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Kasbekar M, Mitchell CA, Proven MA, Passegué E. Hematopoietic stem cells through the ages: A lifetime of adaptation to organismal demands. Cell Stem Cell 2023; 30:1403-1420. [PMID: 37865087 PMCID: PMC10842631 DOI: 10.1016/j.stem.2023.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
Hematopoietic stem cells (HSCs), which govern the production of all blood lineages, transition through a series of functional states characterized by expansion during fetal development, functional quiescence in adulthood, and decline upon aging. We describe central features of HSC regulation during ontogeny to contextualize how adaptive responses over the life of the organism ultimately form the basis for HSC functional degradation with age. We particularly focus on the role of cell cycle regulation, inflammatory response pathways, epigenetic changes, and metabolic regulation. We then explore how the knowledge of age-related changes in HSC regulation can inform strategies for the rejuvenation of old HSCs.
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Affiliation(s)
- Monica Kasbekar
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Division of Hematology and Medical Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Carl A Mitchell
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Melissa A Proven
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY 10032, USA.
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2
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Semaan A, Bernard V, Wong J, Makino Y, Swartzlander DB, Rajapakshe KI, Lee JJ, Officer A, Schmidt CM, Wu HH, Scaife CL, Affolter KE, Nachmanson D, Firpo MA, Yip-Schneider M, Lowy AM, Harismendy O, Sen S, Maitra A, Jakubek YA, Guerrero PA. Integrated Molecular Characterization of Intraductal Papillary Mucinous Neoplasms: An NCI Cancer Moonshot Precancer Atlas Pilot Project. Cancer Res Commun 2023; 3:2062-2073. [PMID: 37721516 PMCID: PMC10563795 DOI: 10.1158/2767-9764.crc-22-0419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Intraductal papillary mucinous neoplasms (IPMN) are cystic precursor lesions to pancreatic ductal adenocarcinoma (PDAC). IPMNs undergo multistep progression from low-grade (LG) to high-grade (HG) dysplasia, culminating in invasive neoplasia. While patterns of IPMN progression have been analyzed using multiregion sequencing for somatic mutations, there is no integrated assessment of molecular events, including copy-number alterations (CNA) and transcriptional changes that accompany IPMN progression. We performed laser capture microdissection on surgically resected IPMNs of varying grades of histologic dysplasia obtained from 23 patients, followed by whole-exome and whole-transcriptome sequencing. Overall, HG IPMNs displayed a significantly greater aneuploidy score than LG lesions, with chromosome 1q amplification being associated with HG progression and with cases that harbored co-occurring PDAC. Furthermore, the combined assessment of single-nucleotide variants (SNV) and CNAs identified both linear and branched evolutionary trajectories, underscoring the heterogeneity in the progression of LG lesions to HG and PDAC. At the transcriptome level, upregulation of MYC-regulated targets and downregulation of transcripts associated with the MHC class I antigen presentation machinery as well as pathways related to glycosylation were a common feature of progression to HG. In addition, the established PDAC transcriptional subtypes (basal-like and classical) were readily apparent within IPMNs. Taken together, this work emphasizes the role of 1q copy-number amplification as a putative biomarker of high-risk IPMNs, underscores the importance of immune evasion even in noninvasive precursor lesions, and reinforces that evolutionary pathways in IPMNs are heterogenous, comprised of both SNV and CNA-driven events. SIGNIFICANCE Integrated molecular analysis of genomic and transcriptomic alterations in the multistep progression of IPMNs, which are bona fide precursors of pancreatic cancer, identifies features associated with progression of low-risk lesions to high-risk lesions and cancer, which might enable patient stratification and cancer interception strategies.
