1
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Laverty DJ, Gupta SK, Bradshaw GA, Hunter AS, Carlson BL, Calmo NM, Chen J, Tian S, Sarkaria JN, Nagel ZD. ATM inhibition exploits checkpoint defects and ATM-dependent double strand break repair in TP53-mutant glioblastoma. Nat Commun 2024; 15:5294. [PMID: 38906885 DOI: 10.1038/s41467-024-49316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/28/2024] [Indexed: 06/23/2024] Open
Abstract
Determining the balance between DNA double strand break repair (DSBR) pathways is essential for understanding treatment response in cancer. We report a method for simultaneously measuring non-homologous end joining (NHEJ), homologous recombination (HR), and microhomology-mediated end joining (MMEJ). Using this method, we show that patient-derived glioblastoma (GBM) samples with acquired temozolomide (TMZ) resistance display elevated HR and MMEJ activity, suggesting that these pathways contribute to treatment resistance. We screen clinically relevant small molecules for DSBR inhibition with the aim of identifying improved GBM combination therapy regimens. We identify the ATM kinase inhibitor, AZD1390, as a potent dual HR/MMEJ inhibitor that suppresses radiation-induced phosphorylation of DSBR proteins, blocks DSB end resection, and enhances the cytotoxic effects of TMZ in treatment-naïve and treatment-resistant GBMs with TP53 mutation. We further show that a combination of G2/M checkpoint deficiency and reliance upon ATM-dependent DSBR renders TP53 mutant GBMs hypersensitive to TMZ/AZD1390 and radiation/AZD1390 combinations. This report identifies ATM-dependent HR and MMEJ as targetable resistance mechanisms in TP53-mutant GBM and establishes an approach for simultaneously measuring multiple DSBR pathways in treatment selection and oncology research.
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Affiliation(s)
- Daniel J Laverty
- Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | | | | | | | | | | | - Jiajia Chen
- Mayo Clinic, Rochester, MN, 55905, USA
- Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | | | | | - Zachary D Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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2
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Wang J, Sadeghi CA, Frock RL. DNA-PKcs suppresses illegitimate chromosome rearrangements. Nucleic Acids Res 2024; 52:5048-5066. [PMID: 38412274 PMCID: PMC11109964 DOI: 10.1093/nar/gkae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
Two DNA repair pathways, non-homologous end joining (NHEJ) and alternative end joining (A-EJ), are involved in V(D)J recombination and chromosome translocation. Previous studies reported distinct repair mechanisms for chromosome translocation, with NHEJ involved in humans and A-EJ in mice predominantly. NHEJ depends on DNA-PKcs, a critical partner in synapsis formation and downstream component activation. While DNA-PKcs inhibition promotes chromosome translocations harboring microhomologies in mice, its synonymous effect in humans is not known. We find partial DNA-PKcs inhibition in human cells leads to increased translocations and the continued involvement of a dampened NHEJ. In contrast, complete DNA-PKcs inhibition substantially increased microhomology-mediated end joining (MMEJ), thus bridging the two different translocation mechanisms between human and mice. Similar to a previous study on Ku70 deletion, DNA-PKcs deletion in G1/G0-phase mouse progenitor B cell lines, significantly impairs V(D)J recombination and generated higher rates of translocations as a consequence of dysregulated coding and signal end joining. Genetic DNA-PKcs inhibition suppresses NHEJ entirely, with repair phenotypically resembling Ku70-deficient A-EJ. In contrast, we find DNA-PKcs necessary in generating the near-exclusive MMEJ associated with Lig4 deficiency. Our study underscores DNA-PKcs in suppressing illegitimate chromosome rearrangement while also contributing to MMEJ in both species.
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Affiliation(s)
- Jinglong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne A Sadeghi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard L Frock
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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3
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Moore J, Gkantalis J, Guix I, Chou W, Yuen K, Lazar AA, Spitzer M, Combes AJ, Barcellos-Hoff MH. Lack of TGFβ signaling competency predicts immune poor cancer conversion to immune rich and response to checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583752. [PMID: 38496519 PMCID: PMC10942434 DOI: 10.1101/2024.03.06.583752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Transforming growth factor beta (TGFβ) is well-recognized as an immunosuppressive player in the tumor microenvironment but also has a significant impact on cancer cell phenotypes. Loss of TGFβ signaling impairs DNA repair competency, which is described by a transcriptomic score, βAlt. Cancers with high βAlt have more genomic damage and are more responsive to genotoxic therapy. The growing appreciation that cancer DNA repair deficits are important determinants of immune response prompted us to investigate the association of βAlt with response to immune checkpoint blockade (ICB). We predicted that high βAlt tumors would be infiltrated with lymphocytes because of DNA damage burden and hence responsive to ICB. Methods We analyzed public transcriptomic data from clinical trials and preclinical models using transcriptomic signatures of TGFβ targets, DNA repair genes, tumor educated immune cells and interferon. A high βAlt, immune poor mammary tumor derived transplant model resistant to programmed death ligand 1 (PD-L1) antibodies was studied using multispectral flow cytometry to interrogate the immune system. Results Metastatic bladder patients in IMvigor 210 who responded to ICB had significantly increased βAlt scores and experienced significantly longer overall survival compared to those with low βAlt scores (hazard ratio 0.62, P=0.011) . Unexpectedly, 75% of high βAlt cancers were immune poor as defined by low expression of tumor educated immune cell and interferon signatures. The association of high βAlt with immune poor cancer was also evident in TCGA and preclinical cancer models. We used a high βAlt, immune poor cancer to test therapeutic strategies to overcome its inherent anti-PD-L1 resistance. Combination treatment with radiation and TGFβ inhibition were necessary for lymphocytic infiltration and activated NK cells were required for ICB response. Bioinformatic analysis identified high βAlt, immune poor B16 and CT26 preclinical models and paired biopsies of cancer patients that also demonstrated NK cell activation upon response to ICB. Conclusions Our studies support βAlt as a biomarker that predicts response to ICB albeit in immune poor cancers, which has implications for the development of therapeutic strategies to increase the number of cancer patients who will benefit from immunotherapy.
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Affiliation(s)
- Jade Moore
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Jim Gkantalis
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ines Guix
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - William Chou
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Kobe Yuen
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Ann A Lazar
- Division of Oral Epidemiology and Division of Biostatistics, University of California, San Francisco, CA, USA
| | - Mathew Spitzer
- Parker Institute for Cancer Immunotherapy, Department of Otolaryngology- Head and Neck Surgery, Department of Microbiology and Immunology, University of California, San Francisco, CA USA
- A member of the imCORE Network
| | - Alexis J Combes
- Department of Pathology, CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- A member of the imCORE Network
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4
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Jones KM, Bryan A, McCunn E, Lantz PE, Blalock H, Ojeda IC, Mehta K, Cosper PF. The Causes and Consequences of DNA Damage and Chromosomal Instability Induced by Human Papillomavirus. Cancers (Basel) 2024; 16:1662. [PMID: 38730612 PMCID: PMC11083350 DOI: 10.3390/cancers16091662] [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: 03/31/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
High-risk human papillomaviruses (HPVs) are the main cause of cervical, oropharyngeal, and anogenital cancers, which are all treated with definitive chemoradiation therapy when locally advanced. HPV proteins are known to exploit the host DNA damage response to enable viral replication and the epithelial differentiation protocol. This has far-reaching consequences for the host genome, as the DNA damage response is critical for the maintenance of genomic stability. HPV+ cells therefore have increased DNA damage, leading to widespread genomic instability, a hallmark of cancer, which can contribute to tumorigenesis. Following transformation, high-risk HPV oncoproteins induce chromosomal instability, or chromosome missegregation during mitosis, which is associated with a further increase in DNA damage, particularly due to micronuclei and double-strand break formation. Thus, HPV induces significant DNA damage and activation of the DNA damage response in multiple contexts, which likely affects radiation sensitivity and efficacy. Here, we review how HPV activates the DNA damage response, how it induces chromosome missegregation and micronuclei formation, and discuss how these factors may affect radiation response. Understanding how HPV affects the DNA damage response in the context of radiation therapy may help determine potential mechanisms to improve therapeutic response.
