1
|
Schmitz EG, Griffith M, Griffith OL, Cooper MA. Identifying genetic errors of immunity due to mosaicism. J Exp Med 2025; 222:e20241045. [PMID: 40232243 PMCID: PMC11998702 DOI: 10.1084/jem.20241045] [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: 01/08/2025] [Revised: 02/24/2025] [Accepted: 03/24/2025] [Indexed: 04/16/2025] Open
Abstract
Inborn errors of immunity are monogenic disorders of the immune system that lead to immune deficiency and/or dysregulation in patients. Identification of precise genetic causes of disease aids diagnosis and advances our understanding of the human immune system; however, a significant portion of patients lack a molecular diagnosis. Somatic mosaicism, genetic changes in a subset of cells, is emerging as an important mechanism of immune disease in both young and older patients. Here, we review the current landscape of somatic genetic errors of immunity and methods for the detection and validation of somatic variants.
Collapse
Affiliation(s)
- Elizabeth G. Schmitz
- Division of Rheumatology/Immunology, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Megan A. Cooper
- Division of Rheumatology/Immunology, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| |
Collapse
|
2
|
Kang E, Suh JK, Kim SD. Constitutional Mismatch Repair Deficiency, the Most Aggressive Cancer Predisposition Syndrome : Clinical Presentation, Surveillance, and Management. J Korean Neurosurg Soc 2025; 68:294-304. [PMID: 40289693 PMCID: PMC12062528 DOI: 10.3340/jkns.2025.0024] [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: 01/21/2025] [Revised: 04/15/2025] [Accepted: 04/20/2025] [Indexed: 04/30/2025] Open
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a rare and highly aggressive cancer predisposition syndrome caused by biallelic germline mutations in mismatch repair genes. This condition is characterized by early-onset malignancies across multiple organ systems, including central nervous system tumors, hematological cancers, and gastrointestinal malignancies. CMMRD-associated tumors exhibit hypermutation and microsatellite instability, resulting in a high tumor mutation burden and rendering these malignancies responsive to immune checkpoint inhibitors (ICIs). ICIs targeting programmed cell death protein-1 and programmed cell death ligand 1 have demonstrated remarkable efficacy, particularly in hypermutated tumors, providing durable responses and improving survival outcomes. Advances in genetic and molecular diagnostics have enhanced the ability to identify CMMRD early, allowing for the implementation of comprehensive surveillance programs and improved management strategies. A multidisciplinary and individualized approach is essential for managing CMMRD patients. This review underscores the importance of early diagnosis, surveillance, and emerging therapeutic approaches to improve outcomes and quality of life for individuals and families affected by this devastating syndrome.
Collapse
Affiliation(s)
- Eungu Kang
- Department of Pediatrics, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Jin Kyung Suh
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang-Dae Kim
- Department of Neurosurgery, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| |
Collapse
|
3
|
Josephides JM, Chen CL. Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression. Nat Commun 2025; 16:1472. [PMID: 39922809 PMCID: PMC11807193 DOI: 10.1038/s41467-025-56783-0] [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: 02/15/2024] [Accepted: 01/29/2025] [Indexed: 02/10/2025] Open
Abstract
Genomic heterogeneity has largely been overlooked in single-cell replication timing (scRT) studies. Here, we develop MnM, an efficient machine learning-based tool that allows disentangling scRT profiles from heterogenous samples. We use single-cell copy number data to accurately perform missing value imputation, identify cell replication states, and detect genomic heterogeneity. This allows us to separate somatic copy number alterations from copy number changes resulting from DNA replication. Our methodology brings critical insights into chromosomal aberrations and highlights the ubiquitous aneuploidy process during tumorigenesis. The copy number and scRT profiles obtained by analysing >119,000 high-quality human single cells from different cell lines, patient tumours and patient-derived xenograft samples leads to a multi-sample heterogeneity-resolved scRT atlas. This atlas is an important resource for cancer research and demonstrates that scRT profiles can be used to study replication timing heterogeneity in cancer. Our findings also highlight the importance of studying cancer tissue samples to comprehensively grasp the complexities of DNA replication because cell lines, although convenient, lack dynamic environmental factors. These results facilitate future research at the interface of genomic instability and replication stress during cancer progression.
Collapse
Affiliation(s)
- Joseph M Josephides
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, Paris, France
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, Paris, France.
| |
Collapse
|
4
|
Shultes PV, Weaver DT, Tadele DS, Barker-Clarke RJ, Scott JG. Cell-cell fusion in cancer: The next cancer hallmark? Int J Biochem Cell Biol 2024; 175:106649. [PMID: 39186970 PMCID: PMC11752790 DOI: 10.1016/j.biocel.2024.106649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/13/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024]
Abstract
In this review, we consider the role of cell-cell fusion in cancer development and progression through an evolutionary lens. We begin by summarizing the origins of fusion proteins (fusogens), of which there are many distinct classes that have evolved through convergent evolution. We then use an evolutionary framework to highlight how the persistence of fusion over generations and across different organisms can be attributed to traits that increase fitness secondary to fusion; these traits map well to the expanded hallmarks of cancer. By studying the tumor microenvironment, we can begin to identify the key selective pressures that may favor higher rates of fusion compared to healthy tissues. The paper concludes by discussing the increasing number of research questions surrounding fusion, recommendations for how to answer them, and the need for a greater interest in exploring cell fusion and evolutionary principles in oncology moving forward.
Collapse
Affiliation(s)
- Paulameena V Shultes
- Translational Hematology and Oncology (THOR), Cleveland Clinic, Cleveland, OH 44120, USA; School of Medicine, Case Western Reserve University, Cleveland, OH 44120, USA
| | - Davis T Weaver
- Translational Hematology and Oncology (THOR), Cleveland Clinic, Cleveland, OH 44120, USA; School of Medicine, Case Western Reserve University, Cleveland, OH 44120, USA
| | - Dagim S Tadele
- Translational Hematology and Oncology (THOR), Cleveland Clinic, Cleveland, OH 44120, USA; Oslo University Hospital, Ullevål, Department of Medical Genetics, Oslo, Norway
| | - Rowan J Barker-Clarke
- Translational Hematology and Oncology (THOR), Cleveland Clinic, Cleveland, OH 44120, USA
| | - Jacob G Scott
- Translational Hematology and Oncology (THOR), Cleveland Clinic, Cleveland, OH 44120, USA; School of Medicine, Case Western Reserve University, Cleveland, OH 44120, USA; Physics Department, Case Western Reserve University, Cleveland, OH 44120, USA.
| |
Collapse
|
5
|
Pushkaran AC, Arabi AA. A review on point mutations via proton transfer in DNA base pairs in the absence and presence of electric fields. Int J Biol Macromol 2024; 277:134051. [PMID: 39069038 DOI: 10.1016/j.ijbiomac.2024.134051] [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: 01/03/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
This comprehensive review focuses on spontaneous mutations that may occur during DNA replication, the fundamental process responsible for transferring genetic information. In 1963, Löwdin postulated that these mutations are primarily a result of proton transfer reactions within the hydrogen-bonded DNA base pairs. The single and double proton transfer reactions within the base pairs in DNA result in zwitterions and rare tautomers, respectively. For persistent mutations, these products must be generated at high rates and should be thermodynamically stable. This review covers the proton transfer reactions studied experimentally and computationally. The review also examines the influence of externally applied electric fields on the thermodynamics and kinetics of proton transfer reactions within DNA base pairs, and their biological implications.