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Affiliation(s)
- Alexander Semaan
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vincent Bernard
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Justin Wong
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuki Makino
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel B. Swartzlander
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kimal I. Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jaewon J. Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program and Moores Cancer Center, University of California San Diego School of Medicine, San Diego, California
| | | | - Howard H. Wu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | | | | | - Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program and Moores Cancer Center, University of California San Diego School of Medicine, San Diego, California
| | | | | | - Andrew M. Lowy
- Department of Surgery, Division of Surgical Oncology, University of California San Diego, San Diego, California
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Graduate Program and Moores Cancer Center, University of California San Diego School of Medicine, San Diego, California
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yasminka A. Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paola A. Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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3
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Sullivan-Reed K, Toma MM, Drzewiecka M, Nieborowska-Skorska M, Nejati R, Karami A, Wasik MA, Sliwinski T, Skorski T. Simultaneous Targeting of DNA Polymerase Theta and PARP1 or RAD52 Triggers Dual Synthetic Lethality in Homologous Recombination-Deficient Leukemia Cells. Mol Cancer Res 2023; 21:1017-1022. [PMID: 37358557 PMCID: PMC10654933 DOI: 10.1158/1541-7786.mcr-22-1035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/09/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Abstract
DNA polymerase theta (Polθ, encoded by POLQ gene) plays an essential role in Polθ-mediated end-joining (TMEJ) of DNA double-strand breaks (DSB). Inhibition of Polθ is synthetic lethal in homologous recombination (HR)-deficient tumor cells. However, DSBs can be also repaired by PARP1 and RAD52-mediated mechanisms. Because leukemia cells accumulate spontaneous DSBs, we tested if simultaneous targeting of Polθ and PARP1 or RAD52 enhance the synthetic lethal effect in HR-deficient leukemia cells. Transformation potential of the oncogenes inducing BRCA1/2-deficiency (BCR-ABL1 and AML1-ETO) was severely limited in Polq-/-;Parp1-/- and Polq-/-;Rad52-/- cells when compared with single knockouts, which was associated with accumulation of DSBs. Small-molecule inhibitor of Polθ (Polθi) when combined with PARP or RAD52 inhibitors (PARPi, RAD52i) caused accumulation of DSBs and exerted increased effect against HR-deficient leukemia and myeloproliferative neoplasm cells. IMPLICATIONS In conclusion, we show that PARPi or RAD52i might improve therapeutic effect of Polθi against HR-deficient leukemias.
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Affiliation(s)
- Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Monika M. Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Malgorzata Drzewiecka
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Adam Karami
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Mariusz A. Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
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4
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Yu X, Zhu L, Wang T, Li L, Liu J, Che G, Zhou Q. Enhancing the anti-tumor response by combining DNA damage repair inhibitors in the treatment of solid tumors. Biochim Biophys Acta Rev Cancer 2023; 1878:188910. [PMID: 37172653 DOI: 10.1016/j.bbcan.2023.188910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/12/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
The anti-cancer efficacy of anti-malignancy therapies is related to DNA damage. However, DNA damage-response mechanisms can repair DNA damage, failing anti-tumor therapy. The resistance to chemotherapy, radiotherapy, and immunotherapy remains a clinical challenge. Thus, new strategies to overcome these therapeutic resistance mechanisms are needed. DNA damage repair inhibitors (DDRis) continue to be investigated, with polyadenosine diphosphate ribose polymerase inhibitors being the most studied inhibitors. Evidence of their clinical benefits and therapeutic potential in preclinical studies is growing. In addition to their potential as a monotherapy, DDRis may play an important synergistic role with other anti-cancer therapies or in reversing acquired treatment resistance. Here we review the impact of DDRis on solid tumors and the potential value of combinations of different treatment modalities with DDRis for solid tumors.
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Affiliation(s)
- Xianzhe Yu
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China; Department of Gastrointestinal Surgery, Chengdu Second People's Hospital, No. 10 Qinyun Nan Street, Chengdu 610041, Sichuan Province, People's Republic of China
| | - Lingling Zhu
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China
| | - Ting Wang
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China
| | - Lu Li
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China
| | - Jiewei Liu
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China.
| | - Guowei Che
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China.
| | - Qinghua Zhou
- Lung Cancer Institute/Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, People's Republic of China.
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Vekariya U, Toma M, Nieborowska-Skorska M, Le BV, Caron MC, Kukuyan AM, Sullivan-Reed K, Podszywalow-Bartnicka P, Chitrala KN, Atkins J, Drzewiecka M, Feng W, Chan J, Chatla S, Golovine K, Jelinek J, Sliwinski T, Ghosh J, Matlawska-Wasowska K, Chandramouly G, Nejati R, Wasik M, Sykes SM, Piwocka K, Hadzijusufovic E, Valent P, Pomerantz RT, Morton G, Childers W, Zhao H, Paietta EM, Levine RL, Tallman MS, Fernandez HF, Litzow MR, Gupta GP, Masson JY, Skorski T. DNA polymerase θ protects leukemia cells from metabolically induced DNA damage. Blood 2023; 141:2372-2389. [PMID: 36580665 PMCID: PMC10273171 DOI: 10.1182/blood.2022018428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/1-carbon cycle metabolism contributed to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases (OTKs: FLT3(internal tandem duplication [ITD]), JAK2(V617F), BCR-ABL1). To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) via ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in the efficient repair of DPC-containing DNA double-strand breaks by POLθ-mediated end-joining. The transforming activities of OTKs and other leukemia-inducing oncogenes, especially of those causing the inhibition of BRCA1/2-mediated homologous recombination with and without concomitant inhibition of DNA-PK-dependent nonhomologous end-joining, was abrogated in Polq-/- murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitors or DPC-inducing drug etoposide enhanced the antileukemia effect of POLθ inhibitor in vitro and in vivo. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions triggered by formaldehyde, and it can be targeted to achieve a therapeutic effect.