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Affiliation(s)
- Kathryn M. Jones
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Ava Bryan
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Emily McCunn
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Pate E. Lantz
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Hunter Blalock
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
- University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Isabel C. Ojeda
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
- University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Kavi Mehta
- Department of Comparative Biosciences, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
| | - Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
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5
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Shokrollahi M, Stanic M, Hundal A, Chan JNY, Urman D, Jordan CA, Hakem A, Espin R, Hao J, Krishnan R, Maass PG, Dickson BC, Hande MP, Pujana MA, Hakem R, Mekhail K. DNA double-strand break-capturing nuclear envelope tubules drive DNA repair. Nat Struct Mol Biol 2024:10.1038/s41594-024-01286-7. [PMID: 38632359 DOI: 10.1038/s41594-024-01286-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024]
Abstract
Current models suggest that DNA double-strand breaks (DSBs) can move to the nuclear periphery for repair. It is unclear to what extent human DSBs display such repositioning. Here we show that the human nuclear envelope localizes to DSBs in a manner depending on DNA damage response (DDR) kinases and cytoplasmic microtubules acetylated by α-tubulin acetyltransferase-1 (ATAT1). These factors collaborate with the linker of nucleoskeleton and cytoskeleton complex (LINC), nuclear pore complex (NPC) protein NUP153, nuclear lamina and kinesins KIF5B and KIF13B to generate DSB-capturing nuclear envelope tubules (dsbNETs). dsbNETs are partly supported by nuclear actin filaments and the circadian factor PER1 and reversed by kinesin KIFC3. Although dsbNETs promote repair and survival, they are also co-opted during poly(ADP-ribose) polymerase (PARP) inhibition to restrain BRCA1-deficient breast cancer cells and are hyper-induced in cells expressing the aging-linked lamin A mutant progerin. In summary, our results advance understanding of nuclear structure-function relationships, uncover a nuclear-cytoplasmic DDR and identify dsbNETs as critical factors in genome organization and stability.
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Affiliation(s)
- Mitra Shokrollahi
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mia Stanic
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anisha Hundal
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Defne Urman
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chris A Jordan
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anne Hakem
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Roderic Espin
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jun Hao
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada
| | - Philipp G Maass
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Manoor P Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Miquel A Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Razqallah Hakem
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Research Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Temerty Centre for AI Research and Education in Medicine, University of Toronto, Toronto, Ontario, Canada.
- College of New Scholars, Artists and Scientists, Royal Society of Canada, Ottawa, Ontario, Canada.
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6
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Paine PT, Rechsteiner C, Morandini F, Desdín-Micó G, Mrabti C, Parras A, Haghani A, Brooke R, Horvath S, Seluanov A, Gorbunova V, Ocampo A. Initiation phase cellular reprogramming ameliorates DNA damage in the ERCC1 mouse model of premature aging. FRONTIERS IN AGING 2024; 4:1323194. [PMID: 38322248 PMCID: PMC10844398 DOI: 10.3389/fragi.2023.1323194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
Abstract
Unlike aged somatic cells, which exhibit a decline in molecular fidelity and eventually reach a state of replicative senescence, pluripotent stem cells can indefinitely replenish themselves while retaining full homeostatic capacity. The conferment of beneficial-pluripotency related traits via in vivo partial cellular reprogramming in vivo partial reprogramming significantly extends lifespan and restores aging phenotypes in mouse models. Although the phases of cellular reprogramming are well characterized, details of the rejuvenation processes are poorly defined. To understand whether cellular reprogramming can ameliorate DNA damage, we created a reprogrammable accelerated aging mouse model with an ERCC1 mutation. Importantly, using enhanced partial reprogramming by combining small molecules with the Yamanaka factors, we observed potent reversion of DNA damage, significant upregulation of multiple DNA damage repair processes, and restoration of the epigenetic clock. In addition, we present evidence that pharmacological inhibition of ALK5 and ALK2 receptors in the TGFb pathway are able to phenocopy some benefits including epigenetic clock restoration suggesting a role in the mechanism of rejuvenation by partial reprogramming.
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Affiliation(s)
- Patrick Treat Paine
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Center for Virology and Vaccine Research, Harvard Medical School, Boston, MA, United States
| | | | - Francesco Morandini
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Gabriela Desdín-Micó
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
| | | | - Robert Brooke
- Epigenetic Clock Development Foundation, Torrance, CA, United States
| | - Steve Horvath
- Altos Labs, San Diego, CA, United States
- Epigenetic Clock Development Foundation, Torrance, CA, United States
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
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7
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Lin C, Schoenherr RM, Voytovich UJ, Ivey RG, Kennedy JJ, Whiteaker JR, Wang P, Paulovich AG. RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage. Sci Data 2024; 11:27. [PMID: 38177134 PMCID: PMC10766633 DOI: 10.1038/s41597-023-02829-1] [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: 07/25/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of TP53 or PTEN loss, we profiled the RNA and phosphoproteomes of the MCF10A epithelial cell line, along with its congenic TP53- or PTEN-knockout derivatives, upon perturbation with the monofunctional DNA alkylating agent methyl methanesulfonate (MMS) vs. mock treatment. To enable quantitative and reproducible mass spectrometry data generation, the cell lines were SILAC-labeled (stable isotope labeling with amino acids in cell culture), and the experimental design included label swapping and biological replicates. All data are publicly available and may be used to advance our understanding of the TP53 and PTEN tumor suppressor genes and to provide functional signatures for bioinformatic analyses of proteogenomic datasets.
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Affiliation(s)
- ChenWei Lin
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | | | - Pei Wang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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8
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Schuhwerk H, Brabletz T. Mutual regulation of TGFβ-induced oncogenic EMT, cell cycle progression and the DDR. Semin Cancer Biol 2023; 97:86-103. [PMID: 38029866 DOI: 10.1016/j.semcancer.2023.11.009] [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: 06/27/2023] [Revised: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
TGFβ signaling and the DNA damage response (DDR) are two cellular toolboxes with a strong impact on cancer biology. While TGFβ as a pleiotropic cytokine affects essentially all hallmarks of cancer, the multifunctional DDR mostly orchestrates cell cycle progression, DNA repair, chromatin remodeling and cell death. One oncogenic effect of TGFβ is the partial activation of epithelial-to-mesenchymal transition (EMT), conferring invasiveness, cellular plasticity and resistance to various noxae. Several reports show that both individual networks as well as their interface affect chemo-/radiotherapies. However, the underlying mechanisms remain poorly resolved. EMT often correlates with TGFβ-induced slowing of proliferation, yet numerous studies demonstrate that particularly the co-activated EMT transcription factors counteract anti-proliferative signaling in a partially non-redundant manner. Collectively, evidence piled up over decades underscore a multifaceted, reciprocal inter-connection of TGFβ signaling / EMT with the DDR / cell cycle progression, which we will discuss here. Altogether, we conclude that full cell cycle arrest is barely compatible with the propagation of oncogenic EMT traits and further propose that 'EMT-linked DDR plasticity' is a crucial, yet intricate facet of malignancy, decisively affecting metastasis formation and therapy resistance.