Collapse
Affiliation(s)
- Anju Choorakottayil Pushkaran
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box: 15551, United Arab Emirates
| | - Alya A Arabi
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box: 15551, United Arab Emirates.
| |
Collapse
|
6
|
Wolf SP, Leisegang M, Steiner M, Wallace V, Kiyotani K, Hu Y, Rosenberger L, Huang J, Schreiber K, Nakamura Y, Schietinger A, Schreiber H. CD4 + T cells with convergent TCR recombination reprogram stroma and halt tumor progression in adoptive therapy. Sci Immunol 2024; 9:eadp6529. [PMID: 39270007 PMCID: PMC11560124 DOI: 10.1126/sciimmunol.adp6529] [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: 04/05/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024]
Abstract
Cancers eventually kill hosts even when infiltrated by cancer-specific T cells. We examined whether cancer-specific T cell receptors of CD4+ T cells (CD4TCRs) from tumor-bearing hosts can be exploited for adoptive TCR therapy. We focused on CD4TCRs targeting an autochthonous mutant neoantigen that is only presented by stroma surrounding the MHC class II-negative cancer cells. The 11 most common tetramer-sorted CD4TCRs were tested using TCR-engineered CD4+ T cells. Three TCRs were characterized by convergent recombination for which multiple T cell clonotypes differed in their nucleotide sequences but encoded identical TCR α and β chains. These preferentially selected TCRs destroyed tumors equally well and halted progression through reprogramming of the tumor stroma. TCRs represented by single T cell clonotypes were similarly effective only if they shared CDR elements with preferentially selected TCRs in both α and β chains. Selecting candidate TCRs on the basis of these characteristics can help identify TCRs that are potentially therapeutically effective.
Collapse
Affiliation(s)
- Steven P. Wolf
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago; Chicago, USA
- Department of Pathology, The University of Chicago; Chicago, USA
| | - Matthias Leisegang
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago; Chicago, USA
- Institute of Immunology, Campus Buch, Charité - Universitätsmedizin Berlin; Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Madeline Steiner
- Department of Pathology, The University of Chicago; Chicago, USA
| | - Veronika Wallace
- Department of Pathology, The University of Chicago; Chicago, USA
| | - Kazuma Kiyotani
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research; Tokyo, Japan
- Laboratory of Immunogenomics, Center for Intractable Diseases and ImmunoGenomics (CiDIG), National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-shi, Osaka, Japan
| | - Yifei Hu
- Pritzker School of Molecular Engineering, University of Chicago; Chicago, USA
- Pritzker School of Medicine, University of Chicago; Chicago, USA
| | - Leonie Rosenberger
- Institute of Immunology, Campus Buch, Charité - Universitätsmedizin Berlin; Berlin, Germany
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago; Chicago, USA
- Committees on Cancer Biology and Immunology and the Cancer Center, The University of Chicago; Chicago, USA
| | - Karin Schreiber
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago; Chicago, USA
- Department of Pathology, The University of Chicago; Chicago, USA
| | - Yusuke Nakamura
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research; Tokyo, Japan
- Laboratory of Immunogenomics, Center for Intractable Diseases and ImmunoGenomics (CiDIG), National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-shi, Osaka, Japan
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center; New York, USA
| | - Hans Schreiber
- David and Etta Jonas Center for Cellular Therapy, The University of Chicago; Chicago, USA
- Department of Pathology, The University of Chicago; Chicago, USA
- Committees on Cancer Biology and Immunology and the Cancer Center, The University of Chicago; Chicago, USA
| |
Collapse
|
7
|
Ryu E, Yoo J, Kang MS, Ha NY, Jang Y, Kim J, Kim Y, Kim BG, Kim S, Myung K, Kang S. ATAD5 functions as a regulatory platform for Ub-PCNA deubiquitination. Proc Natl Acad Sci U S A 2024; 121:e2315759121. [PMID: 39145935 PMCID: PMC11348035 DOI: 10.1073/pnas.2315759121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 07/11/2024] [Indexed: 08/16/2024] Open
Abstract
Ubiquitination status of proliferating cell nuclear antigen (PCNA) is crucial for regulating DNA lesion bypass. After the resolution of fork stalling, PCNA is subsequently deubiquitinated, but the underlying mechanism remains undefined. We found that the N-terminal domain of ATAD5 (ATAD5-N), the largest subunit of the PCNA-unloading complex, functions as a scaffold for Ub-PCNA deubiquitination. ATAD5 recognizes DNA-loaded Ub-PCNA through distinct DNA-binding and PCNA-binding motifs. Furthermore, ATAD5 forms a heterotrimeric complex with UAF1-USP1 deubiquitinase, facilitating the deubiquitination of DNA-loaded Ub-PCNA. ATAD5 also enhances the Ub-PCNA deubiquitination by USP7 and USP11 through specific interactions. ATAD5 promotes the distinct deubiquitination process of UAF1-USP1, USP7, and USP11 for poly-Ub-PCNA. Additionally, ATAD5 mutants deficient in UAF1-binding had increased sensitivity to DNA-damaging agents. Our results ultimately reveal that ATAD5 and USPs cooperate to efficiently deubiquitinate Ub-PCNA prior to its release from the DNA in order to safely deactivate the DNA repair process.
Collapse
Affiliation(s)
- Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Juyeong Yoo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Na Young Ha
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Yewon Jang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Jinwoo Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Yeongjae Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Shinseog Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| |
Collapse
|
8
|
Das A, MacFarland SP, Meade J, Hansford JR, Schneider KW, Kuiper RP, Jongmans MCJ, Lesmana H, Schultz KAP, Nichols KE, Durno C, Zelley K, Porter CC, States LJ, Ben-Shachar S, Savage SA, Kalish JM, Walsh MF, Scott HS, Plon SE, Tabori U. Clinical Updates and Surveillance Recommendations for DNA Replication Repair Deficiency Syndromes in Children and Young Adults. Clin Cancer Res 2024; 30:3378-3387. [PMID: 38860976 DOI: 10.1158/1078-0432.ccr-23-3994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/29/2024] [Accepted: 05/02/2024] [Indexed: 06/12/2024]
Abstract
Replication repair deficiency (RRD) is a pan-cancer mechanism characterized by abnormalities in the DNA mismatch repair (MMR) system due to pathogenic variants in the PMS2, MSH6, MSH2, or MLH1 genes, and/or in the polymerase-proofreading genes POLE and POLD1. RRD predisposition syndromes (constitutional MMR deficiency, Lynch, and polymerase proofreading-associated polyposis) share overlapping phenotypic and biological characteristics. Moreover, cancers stemming from germline defects of one mechanism can acquire somatic defects in another, leading to complete RRD. Here we describe the recent advances in the diagnostics, surveillance, and clinical management for children with RRD syndromes. For patients with constitutional MMR deficiency, new data combining clinical insights and cancer genomics have revealed genotype-phenotype associations and helped in the development of novel functional assays, diagnostic guidelines, and surveillance recommendations. Recognition of non-gastrointestinal/genitourinary malignancies, particularly aggressive brain tumors, in select children with Lynch and polymerase proofreading-associated polyposis syndromes harboring an RRD biology have led to new management considerations. Additionally, universal hypermutation and microsatellite instability have allowed immunotherapy to be a paradigm shift in the treatment of RRD cancers independent of their germline etiology. These advances have also stimulated a need for expert recommendations about genetic counseling for these patients and their families. Future collaborative work will focus on newer technologies such as quantitative measurement of circulating tumor DNA and functional genomics to tailor surveillance and clinical care, improving immune surveillance; develop prevention strategies; and deliver these novel discoveries to resource-limited settings to maximize benefits for patients globally.