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Affiliation(s)
- Umeshkumar Vekariya
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Monika Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Margaret Nieborowska-Skorska
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Bac Viet Le
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Marie-Christine Caron
- CHU de Québec Research Centre (Oncology Division) and Laval University Cancer Research Center, Québec City, QC, Canada
| | - Anna-Mariya Kukuyan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Kumaraswamy N. Chitrala
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Jessica Atkins
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Malgorzata Drzewiecka
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joe Chan
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Srinivas Chatla
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Konstantin Golovine
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA
| | - Stephen M. Sykes
- Division of Hematology/Oncology, Department of Pediatrics, Washington University at St. Louis, St. Louis, MO
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Emir Hadzijusufovic
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
- Department for Companion Animals & Horses, Clinic for Internal Medicine and Infectious Diseases, University of Veterinary Medicine Vienna, Austria
| | - Peter Valent
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Richard T. Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - George Morton
- Moulder Center for Drug Discovery, Temple University School of Pharmacy, Philadelphia, PA
| | - Wayne Childers
- Moulder Center for Drug Discovery, Temple University School of Pharmacy, Philadelphia, PA
| | - Huaqing Zhao
- Department of Clinical Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Elisabeth M. Paietta
- Department of Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
| | - Ross L. Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin S. Tallman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hugo F. Fernandez
- Moffitt Malignant Hematology & Cellular Therapy at Memorial Healthcare System, Pembroke Pines, FL
| | - Mark R. Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jean-Yves Masson
- CHU de Québec Research Centre (Oncology Division) and Laval University Cancer Research Center, Québec City, QC, Canada
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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Kruchinin AA, Makarova AV. Multifaceted Nature of DNA Polymerase θ. Int J Mol Sci 2023; 24. [PMID: 36835031 DOI: 10.3390/ijms24043619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
DNA polymerase θ belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol θ is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol θ, its multiple roles in protection of genome stability and the potential of Pol θ as a target for cancer treatment.
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7
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Chandramouly G, Jamsen J, Borisonnik N, Tyagi M, Calbert ML, Tredinnick T, Ozdemir AY, Kent T, Demidova EV, Arora S, Wilson SH, Pomerantz RT. Polλ promotes microhomology-mediated end-joining. Nat Struct Mol Biol 2023; 30:107-14. [PMID: 36536104 DOI: 10.1038/s41594-022-00895-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
The double-strand break (DSB) repair pathway called microhomology-mediated end-joining (MMEJ) is thought to be dependent on DNA polymerase theta (Polθ) and occur independently of nonhomologous end-joining (NHEJ) factors. An unresolved question is whether MMEJ is facilitated by a single Polθ-mediated end-joining pathway or consists of additional undiscovered pathways. We find that human X-family Polλ, which functions in NHEJ, additionally exhibits robust MMEJ activity like Polθ. Polλ promotes MMEJ in mammalian cells independently of essential NHEJ factors LIG4/XRCC4 and Polθ, which reveals a distinct Polλ-dependent MMEJ mechanism. X-ray crystallography employing in situ photo-induced DSB formation captured Polλ in the act of stabilizing a microhomology-mediated DNA synapse with incoming nucleotide at 2.0 Å resolution and reveals how Polλ performs replication across a DNA synapse joined by minimal base-pairing. Last, we find that Polλ is semisynthetic lethal with BRCA1 and BRCA2. Together, these studies indicate Polλ MMEJ as a distinct DSB repair mechanism.