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Affiliation(s)
- Harald Schuhwerk
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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9
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2023; 186:3476-3498.e35. [PMID: 37541199 PMCID: PMC10414761 DOI: 10.1016/j.cell.2023.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.
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Affiliation(s)
- Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Department of Population Health Science and Policy, Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Uliana J Voytovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yajue Huang
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hee Lee
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Lindsay Bergan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Fenyo
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua Wang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Mary Helen Barcellos-Hoff
- Helen Diller Family Comprehensive Cancer Center, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris J Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles Drescher
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcin Cieslik
- Department of Pathology, Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Michael J Birrer
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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10
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Stagg J, Golden E, Wennerberg E, Demaria S. The interplay between the DNA damage response and ectonucleotidases modulates tumor response to therapy. Sci Immunol 2023; 8:eabq3015. [PMID: 37418547 PMCID: PMC10394739 DOI: 10.1126/sciimmunol.abq3015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/14/2023] [Indexed: 07/09/2023]
Abstract
The extracellular nucleoside adenosine reduces tissue inflammation and is generated by irreversible dephosphorylation of adenosine monophosphate (AMP) mediated by the ectonucleotidase CD73. The pro-inflammatory nucleotides adenosine triphosphate, nicotinamide adenine dinucleotide, and cyclic guanosine -monophosphate-AMP (cGAMP), which are produced in the tumor microenvironment (TME) during therapy-induced immunogenic cell death and activation of innate immune signaling, can be converted into AMP by ectonucleotidases CD39, CD38, and CD203a/ENPP1. Thus, ectonucleotidases shape the TME by converting immune-activating signals into an immunosuppressive one. Ectonucleotidases also hinder the ability of therapies including radiation therapy, which enhance the release of pro-inflammatory nucleotides in the extracellular milieu, to induce immune-mediated tumor rejection. Here, we review the immunosuppressive effects of adenosine and the role of different ectonucleotidases in modulating antitumor immune responses. We discuss emerging opportunities to target adenosine generation and/or its ability to signal via adenosine receptors expressed by immune and cancer cells in the context of combination immunotherapy and radiotherapy.
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Affiliation(s)
- John Stagg
- Centre de Recherche du Centre Hospitalier de
l’Université de Montréal, 900 St-Denis street, Montreal,
Quebec, Canada, H2X 0A9
| | - Encouse Golden
- Department of Radiation Oncology, Weill Cornell Medicine,
New York, NY 10065, USA
| | - Erik Wennerberg
- Division of Radiotherapy and Imaging, Institute of Cancer
Research, London SM2 5NG, UK
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine,
New York, NY 10065, USA
- Department of Pathology and Laboratory Medicine, Weill
Cornell Medicine, New York, NY, 10065, USA
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11
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Gregucci F, Spada S, Barcellos-Hoff MH, Bhardwaj N, Chan Wah Hak C, Fiorentino A, Guha C, Guzman ML, Harrington K, Herrera FG, Honeychurch J, Hong T, Iturri L, Jaffee E, Karam SD, Knott SR, Koumenis C, Lyden D, Marciscano AE, Melcher A, Mondini M, Mondino A, Morris ZS, Pitroda S, Quezada SA, Santambrogio L, Shiao S, Stagg J, Telarovic I, Timmerman R, Vozenin MC, Weichselbaum R, Welsh J, Wilkins A, Xu C, Zappasodi R, Zou W, Bobard A, Demaria S, Galluzzi L, Deutsch E, Formenti SC. Updates on radiotherapy-immunotherapy combinations: Proceedings of 6 th annual ImmunoRad conference. Oncoimmunology 2023; 12:2222560. [PMID: 37363104 PMCID: PMC10286673 DOI: 10.1080/2162402x.2023.2222560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Focal radiation therapy (RT) has attracted considerable attention as a combinatorial partner for immunotherapy (IT), largely reflecting a well-defined, predictable safety profile and at least some potential for immunostimulation. However, only a few RT-IT combinations have been tested successfully in patients with cancer, highlighting the urgent need for an improved understanding of the interaction between RT and IT in both preclinical and clinical scenarios. Every year since 2016, ImmunoRad gathers experts working at the interface between RT and IT to provide a forum for education and discussion, with the ultimate goal of fostering progress in the field at both preclinical and clinical levels. Here, we summarize the key concepts and findings presented at the Sixth Annual ImmunoRad conference.
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Affiliation(s)
- Fabiana Gregucci
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Radiation Oncology, Miulli General Regional Hospital, Acquaviva delle Fonti, Bari, Italy
| | - Sheila Spada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, School of Medicine, University of California, San Francisco, CA, USA
| | - Nina Bhardwaj
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Alba Fiorentino
- Department of Radiation Oncology, Miulli General Regional Hospital, Acquaviva delle Fonti, Bari, Italy
- Department of Medicine and Surgery, LUM University, Casamassima, Bari, Italy
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, USA
| | - Monica L. Guzman
- Division of Hematology/Oncology, Department of Medicine, Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Kevin Harrington
- The Institute of Cancer Research/The Royal Marsden NHS Foundation Trust, National Institute for Health Research Biomedical Research Centre, London, UK
| | - Fernanda G. Herrera
- Centre Hospitalier Universitaire Vaudois, University of Lausanne and Ludwig Institute for Cancer Research at the Agora Cancer Research Center, Lausanne, Switzerland
| | - Jamie Honeychurch
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Theodore Hong
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorea Iturri
- Institut Curie, Université PSL, CNRS UMR3347, INSERM U1021, Signalisation Radiobiologie et Cancer, Orsay, France
| | - Elisabeth Jaffee
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado, Aurora, CO, USA
| | - Simon R.V. Knott
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | - Alan Melcher
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - Michele Mondini
- Department of Radiation Oncology, Gustave Roussy Cancer Campus, Villejuif, France
- Université of Paris-Saclay, Saclay, France
- INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Anna Mondino
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Zachary S. Morris
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sean Pitroda
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
| | - Sergio A. Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Stephen Shiao
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - John Stagg
- Centre de Recherche du Centre Hospitalier de l’Universite de Montreal, Faculty of Pharmacy, Montreal, Canada
| | - Irma Telarovic
- Laboratory for Applied Radiobiology, Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Robert Timmerman
- Departments of Radiation Oncology and Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marie-Catherine Vozenin
- Laboratory of Radiation Oncology, Radiation Oncology Service, Department of Oncology, CHUV, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ralph Weichselbaum
- Department of Radiation and Cellular Oncology, Ludwig Center for Metastases Research, University of Chicago, IL, USA
| | - James Welsh
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Wilkins
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom, Royal Marsden Hospital, Sutton, UK
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Roberta Zappasodi
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Weiping Zou
- Departments of Surgery and Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Eric Deutsch
- Department of Radiation Oncology, Gustave Roussy Cancer Campus, Villejuif, France
- Université of Paris-Saclay, Saclay, France
- INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Silvia C. Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
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12
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Ma L, Gonzalez-Junca A, Chou W, Barcellos-Hoff MH. Monitoring TGFβ signaling in irradiated tumors. Methods Cell Biol 2023; 180:49-67. [PMID: 37890932 DOI: 10.1016/bs.mcb.2023.02.009] [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: 10/29/2023]
Abstract
Transforming growth factor β (TGFβ) is exquisitely regulated under physiological conditions but its activity is highly dysregulated in cancer. All cells make TGFβ and have receptors for the ligand, which is sequestered in the extracellular matrix in a latent form. Ionizing radiation elicits rapid release of TGFβ from these stores, so-called activation, over a wide range of doses and exposures, including low dose (<1Gy) whole-body irradiation, creating an extraordinarily potent signal in the irradiated tissue or tumor. Hence, accurate evaluation of TGFβ activity is complicated because of its ubiquitous distribution as a latent complex. Here we describe conditions for assays that reveal TGFβ activity in situ using either tissue preparations or functional imaging.