Collapse
Affiliation(s)
- Anirban Das
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Suzanne P MacFarland
- Division of Oncology, Cancer Predisposition Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Julia Meade
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jordan R Hansford
- Michael Rice Centre for Hematology and Oncology, Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Kami W Schneider
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Harry Lesmana
- Department of Pediatric Hematology/Oncology and BMT, Cleveland Clinic, Cleveland, Ohio
| | - Kris Ann P Schultz
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Carol Durno
- Division of Gastroenterology and Hepatology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Zane Cohen Center, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kristin Zelley
- Hereditary Cancer Predisposition Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Lisa J States
- Department of Radiology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shay Ben-Shachar
- Clalit Research Institute, Ramat-Gan, Tel Aviv University, Tel-Aviv, Israel
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Pediatrics and Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael F Walsh
- Divisions of Solid Tumor and Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hamish S Scott
- Center for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Sharon E Plon
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Uri Tabori
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
9
|
Ash LJ, Busia-Bourdain O, Okpattah D, Kamel A, Liberchuk A, Wolfe AL. KRAS: Biology, Inhibition, and Mechanisms of Inhibitor Resistance. Curr Oncol 2024; 31:2024-2046. [PMID: 38668053 PMCID: PMC11049385 DOI: 10.3390/curroncol31040150] [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: 03/13/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
KRAS is a small GTPase that is among the most commonly mutated oncogenes in cancer. Here, we discuss KRAS biology, therapeutic avenues to target it, and mechanisms of resistance that tumors employ in response to KRAS inhibition. Several strategies are under investigation for inhibiting oncogenic KRAS, including small molecule compounds targeting specific KRAS mutations, pan-KRAS inhibitors, PROTACs, siRNAs, PNAs, and mutant KRAS-specific immunostimulatory strategies. A central challenge to therapeutic effectiveness is the frequent development of resistance to these treatments. Direct resistance mechanisms can involve KRAS mutations that reduce drug efficacy or copy number alterations that increase the expression of mutant KRAS. Indirect resistance mechanisms arise from mutations that can rescue mutant KRAS-dependent cells either by reactivating the same signaling or via alternative pathways. Further, non-mutational forms of resistance can take the form of epigenetic marks, transcriptional reprogramming, or alterations within the tumor microenvironment. As the possible strategies to inhibit KRAS expand, understanding the nuances of resistance mechanisms is paramount to the development of both enhanced therapeutics and innovative drug combinations.
Collapse
Affiliation(s)
- Leonard J. Ash
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Molecular, Cellular, and Developmental Biology Subprogram of the Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
| | - Ottavia Busia-Bourdain
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
| | - Daniel Okpattah
- Biochemistry Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
| | - Avrosina Kamel
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Macaulay Honors College, Hunter College, City University of New York, New York, NY 10065, USA
| | - Ariel Liberchuk
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Macaulay Honors College, Hunter College, City University of New York, New York, NY 10065, USA
| | - Andrew L. Wolfe
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Molecular, Cellular, and Developmental Biology Subprogram of the Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
- Biochemistry Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| |
Collapse
|
10
|
Mao Y, Qian SB. Making sense of mRNA translational "noise". Semin Cell Dev Biol 2024; 154:114-122. [PMID: 36925447 PMCID: PMC10500040 DOI: 10.1016/j.semcdb.2023.03.004] [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: 03/16/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
The importance of translation fidelity has been apparent since the discovery of genetic code. It is commonly believed that translation deviating from the main coding region is to be avoided at all times inside cells. However, ribosome profiling and mass spectrometry have revealed pervasive noncanonical translation. Both the scope and origin of translational "noise" are just beginning to be appreciated. Although largely overlooked, those translational "noises" are associated with a wide range of cellular functions, such as producing unannotated protein products. Furthermore, the dynamic nature of translational "noise" is responsive to stress conditions, highlighting the beneficial effect of translational "noise" in stress adaptation. Mechanistic investigation of translational "noise" will provide better insight into the mechanisms of translational regulation. Ultimately, they are not "noise" at all but represent a signature of cellular activities under pathophysiological conditions. Deciphering translational "noise" holds the therapeutic and diagnostic potential in a wide spectrum of human diseases.
Collapse
Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
11
|
Das A, Fernandez NR, Levine A, Bianchi V, Stengs LK, Chung J, Negm L, Dimayacyac JR, Chang Y, Nobre L, Ercan AB, Sanchez-Ramirez S, Sudhaman S, Edwards M, Larouche V, Samuel D, Van Damme A, Gass D, Ziegler DS, Bielack SS, Koschmann C, Zelcer S, Yalon-Oren M, Campino GA, Sarosiek T, Nichols KE, Loret De Mola R, Bielamowicz K, Sabel M, Frojd CA, Wood MD, Glover JM, Lee YY, Vanan M, Adamski JK, Perreault S, Chamdine O, Hjort MA, Zapotocky M, Carceller F, Wright E, Fedorakova I, Lossos A, Tanaka R, Osborn M, Blumenthal DT, Aronson M, Bartels U, Huang A, Ramaswamy V, Malkin D, Shlien A, Villani A, Dirks PB, Pugh TJ, Getz G, Maruvka YE, Tsang DS, Ertl-Wagner B, Hawkins C, Bouffet E, Morgenstern DA, Tabori U. Combined Immunotherapy Improves Outcome for Replication-Repair-Deficient (RRD) High-Grade Glioma Failing Anti-PD-1 Monotherapy: A Report from the International RRD Consortium. Cancer Discov 2024; 14:258-273. [PMID: 37823831 PMCID: PMC10850948 DOI: 10.1158/2159-8290.cd-23-0559] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/28/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023]
Abstract
Immune checkpoint inhibition (ICI) is effective for replication-repair-deficient, high-grade gliomas (RRD-HGG). The clinical/biological impact of immune-directed approaches after failing ICI monotherapy is unknown. We performed an international study on 75 patients treated with anti-PD-1; 20 are progression free (median follow-up, 3.7 years). After second progression/recurrence (n = 55), continuing ICI-based salvage prolonged survival to 11.6 months (n = 38; P < 0.001), particularly for those with extreme mutation burden (P = 0.03). Delayed, sustained responses were observed, associated with changes in mutational spectra and the immune microenvironment. Response to reirradiation was explained by an absence of deleterious postradiation indel signatures (ID8). CTLA4 expression increased over time, and subsequent CTLA4 inhibition resulted in response/stable disease in 75%. RAS-MAPK-pathway inhibition led to the reinvigoration of peripheral immune and radiologic responses. Local (flare) and systemic immune adverse events were frequent (biallelic mismatch-repair deficiency > Lynch syndrome). We provide a mechanistic rationale for the sustained benefit in RRD-HGG from immune-directed/synergistic salvage therapies. Future approaches need to be tailored to patient and tumor biology. SIGNIFICANCE Hypermutant RRD-HGG are susceptible to checkpoint inhibitors beyond initial progression, leading to improved survival when reirradiation and synergistic immune/targeted agents are added. This is driven by their unique biological and immune properties, which evolve over time. Future research should focus on combinatorial regimens that increase patient survival while limiting immune toxicity. This article is featured in Selected Articles from This Issue, p. 201.