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8
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Wang L, Wang W, Beird HC, Cheng X, Fang H, Tang G, Toruner GA, Yin CC, You MJ, Issa GC, Borthakur G, Peng G, Khoury JD, Medeiros LJ, Tang Z. PPP1R7 Is a Novel Translocation Partner of CBFB via t(2;16)(q37;q22) in Acute Myeloid Leukemia. Genes (Basel) 2022; 13:1367. [PMID: 36011278 PMCID: PMC9407081 DOI: 10.3390/genes13081367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
In a subset of acute myeloid leukemia (AML) cases, the core binding factor beta subunit gene (CBFB) was rearranged via inv(16)(p13.1q22) or t(16;16)(p13.1;q22), in which the smooth muscle myosin heavy chain 11 gene (MYH11) was the partner (CBFB::MYH11). Rare variants of CBFB rearrangement occurring via non-classic chromosomal aberrations have been reported, such as t(1;16), t(2;16), t(3;16), t(5;16), and t(16;19), but the partners of CBFB have not been characterized. We report a case of AML with a complex karyotype, including t(2;16)(q37;q22), in which the protein phosphatase 1 regulatory subunit 7 gene (PPP1R7) at chromosome 2q37 was rearranged with CBFB (CBFB::PPP1R7). This abnormality was inconspicuous by conventional karyotype and interphase fluorescence in situ hybridization (FISH), thus leading to an initial interpretation of inv(16)(p13.1q22); however, metaphase FISH showed that the CBFB rearrangement involved chromosome 2. Using whole genome and Sanger sequencing, the breakpoints were identified as being located in intron 5 of CBFB and intron 7 of PPP1R7. A microhomology of CAG was found in the break and reconnection sites of CBFB and PPP1R7, thus supporting the formation of CBFB::PPP1R7 by microhomology-mediated end joining.
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9
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Miskel D, Poirier M, Beunink L, Rings F, Held E, Tholen E, Tesfaye D, Schellander K, Salilew-Wondim D, Blaschka C, Große-Brinkhaus C, Brenig B, Hoelker M. The cell cycle stage of bovine zygotes electroporated with CRISPR/Cas9-RNP affects frequency of Loss-of-heterozygosity editing events. Sci Rep 2022; 12:10793. [PMID: 35750764 PMCID: PMC9232522 DOI: 10.1038/s41598-022-14699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 06/10/2022] [Indexed: 12/14/2022] Open
Abstract
At the embryonic level, CRISPR technologies have been used to edit genomes reliably and efficiently in various mammalian models, with Ribonucleoprotein (RNP) electroporation potentially representing a superior delivery method into mammalian zygotes. However, detailed insights of the interactions between varying technical settings as well as the time point of electroporation in a bovine zygote's cell cycle on developmental metrics and the frequency and type of editing events are largely unknown. The present study uncovers that increasing pulse lengths result in higher Full Edit rates, with Mosaicism in Full-Edit embryos being significantly affected by adjusting RNP-electroporation relative to zygote cell cycle. A considerable proportion of Full Edit embryos demonstrated loss-of-heterozygosity after RNP-electroporation prior to S-phase. Some of these loss-of-heterozygosity events are a consequence of chromosomal disruptions along large sections of the target chromosomes making it necessary to check for their presence prior use of this technique in animal breeding. One out of 2 of these loss-of-heterozygosity events, however, was not associated with loss of an entire chromosome or chromosomal sections. Whether analysed loss-of-heterozygosity in these cases, however, was a false negative result due to loss of PCR primer sequences after INDEL formation at the target side or indeed due to interhomolog recombination needs to be clarified in follow up studies since the latter would for sure offer attractive options for future breeding schedules.
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Affiliation(s)
- Dennis Miskel
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Mikhael Poirier
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Luisa Beunink
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Franca Rings
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Eva Held
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Ernst Tholen
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Dawit Tesfaye
- grid.47894.360000 0004 1936 8083Department of Biomedical Sciences, Animal Reproduction and Biotechnology Laboratory, Colorado State University, 3105 Rampart Rd, Fort Collins, CO 80521 USA
| | - Karl Schellander
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Dessie Salilew-Wondim
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Carina Blaschka
- grid.7450.60000 0001 2364 4210Department of Animal Science, Biotechnology and Reproduction of Farm Animals, Georg August University Goettingen, Burckhardtweg 2, 37077 Goettingen, Germany
| | - Christine Große-Brinkhaus
- grid.10388.320000 0001 2240 3300Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Bertram Brenig
- grid.7450.60000 0001 2364 4210Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg August University Goettingen, Burckhardtweg 2, 37077 Goettingen, Germany
| | - Michael Hoelker
- grid.7450.60000 0001 2364 4210Department of Animal Science, Biotechnology and Reproduction of Farm Animals, Georg August University Goettingen, Burckhardtweg 2, 37077 Goettingen, Germany
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10
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Alagpulinsa DA, Toribio MP, Alhallak I, Shmookler Reis RJ. Advances in understanding the molecular basis of clonal hematopoiesis. Trends Mol Med 2022; 28:360-377. [PMID: 35341686 DOI: 10.1016/j.molmed.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/28/2022]
Abstract