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Affiliation(s)
- Lin Ma
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Alba Gonzalez-Junca
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - William Chou
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States.
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13
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Barcellos-Hoff MH, Gulley JL. Molecular Pathways and Mechanisms of TGFβ in Cancer Therapy. Clin Cancer Res 2023; 29:2025-2033. [PMID: 36598437 PMCID: PMC10238558 DOI: 10.1158/1078-0432.ccr-21-3750] [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: 04/26/2022] [Revised: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023]
Abstract
Even though the number of agents that inhibit TGFβ being tested in patients with cancer has grown substantially, clinical benefit from TGFβ inhibition has not yet been achieved. The myriad mechanisms in which TGFβ is protumorigenic may be a key obstacle to its effective deployment; cancer cells frequently employ TGFβ-regulated programs that engender plasticity, enable a permissive tumor microenvironment, and profoundly suppress immune recognition, which is the target of most current early-phase trials of TGFβ inhibitors. Here we discuss the implications of a less well-recognized aspect of TGFβ biology regulating DNA repair that mediates responses to radiation and chemotherapy. In cancers that are TGFβ signaling competent, TGFβ promotes effective DNA repair and suppresses error-prone repair, thus conferring resistance to genotoxic therapies and limiting tumor control. Cancers in which TGFβ signaling is intrinsically compromised are more responsive to standard genotoxic therapy. Recognition that TGFβ is a key moderator of both DNA repair and immunosuppression might be used to synergize combinations of genotoxic therapy and immunotherapy to benefit patients with cancer.
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Affiliation(s)
- Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James L. Gulley
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Zuo N, Ma L, Liu T, Hu W, Luo Y, Meng H, Ren Q, Deng Y, Wei L, Liu Q. Human papillomavirus associated XPF deficiency increases alternative end joining and cisplatin sensitivity in head and neck squamous cell carcinoma. Oral Oncol 2023; 140:106367. [PMID: 36996606 DOI: 10.1016/j.oraloncology.2023.106367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/02/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023]
Abstract
OBJECTIVES Human papillomavirus (HPV) positive head and neck squamous cell carcinoma (HNSCC) showed a considerably better prognosis with greater cisplatin sensitivity compared to their HPV-negative counterparts. Deciphering the underlying molecular mechanisms for HPV-induced cisplatin sensitivity is imperative to improve the prognosis of HPV-negative HNSCC. MATERIALS AND METHODS The Fanconi anemia (FA) pathway status in HNSCC cells was analysed by detecting the cell cycle and chromosomal aberrations. XPF expression was validated using PCR, western blot, and immunohistochemistry. Droplet digital PCR and GFP expressing reporter assay were used to analyse the changes in alternative end-joining (alt-EJ) levels. The cisplatin sensitization was verified by cell proliferation assay, clonogenic cell survival assay, and TUNEL. RESULTS HPV-positive HNSCC cells showed significant prolonged G2-M cell cycle arrest and aberrant chromosome formation under interstrand crosslinker treatment. Both mRNA and protein expression of XPF were considerably decreased in HPV-positive HNSCC, according to the analysis of cellular and clinical data. XPF inhibition upregulated the activity of the alt-EJ pathway in HPV-negative HNSCC cells by 32.02% (P < 0.001) but had little effect on HPV-positive HNSCC. Consistent with this, simultaneous suppression of XPF and alt-EJ enhanced cisplatin sensitivity of HPV-negative HNSCC in vitro and in vivo. CONCLUSION HPV-positive HNSCC cells exhibit a profound FA pathway deficiency associated with reduced XPF expression. HNSCC cells with compromised XPF function are more reliant on the alt-EJ pathway for genomic stability. Combining FA and alt-EJ inhibition may be used to cope with the hard-to-treat HPV-negative HNSCC.
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15
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Qin X, Wang J, Wang X, Huang T, Fang Z, Yan L, Fan Y, Xu D. Widespread genomic/molecular alterations of DNA helicases and their clinical/therapeutic implications across human cancer. Biomed Pharmacother 2023; 158:114193. [PMID: 36586240 DOI: 10.1016/j.biopha.2022.114193] [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: 10/08/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
DNA helicases are essential to genomic stability by regulating DNA metabolisms and their loss-of-function mutations lead to genomic instability and predisposition to cancer. Paradoxically, overexpression of DNA helicases is observed in several cancers. Here we analyzed genomic and molecular alterations in 12 important DNA helicases in TCGA pan-cancers to provide an overview of their aberrations. Significant expression heterogeneity of 12 DNA helicases was observed. We calculated DNA helicase score (DHS) based on their expression, and categorized tumors into high, low and intermediate subtypes. High DHS subtypes were robustly associated with stemness, proliferation, hyperactivated oncogenic signaling, longer telomeres, total mutation burden, copy number alterations (CNAs) and shorter survival. Importantly, tumors with high DHSs exhibited stronger expression of alternative end-join (alt-EJ) factors, indicative of sensitivity to chemo- and radio-therapies. High DHSs were also associated with homologous recombination deficiency (HRD), BRCA1/2 mutations and sensitivity to PARP inhibitors. Moreover, several drugs are identified to inhibit DNA helicases, with the Auror A kinase inhibitor Danusertib as the strongest candidate that was confirmed experimentally. The aberrant expression of DNA helicases was associated with CNAs, DNA methylation and m6A regulators. Our findings thus reveal widespread dysregulation of DNA helicases and their broad connection with featured oncogenic aberrations across human cancers. The close association of DHS with the alt-EJ pathway and HRD, and identification of Danusertib as a putative DNA helicase inhibitor have translational significance. Taken together, these findings will contribute to DNA helicase-based cancer therapy.
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Affiliation(s)
- Xin Qin
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jing Wang
- Department of Urologic Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Xing Wang
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Wannan Medical College, Wuhu 241000, China
| | - Tao Huang
- Department of Urologic Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Lei Yan
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm 171 76, Sweden.