Collapse
Affiliation(s)
- Anirban Das
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatric Haematology and Oncology, Tata Medical Center, Kolkata, India
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Nicholas R. Fernandez
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Adrian Levine
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Lucie K. Stengs
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Jiil Chung
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Logine Negm
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Jose Rafael Dimayacyac
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Yuan Chang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Liana Nobre
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Ayse B. Ercan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Santiago Sanchez-Ramirez
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Valerie Larouche
- Pediatric Haematology/Oncology Department, CHU de Québec-Université Laval, Quebec City, Canada
| | - David Samuel
- Department of Paediatric Oncology, Valley Children's Hospital, Madera, California
| | - An Van Damme
- Department of Paediatric Haematology and Oncology, Saint Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - David Gass
- Atrium Health/Levine Children's Hospital, Charlotte, North Carolina
| | - David S. Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, Australia
| | - Stefan S. Bielack
- Department of Pediatric Oncology, Hematology and Immunology, Center for Childhood, Adolescent, and Women's Medicine, Stuttgart Cancer Center, Klinikum Stuttgart, Stuttgart, Germany
| | - Carl Koschmann
- Pediatric Hematology/Oncology, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Shayna Zelcer
- Department of Pediatrics, London Health Sciences Centre, London, Canada
| | - Michal Yalon-Oren
- Department of Paediatric Haematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Gadi Abede Campino
- Department of Paediatric Haematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | | | - Kim E. Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Kevin Bielamowicz
- Department of Pediatrics, Section of Pediatric Hematology/Oncology, The University of Arkansas for Medical Sciences/Arkansas Children's Hospital, Little Rock, Arkansas
| | - Magnus Sabel
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg & Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Charlotta A. Frojd
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Matthew D. Wood
- Neuropathology, Oregon Health & Science University Department of Pathology, Portland, Oregon
| | - Jason M. Glover
- Department of Pediatric Hematology/Oncology, Randall Children's Hospital, Portland, Oregon
| | - Yi-Yen Lee
- Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Magimairajan Vanan
- Pediatric Hematology-Oncology, CancerCare Manitoba, Winnipeg, Canada
- CancerCare Manitoba Research Institute, Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
| | - Jenny K. Adamski
- Neuro-oncology Division, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Sebastien Perreault
- Neurosciences Department, Child Neurology Division, CHU Sainte-Justine, Montreal, Canada
| | - Omar Chamdine
- Pediatric Hematology Oncology, King Fahad Specialist Hospital Dammam, Eastern Province, Saudi Arabia
| | - Magnus Aasved Hjort
- Department of Paediatric Haematology and Oncology, St. Olav's University Hospital, Trondheim, Norway
| | - Michal Zapotocky
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - Fernando Carceller
- Paediatric and Adolescent Neuro-Oncology and Drug Development, The Royal Marsden NHS Foundation Trust & Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Erin Wright
- Division of Neuro-Oncology, Akron Children's Hospital, Akron, Ohio
| | - Ivana Fedorakova
- Clinic of Pediatric Oncology and Hematology, University Children's Hospital, Banská Bystrica, Slovakia
| | - Alexander Lossos
- Department of Oncology, Leslie and Michael Gaffin Centre for Neuro-Oncology, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - Ryuma Tanaka
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael Osborn
- Women's and Children's Hospital, North Adelaide, Australia
| | - Deborah T. Blumenthal
- Neuro-Oncology Service, Tel-Aviv Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - Ute Bartels
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Annie Huang
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Anita Villani
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Peter B. Dirks
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Trevor J. Pugh
- Ontario Institute for Cancer Research, Princess Margaret Cancer Centre, Toronto, Canada
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Derek S. Tsang
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Birgit Ertl-Wagner
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Eric Bouffet
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Daniel A. Morgenstern
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Uri Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| |
Collapse
|
12
|
Klement RJ. Cancer as a global health crisis with deep evolutionary roots. GLOBAL TRANSITIONS 2024; 6:45-65. [DOI: 10.1016/j.glt.2024.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
|
13
|
Weber CAM, Krönke N, Volk V, Auber B, Förster A, Trost D, Geffers R, Esmaeilzadeh M, Lalk M, Nabavi A, Samii A, Krauss JK, Feuerhake F, Hartmann C, Wiese B, Brand F, Weber RG. Rare germline variants in POLE and POLD1 encoding the catalytic subunits of DNA polymerases ε and δ in glioma families. Acta Neuropathol Commun 2023; 11:184. [PMID: 37990341 PMCID: PMC10664377 DOI: 10.1186/s40478-023-01689-5] [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: 08/23/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023] Open
Abstract
Pathogenic germline variants in the DNA polymerase genes POLE and POLD1 cause polymerase proofreading-associated polyposis, a dominantly inherited disorder with increased risk of colorectal carcinomas and other tumors. POLE/POLD1 variants may result in high somatic mutation and neoantigen loads that confer susceptibility to immune checkpoint inhibitors (ICIs). To explore the role of POLE/POLD1 germline variants in glioma predisposition, whole-exome sequencing was applied to leukocyte DNA of glioma patients from 61 tumor families with at least one glioma case each. Rare heterozygous POLE/POLD1 missense variants predicted to be deleterious were identified in glioma patients from 10 (16%) families, co-segregating with the tumor phenotype in families with available DNA from several tumor patients. Glioblastoma patients carrying rare POLE variants had a mean overall survival of 21 months. Additionally, germline variants in POLD1, located at 19q13.33, were detected in 2/34 (6%) patients with 1p/19q-codeleted oligodendrogliomas, while POLE variants were identified in 2/4 (50%) glioblastoma patients with a spinal metastasis. In 13/15 (87%) gliomas from patients carrying POLE/POLD1 variants, features of defective polymerase proofreading, e.g. hypermutation, POLE/POLD1-associated mutational signatures, multinucleated cells, and increased intratumoral T cell response, were observed. In a CRISPR/Cas9-derived POLE-deficient LN-229 glioblastoma cell clone, a mutator phenotype and delayed S phase progression were detected compared to wildtype POLE cells. Our data provide evidence that rare POLE/POLD1 germline variants predispose to gliomas that may be susceptible to ICIs. Data compiled here suggest that glioma patients carrying POLE/POLD1 variants may be recognized by cutaneous manifestations, e.g. café-au-lait macules, and benefit from surveillance colonoscopy.
