipra Gandhi
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
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