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16
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Hu C, Bugbee T, Palinski R, Akinyemi IA, McIntosh MT, MacCarthy T, Bhaduri-McIntosh S, Wallace N. Beta human papillomavirus 8E6 promotes alternative end joining. eLife 2023; 12:e81923. [PMID: 36692284 PMCID: PMC9897725 DOI: 10.7554/elife.81923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
Double strand breaks (DSBs) are one of the most lethal DNA lesions in cells. The E6 protein of beta-human papillomavirus (HPV8 E6) impairs two critical DSB repair pathways: homologous recombination (HR) and non-homologous end joining (NHEJ). However, HPV8 E6 only delays DSB repair. How DSBs are repaired in cells with HPV8 E6 remains to be studied. We hypothesize that HPV8 E6 promotes a less commonly used DSB repair pathway, alternative end joining (Alt-EJ). Using CAS9-based Alt-EJ reporters, we show that HPV8 E6 promotes Alt-EJ. Further, using small molecule inhibitors, CRISPR/CAS9 gene knockout, and HPV8 E6 mutant, we find that HPV8 E6 promotes Alt-EJ by binding p300, an acetyltransferase that facilitates DSB repair by HR and NHEJ. At least some of this repair occurs through a subset of Alt-EJ known as polymerase theta dependent end joining. Finally, whole genome sequencing analysis showed HPV8 E6 caused an increased frequency of deletions bearing the microhomology signatures of Alt-EJ. This study fills the knowledge gap of how DSB is repaired in cells with HPV8 E6 and the mutagenic consequences of HPV8 E6 mediated p300 destabilization. Broadly, this study supports the hypothesis that beta-HPV promotes cancer formation by increasing genomic instability.
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Affiliation(s)
- Changkun Hu
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Division of Biology, Kansas State UniversityManhattanUnited States
| | - Taylor Bugbee
- Division of Biology, Kansas State UniversityManhattanUnited States
| | - Rachel Palinski
- Veterinary Diagnostic Laboratory, Kansas State UniversityManhattanUnited States
| | - Ibukun A Akinyemi
- Child Health Research Institute, Department of Pediatrics, University of FloridaGainesvilleUnited States
- Department of Molecular Genetics and Microbiology, University of FloridaGainesvilleUnited States
| | - Michael T McIntosh
- Child Health Research Institute, Department of Pediatrics, University of FloridaGainesvilleUnited States
| | - Thomas MacCarthy
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookUnited States
| | - Sumita Bhaduri-McIntosh
- Child Health Research Institute, Department of Pediatrics, University of FloridaGainesvilleUnited States
- Department of Molecular Genetics and Microbiology, University of FloridaGainesvilleUnited States
| | - Nicholas Wallace
- Division of Biology, Kansas State UniversityManhattanUnited States
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17
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Zhang B, Jia P, Wang J, Pei G, Wang C, Pei S, Li X, Zhao Z, Yi X, Guan XY, Huang Y. Integrated analysis of racial disparities in genomic architecture identifies a trans-ancestry prognostic subtype in bladder cancer. Mol Oncol 2022; 17:564-581. [PMID: 36495164 PMCID: PMC10061287 DOI: 10.1002/1878-0261.13360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
The incidence of bladder cancer and patient survival vary greatly among different populations, but the influence of the associated molecular features and evolutionary processes on its clinical treatment and prognostication remains unknown. Here, we analyze the genomic architectures of 505 bladder cancer patients from Asian/Black/White populations. We identify a previously unknown association between AHNAK mutations and activity of the APOBEC-a mutational signature, the activity of which varied substantially across populations. All significantly mutated genes but only half of arm-level somatic copy number alterations (SCNAs) are enriched with clonal events, indicating large-scale SCNAs as rich sources of bladder cancer clonal diversities. The prevalence of TP53 and ATM clonal mutations as well as the associated burden of SCNAs is significantly higher in Whites/Blacks than in Asians. We identify a trans-ancestry prognostic subtype of bladder cancer characterized by enrichment of non-muscle-invasive patients and muscle-invasive patients with good prognosis, increased CREBBP/FGFR3/HRAS/NFE2L2 mutations, decreased intra-tumor heterogeneity and genome instability, and an activated tumor microenvironment.
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Affiliation(s)
- Baifeng Zhang
- Departments of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, China.,Departments of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, China.,Geneplus-Beijing, China
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, TX, USA
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, China
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, TX, USA
| | | | | | - Xiangchun Li
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, China
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, TX, USA
| | | | - Xin-Yuan Guan
- Departments of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, China.,Departments of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, China
| | - Yi Huang
- Geneplus-Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi, China.,Luohu people's hospital, Shenzhen, China
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18
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Abstract
DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase-like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand-breaking chemicals and radiation. Since some homologous recombination-defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.
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Affiliation(s)
- Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA;
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA;
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19
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Rodríguez A, Epperly M, Filiatrault J, Velázquez M, Yang C, McQueen K, Sambel LA, Nguyen H, Iyer DR, Juárez U, Ayala-Zambrano C, Martignetti DB, Frías S, Fisher R, Parmar K, Greenberger JS, D’Andrea AD. TGFβ pathway is required for viable gestation of Fanconi anemia embryos. PLoS Genet 2022; 18:e1010459. [PMID: 36441774 PMCID: PMC9731498 DOI: 10.1371/journal.pgen.1010459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/08/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
Overexpression of the TGFβ pathway impairs the proliferation of the hematopoietic stem and progenitor cells (HSPCs) pool in Fanconi anemia (FA). TGFβ promotes the expression of NHEJ genes, known to function in a low-fidelity DNA repair pathway, and pharmacological inhibition of TGFβ signaling rescues FA HSPCs. Here, we demonstrate that genetic disruption of Smad3, a transducer of the canonical TGFβ pathway, modifies the phenotype of FA mouse models deficient for Fancd2. We observed that the TGFβ and NHEJ pathway genes are overexpressed during the embryogenesis of Fancd2-/- mice and that the Fancd2-/-Smad3-/- double knockout (DKO) mice undergo high levels of embryonic lethality due to loss of the TGFβ-NHEJ axis. Fancd2-deficient embryos acquire extensive genomic instability during gestation which is not reversed by Smad3 inactivation. Strikingly, the few DKO survivors have activated the non-canonical TGFβ-ERK pathway, ensuring expression of NHEJ genes during embryogenesis and improved survival. Activation of the TGFβ-NHEJ axis was critical for the survival of the few Fancd2-/-Smad3-/- DKO newborn mice but had detrimental consequences for these surviving mice, such as enhanced genomic instability and ineffective hematopoiesis.