Collapse
Affiliation(s)
- Christine A M Weber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Nicole Krönke
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Valery Volk
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Alisa Förster
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | | | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Michael Lalk
- Department of Neurosurgery, KRH Klinikum Nordstadt, Hannover, Germany
| | - Arya Nabavi
- Department of Neurosurgery, KRH Klinikum Nordstadt, Hannover, Germany
| | - Amir Samii
- Department of Neurosurgery, International Neuroscience Institute, Hannover, Germany
| | - Joachim K Krauss
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Friedrich Feuerhake
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
- Institute for Neuropathology, University Clinic Freiburg, Freiburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Bettina Wiese
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
- Department of Neurology, Henriettenstift, Diakovere Krankenhaus gGmbH, Hannover, Germany
| | - Frank Brand
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Ruthild G Weber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| |
Collapse
|
14
|
Strauss JD, Pursell ZF. Replication DNA polymerases, genome instability and cancer therapies. NAR Cancer 2023; 5:zcad033. [PMID: 37388540 PMCID: PMC10304742 DOI: 10.1093/narcan/zcad033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
Collapse
Affiliation(s)
- Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| |
Collapse
|
15
|
Abdullahi A, Wong TWL, Ng SSM. Putative role of non-invasive vagus nerve stimulation in cancer pathology and immunotherapy: Can this be a hidden treasure, especially for the elderly? Cancer Med 2023; 12:19081-19090. [PMID: 37587897 PMCID: PMC10557911 DOI: 10.1002/cam4.6466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
Cancer is globally a disease of significant public health concern owing to its prevalence, and association with morbidity and mortality. Thus, cost-effective treatments for cancer are important to help reduce its significant morbidity and mortality. However, the current therapeutic options for cancer such as chemotherapy, radiotherapy, and surgery may produce serious adverse events such as nausea, vomiting, fatigue, and peripheral neuropathy, especially in the long term. In addition, these therapeutic options may not be well tolerated by the elderly especially those who are frail. The current article is aimed at discussing an alternative therapeutic option, non-invasive vagus nerve stimulation (VNS), and the roles it plays in cancer pathology and immunotherapy. The VNS does this by reducing oxidative stress via silent information regulator 1 (SIRT1); inhibiting inflammation via both hypothalamic-pituitary-axis (HPA) and the release of corticosteroid from the adrenal gland, and cholinergic anti-inflammatory pathway (CAP), and increasing vagal activity which helps in the regulation of cell proliferation, differentiation, apoptosis, and metabolism, and increase chance of survival. Furthermore, it helps with reducing complications due to cancer or its treatments such as postoperative ileus and severity of peripheral neuropathy induced by chemotherapy, and improves cancer-related fatigue, lymphopenia, and quality of life. These suggest that the importance of non-invasive VNS in cancer pathology and immunotherapy cannot be overemphasized. Therefore, considering the safety of non-invasive VNS and its cost-effectiveness, it is a therapeutic option worth trying for these patients, especially in combination with other therapies.
Collapse
Affiliation(s)
- Auwal Abdullahi
- Department of Rehabilitation SciencesThe Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina
| | - Thomson W. L. Wong
- Department of Rehabilitation SciencesThe Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina
| | - Shamay S. M. Ng
- Department of Rehabilitation SciencesThe Hong Kong Polytechnic UniversityKowloonHong Kong Special Administrative RegionChina
| |
Collapse
|
16
|
Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY, Reik W, Sharifi S, Suh Y, Walsh K. Mitigating age-related somatic mutation burden. Trends Mol Med 2023; 29:530-540. [PMID: 37121869 PMCID: PMC11816329 DOI: 10.1016/j.molmed.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
Abstract
Genomes are inherently unstable and require constant DNA repair to maintain their genetic information. However, selective pressure has optimized repair mechanisms in somatic cells only to allow transmitting genetic information to the next generation, not to maximize sequence integrity long beyond the reproductive age. Recent studies have confirmed that somatic mutations, due to errors during genome repair and replication, accumulate in tissues and organs of humans and model organisms. Here, we describe recent advances in the quantitative analysis of somatic mutations in vivo. We also review evidence for or against a possible causal role of somatic mutations in aging. Finally, we discuss options to prevent, delay or eliminate de novo, random somatic mutations as a cause of aging.
Collapse
Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Center for Single-Cell Omics, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University and University Hospital of Cologne, Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Abdulkadir Abakir
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
| | | | | | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wolf Reik
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK; Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| |
Collapse
|
17
|
Zhang L, De Cecco M, Lee M, Hao X, Maslov AY, Montagna C, Campisi J, Dong X, Sedivy JM, Vijg J. Analysis of Somatic Mutations in Senescent Cells Using Single-Cell Whole-Genome Sequencing. AGING BIOLOGY 2023; 1:20230005. [PMID: 39421602 PMCID: PMC11484980 DOI: 10.59368/agingbio.20230005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Somatic mutations accumulate in multiple organs and tissues during aging and are a known cause of cancer. Cellular senescence is a possible cause of functional decline in aging, yet also acts as an anticancer mechanism in vivo. Here, we compared somatic mutation burden between early passage and deeply senescent human fibroblasts using single-cell whole-genome sequencing. The results show that single-nucleotide variants (SNVs) and small insertions and deletions (INDELs) are increased in senescent cells by about twofold but have the same mutational signature as early passage cells. The increase in SNVs and INDELs can be explained by increased replication errors due to the increased number of cell divisions senescent cells are likely to have undergone. By contrast, a stark increase of aneuploidies was observed in deeply senescent cells, with about half of all senescent cells affected but none of the early passage cells analyzed. These results indicate that large chromosomal events rather than small base substitutions or insertions and deletions could be mechanistically linked to cellular senescence.
Collapse
Affiliation(s)
- Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xiaoxiao Hao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technology, Voronezh, Russia
| | - Cristina Montagna
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
18
|
Abildgaard AB, Nielsen SV, Bernstein I, Stein A, Lindorff-Larsen K, Hartmann-Petersen R. Lynch syndrome, molecular mechanisms and variant classification. Br J Cancer 2023; 128:726-734. [PMID: 36434153 PMCID: PMC9978028 DOI: 10.1038/s41416-022-02059-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Patients with the heritable cancer disease, Lynch syndrome, carry germline variants in the MLH1, MSH2, MSH6 and PMS2 genes, encoding the central components of the DNA mismatch repair system. Loss-of-function variants disrupt the DNA mismatch repair system and give rise to a detrimental increase in the cellular mutational burden and cancer development. The treatment prospects for Lynch syndrome rely heavily on early diagnosis; however, accurate diagnosis is inextricably linked to correct clinical interpretation of individual variants. Protein variant classification traditionally relies on cumulative information from occurrence in patients, as well as experimental testing of the individual variants. The complexity of variant classification is due to (1) that variants of unknown significance are rare in the population and phenotypic information on the specific variants is missing, and (2) that individual variant testing is challenging, costly and slow. Here, we summarise recent developments in high-throughput technologies and computational prediction tools for the assessment of variants of unknown significance in Lynch syndrome. These approaches may vastly increase the number of interpretable variants and could also provide important mechanistic insights into the disease. These insights may in turn pave the road towards developing personalised treatment approaches for Lynch syndrome.