Hematopoietic stem cells (HSCs) are polyfunctional, regenerating all blood cells via hematopoiesis throughout life. Clonal hematopoiesis (CH) is said to occur when a substantial proportion of mature blood cells is derived from a single dominant HSC lineage, usually because these HSCs have somatic mutations that confer a fitness and expansion advantage. CH strongly associates with aging and enrichment in some diseases irrespective of age, emerging as an independent causal risk factor for hematologic malignancies, cardiovascular disease, adverse disease outcomes, and all-cause mortality. Defining the molecular mechanisms underlying CH will thus provide a framework to develop interventions for healthy aging and disease treatment. Here, we review the most recent advances in understanding the molecular basis of CH in health and disease.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine & Immunotherapy Center, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Mabel P Toribio
- Metabolism Unit, Division of Endocrinology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Iad Alhallak
- Metabolism Unit, Division of Endocrinology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare System and Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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11
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Ramsden DA, Carvajal-Garcia J, Gupta GP. Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining. Nat Rev Mol Cell Biol 2022; 23:125-140. [PMID: 34522048 DOI: 10.1038/s41580-021-00405-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 02/08/2023]
Abstract
Cellular pathways that repair chromosomal double-strand breaks (DSBs) have pivotal roles in cell growth, development and cancer. These DSB repair pathways have been the target of intensive investigation, but one pathway - alternative end joining (a-EJ) - has long resisted elucidation. In this Review, we highlight recent progress in our understanding of a-EJ, especially the assignment of DNA polymerase theta (Polθ) as the predominant mediator of a-EJ in most eukaryotes, and discuss a potential molecular mechanism by which Polθ-mediated end joining (TMEJ) occurs. We address possible cellular functions of TMEJ in resolving DSBs that are refractory to repair by non-homologous end joining (NHEJ), DSBs generated following replication fork collapse and DSBs present owing to stalling of repair by homologous recombination. We also discuss how these context-dependent cellular roles explain how TMEJ can both protect against and cause genome instability, and the emerging potential of Polθ as a therapeutic target in cancer.
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Affiliation(s)
- Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Kohnke T, Majeti R. Clonal hematopoiesis: from mechanisms to clinical intervention. Cancer Discov 2021; 11:2987-2997. [PMID: 34407958 DOI: 10.1158/2159-8290.cd-21-0901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Our knowledge of how clonal hematopoiesis (CH) relates to diverse health conditions has grown vastly over the past years, touching upon many specialties beyond cancer medicine. Given that CH can act as a precursor to overt disease in many settings, the promise of early intervention has garnered much attention. In this review, we discuss the state of CH research and outline the challenges in developing clinical trials of early interventions. We anticipate that incidental findings of CH will become more common in the near future, but evidence-based efforts of how to manage these findings is currently lacking.
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Affiliation(s)
- Thomas Kohnke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
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13
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Asada S, Kitamura T. Clonal hematopoiesis and associated diseases: A review of recent findings. Cancer Sci 2021; 112:3962-3971. [PMID: 34328684 PMCID: PMC8486184 DOI: 10.1111/cas.15094] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Recent genome‐wide studies have revealed that aging or chronic inflammation can cause clonal expansion of cells in normal tissues. Clonal hematopoiesis has been the most intensively studied form of clonal expansion in the last decade. Clonal hematopoiesis of indeterminate potential (CHIP) is an age‐related phenomenon observed in elderly individuals with no history of hematological malignancy. The most frequently mutated genes in CHIP are DNMT3A, TET2, and ASXL1, which are associated with initiation of leukemia. Importantly, CHIP has been the focus of a number of studies because it is an independent risk factor for myeloid malignancy, cardiovascular disease (CVD), and all‐cause mortality. Animal models recapitulating human CHIP revealed that CHIP‐associated mutations alter the number and function of hematopoietic stem and progenitor cells (HSPCs) and promote leukemic transformation. Moreover, chronic inflammation caused by infection or aging confers a fitness advantage to the CHIP‐associated mutant HSPCs. Myeloid cells, such as macrophages with a CHIP‐associated mutation, accelerate chronic inflammation and are associated with increased levels of inflammatory cytokines. This positive feedback loop between CHIP and chronic inflammation promotes development of atherosclerosis and chronic heart failure and thereby increases the risk for CVD. Notably, HSPCs with a CHIP‐associated mutation may alter not only innate but also acquired immune cells. This suggests that CHIP is involved in the development of solid cancers or immune disorders, such as aplastic anemia. In this review, we provide an overview of recent findings on CHIP. We also discuss potential interventions for treating CHIP and preventing myeloid transformation and CVD progression.
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Affiliation(s)
- Shuhei Asada
- The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan.,Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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