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Affiliation(s)
- Alfredo Rodríguez
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, México
- Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Michael Epperly
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Jessica Filiatrault
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Martha Velázquez
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Chunyu Yang
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for DNA Damage and DNA Repair, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Kelsey McQueen
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for DNA Damage and DNA Repair, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Larissa A. Sambel
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for DNA Damage and DNA Repair, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Huy Nguyen
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for DNA Damage and DNA Repair, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Divya Ramalingam Iyer
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Ulises Juárez
- Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Cecilia Ayala-Zambrano
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Instituto Nacional de Pediatría, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, UNAM, Ciudad Universitaria, México, México
| | - David B. Martignetti
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Sara Frías
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, México
- Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Renee Fisher
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for DNA Damage and DNA Repair, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Joel S. Greenberger
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for DNA Damage and DNA Repair, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail:
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20
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Huang Y, Chen X, Jiang Z, Luo Q, Wan L, Hou X, Yu K, Zhuang J. Transcriptome Sequencing Reveals Tgf-β-Mediated Noncoding RNA Regulatory Mechanisms Involved in DNA Damage in the 661W Photoreceptor Cell Line. Genes (Basel) 2022; 13:2140. [PMID: 36421815 PMCID: PMC9691224 DOI: 10.3390/genes13112140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/24/2022] [Accepted: 11/14/2022] [Indexed: 10/08/2023] Open
Abstract
Transforming growth factor β (Tgf-β), a pleiotropic cytokine, can enhance DNA repair in various cells, including cancer cells and neurons. The noncoding regulatory system plays an important role in Tgf-β-mediated biological activities, whereas few studies have explored its role in DNA damage and repair. In this study, we suggested that Tgf-β improved while its inhibitor LSKL impaired DNA repair and cell viability in UV-irradiated 661W cells. Moreover, RNA-seq was carried out, and a total of 106 differentially expressed (DE)-mRNAs and 7 DE-lncRNAs were identified between UV/LSKL and UV/ctrl 661W cells. Gene ontology and Reactome analysis confirmed that the DE-mRNAs were enriched in multiple DNA damaged- and repair-related biological functions and pathways. We then constructed a ceRNA network that included 3 lncRNAs, 19 miRNAs, and 29 mRNAs with a bioinformatics prediction. Through RT-qPCR and further functional verification, 2 Tgf-β-mediated ceRNA axes (Gm20559-miR-361-5p-Oas2/Gbp7) were further identified. Gm20559 knockout or miR-361-5p mimics markedly impaired DNA repair and cell viability in UV-irradiated 661W cells, which confirms the bioinformatics results. In summary, this study revealed that Tgf-β could reduce DNA damage in 661W cells, provided a Tgf-β-associated ceRNA network for DNA damage and repair, and suggested that the molecular signatures may be useful candidates as targets of treatment for photoreceptor pathology.
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Affiliation(s)
- Yuke Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhigao Jiang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Qian Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Linxi Wan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xiangtao Hou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Keming Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jing Zhuang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
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21
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Barcellos-Hoff MH. The radiobiology of TGFβ. Semin Cancer Biol 2022; 86:857-867. [PMID: 35122974 DOI: 10.1016/j.semcancer.2022.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 01/27/2023]
Abstract
Ionizing radiation is a pillar of cancer therapy that is deployed in more than half of all malignancies. The therapeutic effect of radiation is attributed to induction of DNA damage that kills cancers cells, but radiation also affects signaling that alters the composition of the tumor microenvironment by activating transforming growth factor β (TGFβ). TGFβ is a ubiquitously expressed cytokine that acts as biological lynchpin to orchestrate phenotypes, the stroma, and immunity in normal tissue; these activities are subverted in cancer to promote malignancy, a permissive tumor microenvironment and immune evasion. The radiobiology of TGFβ unites targets at the forefront of oncology-the DNA damage response and immunotherapy. The cancer cell intrinsic and extrinsic network of TGFβ responses in the irradiated tumor form a barrier to both genotoxic treatments and immunotherapy response. Here, we focus on the mechanisms by which radiation induces TGFβ activation, how TGFβ regulates DNA repair, and the dynamic regulation of the tumor immune microenvironment that together oppose effective cancer therapy. Strategies to inhibit TGFβ exploit fundamental radiobiology that may be the missing link to deploying TGFβ inhibitors for optimal patient benefit from cancer treatment.
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Affiliation(s)
- Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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22
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Zuo N, Ma L, Hu W, Deng Y, Wei L, Liu Q. Detection of Alternative End-Joining in HNSC Cell Lines Using DNA Double-Strand Break Reporter Assays. Bio Protoc 2022; 12:e4506. [PMID: 36213110 PMCID: PMC9501725 DOI: 10.21769/bioprotoc.4506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/29/2022] Open
Abstract
The main cellular pathways to repair DNA double-strand breaks (DSBs) and protect the integrity of the genome are homologous recombination (HR), non-homologous end-joining (NHEJ), and alternative end-joining (Alt-EJ). Polymerase theta-regulated Alt-EJ is an error-prone DSB repair pathway characterized by microhomology usage. Considering its importance in cancer treatment, technologies for detection of Alt-EJ in cancer cells may facilitate the study of the mechanisms of carcinogenesis and the development of new therapeutic targets. DSB reporter assay is the classical method for detecting Alt-EJ, which is primarily based on components of EJ2-puro cassette integration, I-SceI cleaving, and flow cytometry analysis. Here, we described an assay based on a modified I-Scel plasmid that can screen head and neck squamous cell carcinoma (HNSC) cells that were successfully transfected using selection medium with hygrovetine. We expect that this protocol will improve the fidelity and accuracy of reporter assays. Graphical abstract: Schematic overview of the workflow for establishment of Alt-EJ reporters.
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Affiliation(s)
- Nan Zuo
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China,Department of Stomatology, the First Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lin Ma
- Department of Stomatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055, China,Institute of Stomatological Research, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Weitao Hu
- Department of Stomatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055, China,Institute of Stomatological Research, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Yongqiang Deng
- Department of Stomatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055, China,Institute of Stomatological Research, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Lanlan Wei
- Department of Stomatology, the First Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qi Liu
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China,*For correspondence:
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23
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Liu T, Ma L, Song L, Yan B, Zhang S, Wang B, Zuo N, Sun X, Deng Y, Ren Q, Li Y, Zhou J, Liu Q, Wei L. CENPM upregulation by E5 oncoprotein of human papillomavirus promotes radiosensitivity in head and neck squamous cell carcinoma. Oral Oncol 2022; 129:105858. [DOI: 10.1016/j.oraloncology.2022.105858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/10/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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24
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Moyret-Lalle C, Prodhomme MK, Burlet D, Kashiwagi A, Petrilli V, Puisieux A, Seimiya H, Tissier A. Role of EMT in the DNA damage response, double-strand break repair pathway choice and its implications in cancer treatment. Cancer Sci 2022; 113:2214-2223. [PMID: 35534984 PMCID: PMC9277259 DOI: 10.1111/cas.15389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022] Open
Abstract
Numerous epithelial–mesenchymal transition (EMT) characteristics have now been demonstrated to participate in tumor development. Indeed, EMT is involved in invasion, acquisition of stem cell properties, and therapy‐associated resistance of cancer cells. Together, these mechanisms offer advantages in adapting to changes in the tumor microenvironment. However, recent findings have shown that EMT‐associated transcription factors (EMT‐TFs) may also be involved in DNA repair. A better understanding of the coordination between the DNA repair pathways and the role played by some EMT‐TFs in the DNA damage response (DDR) should pave the way for new treatments targeting tumor‐specific molecular vulnerabilities, which result in selective destruction of cancer cells. Here we review recent advances, providing novel insights into the role of EMT in the DDR and repair pathways, with a particular focus on the influence of EMT on cellular sensitivity to damage, as well as the implications of these relationships for improving the efficacy of cancer treatments.