Collapse
Affiliation(s)
- Amanda B Abildgaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Inge Bernstein
- Department of Surgical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Institute of Clinical Medicine, Aalborg University Hospital, Aalborg University, Aalborg, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
19
|
Genome-wide siRNA screens identify RBBP9 function as a potential target in Fanconi anaemia-deficient head-and-neck squamous cell carcinoma. Commun Biol 2023; 6:37. [PMID: 36639418 PMCID: PMC9839743 DOI: 10.1038/s42003-022-04389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Fanconi anaemia (FA) is a rare chromosomal-instability syndrome caused by mutations of any of the 22 known FA DNA-repair genes. FA individuals have an increased risk of head-and-neck squamous-cell-carcinomas (HNSCC), often fatal. Systemic intolerance to standard cisplatin-based protocols due to somatic-cell hypersensitivity underscores the urgent need to develop novel therapies. Here, we performed unbiased siRNA screens to unveil genetic interactions synthetic-lethal with FA-pathway deficiency in FA-patient HNSCC cell lines. We identified based on differential-lethality scores between FA-deficient and FA-proficient cells, next to common-essential genes such as PSMC1, PSMB2, and LAMTOR2, the otherwise non-essential RBBP9 gene. Accordingly, low dose of the FDA-approved RBBP9-targeting drug Emetine kills FA-HNSCC. Importantly both RBBP9-silencing as well as Emetine spared non-tumour FA cells. This study provides a minable genome-wide analyses of vulnerabilities to address treatment challenges in FA-HNSCC. Our investigation divulges a DNA-cross-link-repair independent lead, RBBP9, for targeted treatment of FA-HNSCCs without systemic toxicity.
Collapse
|
20
|
Ren P, Dong X, Vijg J. Age-related somatic mutation burden in human tissues. FRONTIERS IN AGING 2022; 3:1018119. [PMID: 36213345 PMCID: PMC9534562 DOI: 10.3389/fragi.2022.1018119] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The genome of multicellular organisms carries the hereditary information necessary for the development of all organs and tissues and to maintain function in adulthood. To ensure the genetic stability of the species, genomes are protected against changes in sequence information. However, genomes are not static. De novo mutations in germline cells are passed on to offspring and generate the variation needed in evolution. Moreover, postzygotic mutations occur in all somatic cells during development and aging. These somatic mutations remain limited to the individual, generating tissues that are genome mosaics. Insight into such mutations and their consequences has been limited due to their extremely low abundance, with most mutations unique for each cell. Recent advances in sequencing, including whole genome sequencing at the single-cell level, have now led to the first insights into somatic mutation burdens in human tissues. Here, we will first briefly describe the latest methodology for somatic mutation analysis, then review our current knowledge of somatic mutation burden in human tissues and, finally, briefly discuss the possible functional impact of somatic mutations on the aging process and age-related diseases, including cancer and diseases other than cancer.
Collapse
Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Xiao Dong
- Department of Genetics, Cell Biology and Development, Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Department of Genetics, Albert Einstein College of Medicine, New York City, NY, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| |
Collapse
|
21
|
Ma X, Dong L, Liu X, Ou K, Yang L. POLE/POLD1 mutation and tumor immunotherapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:216. [PMID: 35780178 PMCID: PMC9250176 DOI: 10.1186/s13046-022-02422-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/17/2022] [Indexed: 12/30/2022]
Abstract
POLE and POLD1 encode the catalytic and proofreading subunits of DNA polymerase ε and polymerase δ, and play important roles in DNA replication and proofreading. POLE/POLD1 exonuclease domain mutations lead to loss of proofreading function, which causes the accumulation of mutant genes in cells. POLE/POLD1 mutations are not only closely related to tumor formation, but are also a potential molecular marker for predicting the efficacy of immunotherapy in pan-carcinomatous species. The association of POLE/POLD1 mutation, ultra-high mutation load, and good prognosis have recently become the focus of clinical research. This article reviews the function of POLE/POLD1, its relationship with deficient mismatch repair/high microsatellite instability, and the role of POLE/POLD1 mutation in the occurrence and development of various tumors.
Collapse
Affiliation(s)
- Xiaoting Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiu Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kai Ou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| |
Collapse
|
22
|
Gatto L, Franceschi E, Tosoni A, Nunno VD, Bartolini S, Brandes AA. Hypermutation as a potential predictive biomarker of immunotherapy efficacy in high-grade gliomas: a broken dream? Immunotherapy 2022; 14:799-813. [PMID: 35670093 DOI: 10.2217/imt-2021-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A high tumor mutational burden and mismatch repair deficiency are observed in 'hypermutated' high-grade gliomas (HGGs); however, the molecular characterization of this distinct subtype and whether it predicts the response to immune checkpoint inhibitors (ICIs) are largely unknown. Pembrolizumab is a valid therapeutic option for the treatment of hypermutated cancers of diverse origin, but only a few clinical trials have explored the activity of ICIs in hypermutated HGGs. HGGs appear to differ from other cancers, likely due to the prevalence of subclonal versus clonal neoantigens, which are unable to elicit an immune response with ICIs. The main aim of this review is to summarize the current knowledge on hypermutation in HGGs, focusing on the broken promises of tumor mutational burden and mismatch repair deficiency as potential biomarkers of response to ICIs.
Collapse
Affiliation(s)
- Lidia Gatto
- Department of Oncology, AUSL Bologna, Bologna, Italy
| | - Enrico Franceschi
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Alicia Tosoni
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Stefania Bartolini
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Alba Ariela Brandes
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| |
Collapse
|
23
|
Nayak DA, Binder RJ. Agents of cancer immunosurveillance: HSPs and dsDNA. Trends Immunol 2022; 43:404-413. [PMID: 35382994 PMCID: PMC9058224 DOI: 10.1016/j.it.2022.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
Tumor immunosurveillance requires tumor cell-derived molecules to initiate responses through corresponding receptors on antigen presenting cells (APCs) and a specific effector response designed to eliminate the emerging tumor cells. This is supported by evidence from immunodeficient individuals and experimental animals. Recent discoveries suggest that adjuvanticity of tumor-derived heat shock proteins (HSPs) and double-stranded DNA (dsDNA) are necessary for tumor-specific immunity. There is also the obligatory early transfer of tumor antigens to APCs. We argue that tumor-derived HSPs deliver sufficient chaperoned antigen for cross-priming within the quantitative limits set by nascent tumors. In contrast to late-stage tumors, we are only just beginning to understand the unique interactions of the immune system with precancerous/nascent neoplastic cells, which is important for improved cancer prevention measures.