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Affiliation(s)
- Caroline Moyret-Lalle
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Mélanie K Prodhomme
- Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Delphine Burlet
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Ayaka Kashiwagi
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Virginie Petrilli
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Alain Puisieux
- Institut Curie, Versailles Saint-Quentin-en-Yvelines University, PSL Research University, Paris, France
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Agnès Tissier
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
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25
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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] [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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26
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Guix I, Liu Q, Pujana MA, Ha P, Piulats J, Linares I, Guedea F, Mao JH, Lazar A, Chapman J, Yom SS, Ashworth A, Barcellos-Hoff MH. Validation of anti-correlated TGFβ signaling and alternative end-joining DNA repair signatures that predict response to genotoxic cancer therapy. Clin Cancer Res 2022; 28:1372-1382. [PMID: 35022323 DOI: 10.1158/1078-0432.ccr-21-2846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/13/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Loss of transforming growth factor β (TGFβ) signaling increases error-prone alternative end-joining (alt-EJ) DNA repair. We previously translated this mechanistic relationship as TGFβ and alt-EJ gene expression signatures, which are anti-correlated across cancer types. A score, βAlt, representing anti-correlation predicts patient outcome in response to genotoxic therapy. Here we sought to verify this biology in live specimens and additional datasets. EXPERIMENTAL DESIGN Human head and neck squamous cell (HNSC) carcinoma explants were treated in vitro to test whether the signatures report TGFβ signaling, indicated by SMAD2 phosphorylation, and unrepaired DNA damage, indicated by persistent 53BP1 foci after irradiation or olaparib. A custom NanoString assay was implemented to analyze the signatures' expression in explants. Each signature gene was then weighted by its association with functional responses to define a modified score, βAltw, that was retested for association with response to genotoxic therapies in independent datasets. RESULTS Most genes in each signature were positively correlated with the expected biological response in tumor explants. Anticorrelation of TGFβ and alt-EJ signatures measured by Nanostring was confirmed in explants. βAltw was significantly (P<0.001) better than βAlt in predicting overall survival in response to genotoxic therapy in TCGA pancancer patients and in independent HNSC and ovarian cancer patient datasets. CONCLUSION Association of the TGFβ and alt-EJ signatures with their biological response validates TGFβ competency as a key mediator of DNA repair that can be readily assayed by gene expression. The predictive value of βAltw supports its development to assist in clinical decision-making.
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Affiliation(s)
- Ines Guix
- Department of Radiation Oncology, University of California, San Francicsco
| | - Qi Liu
- Shenzhen Bay Laboratory, Institute for Biomedical Engineering
| | | | - Patrick Ha
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco
| | - Josep Piulats
- Medical Oncology, Institut Català d'Oncologia-IDIBELL
| | | | | | - Jian-Hua Mao
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, University of California, Berkely
| | - Ann Lazar
- Biostatistics, University of California, San Francisco
| | - Jocelyn Chapman
- Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco
| | - Sue S Yom
- Radiation Oncology, University of California, San Francisco
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Centre
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27
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Derby SJ, Chalmers AJ, Carruthers RD. Radiotherapy-Poly(ADP-ribose) Polymerase Inhibitor Combinations: Progress to Date. Semin Radiat Oncol 2022; 32:15-28. [PMID: 34861992 DOI: 10.1016/j.semradonc.2021.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Radiation resistance remains a huge clinical problem for cancer patients and oncologists in the 21st century. In recent years, the mammalian DNA damage response (DDR) has been extensively characterized and shown to play a key role in determining cellular survival following ionizing radiation exposure. Genomic instability due to altered DDR is a hallmark of cancer, with many tumors exhibiting abnormal DNA repair or lack of redundancy in DDR. Targeting the abnormal DDR phenotype of tumor cells could lead to substantial gains in radiotherapy efficacy, improving local control and survival for patients with cancers that are refractory to current therapies. Poly(ADP-ribose) polymerase inhibitors (PARPi) are the most clinically advanced DDR inhibitors under investigation as radiosensitisers. Preclinical evidence suggests that PARPi may provide tumor specific radiosensitisation in certain contexts. In addition to inhibition of DNA single strand break repair, PARPi may offer other benefits in combination treatment including radiosensitisation of hypoxic cells and targeting of alternative repair pathways such as microhomology mediated end joining which are increasingly recognized to be upregulated in cancer. Several early phase clinical trials of PARPi with radiation have completed or are in progress. Early reports have highlighted tumor specific challenges, with tolerability dependent upon anatomical location and use of concomitant systemic therapies; these challenges were largely predicted by preclinical data. This review discusses the role of PARP in the cellular response to ionizing radiation, summarizes preclinical studies of PARPi in combination with radiotherapy and explores current early phase clinical trials that are evaluating these combinations.
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Affiliation(s)
- Sarah J Derby
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland.
| | - Anthony J Chalmers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland
| | - Ross D Carruthers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland
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28
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Newfeld SJ, O’Connor MB. New aspects of TGF-β superfamily signaling in development and disease (2022 FASEB meeting review). Fac Rev 2022; 11:36. [PMID: 36644295 PMCID: PMC9816873 DOI: 10.12703/r/11-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The 13th Federation of American Societies for Experimental Biology (FASEB) Summer Research Conference, "TGF-β superfamily signaling in development and disease" was convened at the Grand Hotel in Malahide, Ireland in July 2022. The Transforming Growth Factor-β (TGF-β) family of secreted proteins consists of agents of intercellular communication found in all multicellular animals. Attending the meeting was a diverse group of scholars with shared interests in understanding TGF-β signaling mechanisms, normal functions, and the diseases associated with misregulation and mutation. Despite intense study over the previous 35 years, new features of TGF-β activity continue to be discovered. This meeting report offers 21 investigator-provided summaries that illustrate the breadth of the thought-provoking presentations. An emerging theme of the meeting was the power of cross-disciplinary studies, such as one combining immunology, biochemistry, and structural biology, to unravel the secrets of parasitic TGF-β mimics. Please join us at the next meeting.
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Affiliation(s)
- Stuart J Newfeld
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Michael B O’Connor
- Department of Genetics Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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29
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Guhlich M, Hubert L, Mergler CPN, Rave-Fraenk M, Dröge LH, Leu M, Schmidberger H, Rieken S, Hille A, Schirmer MA. Identification of Risk Loci for Radiotoxicity in Prostate Cancer by Comprehensive Genotyping of TGFB1 and TGFBR1. Cancers (Basel) 2021; 13:cancers13215585. [PMID: 34771749 PMCID: PMC8582951 DOI: 10.3390/cancers13215585] [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: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Genetic variability in transforming growth factor beta pathway (TGFB) was suggested to affect adverse events of radiotherapy. We investigated comprehensive variability in TGFB1 (gene coding for TGFβ1 ligand) and TGFBR1 (TGFβ receptor-1) in relation to radiotoxicity. Prostate cancer patients treated with primary radiotherapy (n = 240) were surveyed for acute and late toxicity. Germline polymorphisms (n = 40) selected to cover the common genetic variability in TGFB1 and TGFBR1 were analyzed in peripheral blood cells. Human lymphoblastoid cell lines (LCLs) were used to evaluate a possible impact of TGFB1 and TGFBR1 genetic polymorphisms to DNA repair capacity following single irradiation with 3 Gy. Upon adjustment for multiplicity testing, rs10512263 in TGFBR1 showed a statistically significant association with acute radiation toxicity. Carriers of the Cytosine (C)-variant allele (n = 35) featured a risk ratio of 2.17 (95%-CI 1.41-3.31) for acute toxicity ≥ °2 compared to Thymine/Thymine (TT)-wild type individuals (n = 205). Reduced DNA repair capacity in the presence of the C-allele of rs10512263 might be a mechanistic explanation as demonstrated in LCLs following irradiation. The risk for late radiotoxicity was increased by carrying at least two risk genotypes at three polymorphic sites, including Leu10Pro in TGFB1. Via comprehensive genotyping of TGFB1 and TGFBR1, promising biomarkers for radiotoxicity in prostate cancer were identified.