Collapse
|
24
|
Cadherin‑16 inhibits thyroid carcinoma cell proliferation and invasion. Oncol Lett 2022; 23:145. [PMID: 35350592 PMCID: PMC8941525 DOI: 10.3892/ol.2022.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/04/2022] [Indexed: 11/11/2022] Open
Abstract
Cadherin-16 (CDH16), a member of the cadherin family of adhesion molecules, serves an important role in the formation and maintenance of the thyroid follicular lumen. Decreased expression of CDH16 has been reported to be associated with tumor stage in papillary thyroid cancer (PTC); however, previous analyses have been limited and the biological role of CDH16 in different subtypes of TC is unknown. To investigate the role of CDH16 in the occurrence and development of TC, bioinformatic analysis of three TC subtypes (PTC, follicular cell-derived TC and anaplastic TC) was performed using an extended data set from the Gene Expression Omnibus database, with additional confirmation using data from The Cancer Genome Atlas, as well as biopsies from 35 patients with PTC and TC or follicular cell lines. According to the dataset analysis, CDH16 was downregulated in PTC and follicular cell-derived and anaplastic TC; the downregulation in PTC was independent of DNA copy number variation. Furthermore, low expression levels of CDH16 were significantly correlated with tumor size, lymph node metastasis status and disease stage in 35 patients with PTC. Gene Set Enrichment Analysis suggested that CDH16 participated in DNA replication and cell adhesion pathways. To evaluate CDH16 activity, CDH16 was overexpressed in TC-derived BCPAP cells. CDH16 overexpression inhibited cell proliferation, migration and invasion and induced apoptosis by downregulating proteins associated with DNA replication and cell adhesion. These results support the identification of CDH16 as a valuable target for TC prognosis and therapy and, to the best of our knowledge, represent the first direct demonstration of its mechanistic role in TC.
Collapse
|
25
|
Usman M, Okla MK, Asif HM, AbdElgayed G, Muccee F, Ghazanfar S, Ahmad M, Iqbal MJ, Sahar AM, Khaliq G, Shoaib R, Zaheer H, Hameed Y. A pan-cancer analysis of GINS complex subunit 4 to identify its potential role as a biomarker in multiple human cancers. Am J Cancer Res 2022; 12:986-1008. [PMID: 35411239 PMCID: PMC8984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023] Open
Abstract
This study was initiated to explore the expression variation, clinical significance, and biological importance of the GINS complex subunit 4 (GINS4) in different human cancers as a shared biomarker via pan-cancer analysis through different platforms including UALCAN, Kaplan Meier (KM) plotter, TNMplot, GENT2, GEPIA, DriverDBv3, Human Protein Atlas (HPA), MEXPRESS, cBioportal, STRING, DAVID, MuTarge, Enrichr, TIMER, and CTD. Our findings have verified the up-regulation of GINS4 in 24 major subtypes of human cancers, and its overexpression was found to be substantially associated with poor overall survival (OS), relapse-free survival (RFs), and metastasis in ESCA, KIRC, LIHC, LUAD, and UCEC. This suggested that GINS4 plays a significant role in the development and progression of these five cancers. Furthermore, we noticed that GINS4 is also overexpressed in ESCA, KIRC, LIHC, LUAD, and UCEC patients with different clinicopathological characteristics. Enrichment analysis revealed the involvement of GINS4 associated genes in a variety of diverse GO and KEGG terms. We also explored few significant correlations between GINS4 expression and promoter methylation, genetic alterations, CNVs, other mutant genes, tumor purity, and immune cells infiltration. In conclusion, our results elucidated that GINS4 can serve as a shared diagnostic, prognostic biomarker, and a potential therapeutic target in ESCA, KIRC, LIHC, LUAD, and UCEC patients with different clinicopathological characteristics.
Collapse
Affiliation(s)
- Muhammad Usman
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | - Mohammad K Okla
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Hafiz Muhammad Asif
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
| | - Gehad AbdElgayed
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp2020 Antwerp, Belgium
| | - Fatima Muccee
- Department of Biotechnology, Virtual University of PakistanLahore 54000, Pakistan
| | - Shakira Ghazanfar
- Functional Genomics and Bioinformatics, National Agricultural Research CentreIslamabad 45500, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | | | - Aamina Murad Sahar
- Department of Biosciences, COMSATS University IslamabadIslamabad 4400, Pakistan
| | - Ghania Khaliq
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences BahawalpurBahawalpur 63100, Pakistan
| | - Rabbia Shoaib
- Department of Chemistry, Government College University FaisalabadFaisalabad 3800, Pakistan
| | - Hira Zaheer
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| |
Collapse
|
26
|
Gong X, Cheng J, Zhang K, Wang Y, Li S, Luo Y. Transcriptome sequencing reveals Gastrodia elata Blume could increase the cell viability of eNPCs under hypoxic condition by improving DNA damage repair ability. JOURNAL OF ETHNOPHARMACOLOGY 2022; 282:114646. [PMID: 34530095 DOI: 10.1016/j.jep.2021.114646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gastrodia elata Blume (GEB), known as Tianma in China, is a traditional medicinal herb that has been reported to have various pharmacological effects and neuroprotection, has long been used for treating dizziness, epilepsy, stroke. However, explanation of its underlying mechanisms remains a great challenge. AIM OF THE STUDY The neuroprotective mechanism of GEB on hypoxia-induced neuronal injury in cultured mouse embryonic neural progenitor cells (eNPCs) was investigated, with emphasis on the eNPCs proliferation and DNA damage repair. MATERIALS AND METHODS In this study, hypoxia was focused, which may be caused by stroke or acute cerebral ischemia and is considered as one of the important factors contributing to the Central Nervous System diseases. CoCl2 was adopted to construct a hypoxic/ischemic condition in eNPCs. eNPCs proliferation analysis validated GEB neuroprotective effect under hypoxic/ischemic condition. Transcriptome and weighted gene co-expression network analysis (WGCNA) screened the special gene-network module correlated with what appeared to have significant positive correlation with GEB. Then, Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed to explore the biological functions of selected genes in the modules that had high correlation with GEB. RESULTS GEB has neuroprotective effect and could rescue eNPCs proliferation under hypoxic/ischemic condition induced by CoCl2. Transcriptome and WGCNA unveil the neuroprotective mechanism of GEB on improving DNA damage repair ability by increasing the expression of genes associated with DNA repair and replication. Western blotting and qPCR showed that GEB could improve DNA damage repair ability by increasing the expression of Mcm2, Mcm6, Pold2, Pole, Pole2, Rfc1, Pole4, Dna2 and Rpa2, which were associated with DNA damage and replication. CONCLUSION Through transcriptome and WGCNA, this study unveiled Gastrodia elata Blume could increase the cell viability of eNPCs under hypoxic condition by improving DNA damage repair ability.