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Affiliation(s)
- Manuel Guhlich
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
| | - Laura Hubert
- Institute of Clinical Pharmacology, University Medical Center Göttingen, 37075 Göttingen, Germany; (L.H.); (C.P.N.M.)
| | | | - Margret Rave-Fraenk
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
| | - Leif Hendrik Dröge
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
| | - Martin Leu
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
| | - Heinz Schmidberger
- Department of Radiation Oncology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany;
| | - Stefan Rieken
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
| | - Andrea Hille
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
| | - Markus Anton Schirmer
- Clinic of Radiotherapy and Radiation Oncology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (M.G.); (M.R.-F.); (L.H.D.); (M.L.); (S.R.); (A.H.)
- Institute of Clinical Pharmacology, University Medical Center Göttingen, 37075 Göttingen, Germany; (L.H.); (C.P.N.M.)
- Correspondence: ; Tel.: +49-551-39-64505
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30
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Liu Q, Chen G, Moore J, Guix I, Placantonokis D, Barcellos-Hoff MH. Exploiting Canonical TGFβ Signaling in Cancer Treatment. Mol Cancer Ther 2021; 21:16-24. [PMID: 34670783 PMCID: PMC8742762 DOI: 10.1158/1535-7163.mct-20-0891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/15/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022]
Abstract
Transforming growth factor β (TGFβ) is a pleiotropic cytokine that plays critical roles to define cancer cell phenotypes, construct the tumor microenvironment, and suppress anti-tumor immune responses. As such, TGFβ is a lynchpin for integrating cancer cell intrinsic pathways and communication among host cells in the tumor and beyond that together affect responses to genotoxic, targeted, and immune therapy. Despite decades of preclinical and clinical studies, evidence of clinical benefit from targeting TGFβ in cancer remains elusive. Here, we review the mechanisms by which TGFβ acts to oppose successful cancer therapy, the reported prognostic and predictive value of TGFβ biomarkers, and the potential impact of inhibiting TGFβ in precision oncology. Paradoxically, the diverse mechanisms by which TGFβ impedes therapeutic response are a principal barrier to implementing TGFβ inhibitors because it is unclear which TGFβ mechanism is functional in which patient. Companion diagnostic tools and specific biomarkers of TGFβ targeted biology will be the key to exploiting TGFβ biology for patient benefit.
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Affiliation(s)
- Qi Liu
- Shenzhen Bay Laboratory, Institute for Biomedical Engineering
| | - Genwen Chen
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University
| | - Jade Moore
- Department of Radiation Oncology, University of California, San Francicsco
| | - Ines Guix
- Department of Radiation Oncology, University of California, San Francicsco
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31
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Frock RL, Sadeghi C, Meng J, Wang JL. DNA End Joining: G0-ing to the Core. Biomolecules 2021; 11:biom11101487. [PMID: 34680120 PMCID: PMC8533500 DOI: 10.3390/biom11101487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/28/2022] Open
Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
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32
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Prodhomme MK, Péricart S, Pommier RM, Morel AP, Brunac AC, Franchet C, Moyret-Lalle C, Brousset P, Puisieux A, Hoffmann JS, Tissier A. Opposite Roles for ZEB1 and TMEJ in the Regulation of Breast Cancer Genome Stability. Front Cell Dev Biol 2021; 9:727429. [PMID: 34458275 PMCID: PMC8388841 DOI: 10.3389/fcell.2021.727429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022] Open
Abstract
Breast cancer cells frequently acquire mutations in faithful DNA repair genes, as exemplified by BRCA-deficiency. Moreover, overexpression of an inaccurate DNA repair pathway may also be at the origin of the genetic instability arising during the course of cancer progression. The specific gain in expression of POLQ, encoding the error-prone DNA polymerase Theta (POLθ) involved in theta-mediated end joining (TMEJ), is associated with a characteristic mutational signature. To gain insight into the mechanistic regulation of POLQ expression, this review briefly presents recent findings on the regulation of POLQ in the claudin-low breast tumor subtype, specifically expressing transcription factors involved in epithelial-to-mesenchymal transition (EMT) such as ZEB1 and displaying a paucity in genomic abnormality.
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Affiliation(s)
- Mélanie K Prodhomme
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Sarah Péricart
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Roxane M Pommier
- Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Anne-Pierre Morel
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Anne-Cécile Brunac
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Camille Franchet
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Caroline Moyret-Lalle
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Pierre Brousset
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Alain Puisieux
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Institut Curie, Versailles Saint-Quentin-en-Yvelines University, PSL Research University, Paris, France
| | - Jean-Sébastien Hoffmann
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Agnès Tissier
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
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33
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Hussain SS, Majumdar R, Moore GM, Narang H, Buechelmaier E, Bazil MJ, Ravindran PT, Leeman J, Li Y, Jalan M, Anderson KS, Farina A, Soni R, Mohibullah N, Hamzic E, Rong-Mullins X, Sifuentes C, Damerla RR, Viale A, Powell SN, Higginson D. Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell. Nucleic Acids Res 2021; 49:e74. [PMID: 33877327 PMCID: PMC8287935 DOI: 10.1093/nar/gkab262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
Double strand break (DSB) repair primarily occurs through 3 pathways: non-homologous end-joining (NHEJ), alternative end-joining (Alt-EJ), and homologous recombination (HR). Typical methods to measure pathway usage include integrated cassette reporter assays or visualization of DNA damage induced nuclear foci. It is now well understood that repair of Cas9-induced breaks also involves NHEJ, Alt-EJ, and HR pathways, providing a new format to measure pathway usage. Here, we have developed a simple Cas9-based system with validated repair outcomes that accurately represent each pathway and then converted it to a droplet digital PCR (ddPCR) readout, thus obviating the need for Next Generation Sequencing and bioinformatic analysis with the goal to make Cas9-based system accessible to more laboratories. The assay system has reproduced several important insights. First, absence of the key Alt-EJ factor Pol θ only abrogates ∼50% of total Alt-EJ. Second, single-strand templated repair (SSTR) requires BRCA1 and MRE11 activity, but not BRCA2, establishing that SSTR commonly used in genome editing is not conventional HR. Third, BRCA1 promotes Alt-EJ usage at two-ended DSBs in contrast to BRCA2. This assay can be used in any system, which permits Cas9 delivery and, importantly, allows rapid genotype-to-phenotype correlation in isogenic cell line pairs.
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Affiliation(s)
- Suleman S Hussain
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Grace M Moore
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Himanshi Narang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erika S Buechelmaier
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Maximilian J Bazil
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Jonathan E Leeman
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02189, USA
| | - Yi Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manisha Jalan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kyrie S Anderson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Farina
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rekha Soni
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neeman Mohibullah
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edin Hamzic
- Biocomputix, Sarajevo, 71000, Bosnia and Herzegovina
| | - Xiaoqing Rong-Mullins
- Department of Biostatistics, The Ohio State University College of Public Health, Columbus, OH 43210, USA
| | | | - Rama R Damerla
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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34
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Herskind C, Barcellos-Hoff MH. Editorial: Cell Signaling Mediating Critical Radiation Responses. Front Oncol 2021; 11:695355. [PMID: 34041040 PMCID: PMC8142942 DOI: 10.3389/fonc.2021.695355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Carsten Herskind
- Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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