Collapse
Affiliation(s)
- Xi Gong
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China
| | - Jing Cheng
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China
| | - Kunshan Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Yanlu Wang
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yuping Luo
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 999 Xuefu Rd., Honggutan New District, Nanchang, Jiangxi, 330031, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| |
Collapse
|
27
|
Fang H, Zhu X, Yang H, Oh J, Barbour JA, Wong JWH. Deficiency of replication-independent DNA mismatch repair drives a 5-methylcytosine deamination mutational signature in cancer. SCIENCE ADVANCES 2021; 7:eabg4398. [PMID: 34730999 PMCID: PMC8565909 DOI: 10.1126/sciadv.abg4398] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Multiple mutational signatures have been associated with DNA mismatch repair (MMR)–deficient cancers, but the mechanisms underlying their origin remain unclear. Here, using mutation data from cancer genomes, we identify a previously unknown function of MMR that is able to protect genomes from 5-methylcytosine (5mC) deamination–induced somatic mutations in a replication-independent manner. Cancers with deficiency of MMR proteins MSH2/MSH6 (MutSα) exhibit mutational signature contributions distinct from those that are deficient in MLH1/PMS2 (MutLα). This disparity arises from unrepaired 5mC deamination–induced mismatches rather than replicative DNA polymerase errors. In cancers with biallelic loss of MBD4 DNA glycosylase, repair of 5mC deamination damage is strongly associated with H3K36me3 chromatin, implicating MutSα as the essential factor in its repair. We thus uncover a noncanonical role of MMR in the protection against 5mC deamination–induced mutation in human cancers.
Collapse
|
28
|
Ying J, Yang L, Yin JC, Xia G, Xing M, Chen X, Pang J, Wu Y, Bao H, Wu X, Shao Y, Zhu L, Cheng X. Additive effects of variants of unknown significance in replication repair-associated DNA polymerase genes on mutational burden and prognosis across diverse cancers. J Immunother Cancer 2021; 9:jitc-2021-002336. [PMID: 34479923 PMCID: PMC8420654 DOI: 10.1136/jitc-2021-002336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Defects in replication repair-associated DNA polymerases often manifest an ultra-high tumor mutational burden (TMB), which is associated with higher probabilities of response to immunotherapies. The functional and clinical implications of different polymerase variants remain unclear. METHODS Targeted next-generation sequencing using a 425-cancer gene panel, which covers all exonic regions of three polymerase genes (POLE, POLD1, and POLH), was conducted in a cohort of 12,266 patients across 16 different tumor types from January 2017 to January 2019. Prognostication of POL variant-positive patients was performed using a cohort of 4679 patients from the The Cancer Genome Atlas (TCGA) datasets. RESULTS The overall prevalence of somatic and germline polymerase variants was 4.2% (95% CI 3.8% to 4.5%) and 0.7% (95% CI 0.5% to 0.8%), respectively, with highest frequencies in endometrial, urinary, prostate, and colorectal cancers (CRCs). While most germline polymerase variants showed no clear functional consequences, we identified a candidate p.T466A affecting the exonuclease domain of POLE, which might be underlying the early onset in a case with childhood CRC. Low frequencies of known hot-spot somatic mutations in POLE were detected and were associated with younger age, the male sex, and microsatellite stability. In both the panel and TCGA cohorts, POLE drivers exhibited high frequencies of alterations in genes in the DNA damage and repair (DDR) pathways, including BRCA2, ATM, MSH6, and ATR. Variants of unknown significance (VUS) of different polymerase domains showed variable penetrance with those in the exonuclease domain of POLE and POLD1 displaying high TMB. VUS in POL genes exhibited an additive effect as carriers of multiple VUS had exponentially increased TMB and prolonged overall survival. Similar to cases with driver mutations, the TMB-high POL VUS samples showed DDR pathway involvement and polymerase hypermutation signatures. Combinatorial analysis of POL and DDR pathway status further supported the potential additive effects of POL VUS and DDR pathway genes and revealed distinct prognostic subclasses that were independent of cancer type and TMB. CONCLUSIONS Our results demonstrate the pathogenicity and additive prognostic value of POL VUS and DDR pathway gene alterations and suggest that genetic testing may be warranted in patients with diverse solid tumors.
Collapse
Affiliation(s)
- Jieer Ying
- Department of Abdominal Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Lin Yang
- Department of Medical Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiani C Yin
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Guojie Xia
- Department of Medical Oncology, Traditional Chinese Medical Hospital of Huzhou, Huzhou, China
| | - Minyan Xing
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang University, Haining, Zhejiang, China
| | - Xiaoxi Chen
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yong Wu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lingjun Zhu
- Department of Oncology, Sir Run Run Hospital Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiangdong Cheng
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China .,Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
| |
Collapse
|
29
|
Katerji M, Duerksen-Hughes PJ. DNA damage in cancer development: special implications in viral oncogenesis. Am J Cancer Res 2021; 11:3956-3979. [PMID: 34522461 PMCID: PMC8414375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/04/2021] [Indexed: 06/13/2023] Open
Abstract
DNA lesions arise from a combination of physiological/metabolic sources and exogenous environmental influences. When left unrepaired, these alterations accumulate in the cells and can give rise to mutations that change the function of important proteins (i.e. tumor suppressors, oncoproteins), or cause chromosomal rearrangements (i.e. gene fusions) that also result in the deregulation of key cellular molecules. Progressive acquisition of such genetic changes promotes uncontrolled cell proliferation and evasion of cell death, and hence plays a key role in carcinogenesis. Another less-studied consequence of DNA damage accumulating in the host genome is the integration of oncogenic DNA viruses such as Human papillomavirus, Merkel cell polyomavirus, and Hepatitis B virus. This critical step of viral-induced carcinogenesis is thought to be particularly facilitated by DNA breaks in both viral and host genomes. Therefore, the impact of DNA damage on carcinogenesis is magnified in the case of such oncoviruses via the additional effect of increasing integration frequency. In this review, we briefly present the various endogenous and exogenous factors that cause different types of DNA damage. Next, we discuss the contribution of these lesions in cancer development. Finally, we examine the amplified effect of DNA damage in viral-induced oncogenesis and summarize the limited data existing in the literature related to DNA damage-induced viral integration. To conclude, additional research is needed to assess the DNA damage pathways involved in the transition from viral infection to cancer. Discovering that a certain DNA damaging agent increases the likelihood of viral integration will enable the development of prophylactic and therapeutic strategies designed specifically to prevent such integration, with an ultimate goal of reducing or eliminating these viral-induced malignancies.
Collapse
Affiliation(s)
- Meghri Katerji
- Department of Basic Science, Loma Linda University School of Medicine Loma Linda, CA 92354, USA
| | | |
Collapse
|
30
|
Durno C, Ercan AB, Bianchi V, Edwards M, Aronson M, Galati M, Atenafu EG, Abebe-Campino G, Al-Battashi A, Alharbi M, Azad VF, Baris HN, Basel D, Bedgood R, Bendel A, Ben-Shachar S, Blumenthal DT, Blundell M, Bornhorst M, Bronsema A, Cairney E, Rhode S, Caspi S, Chamdin A, Chiaravalli S, Constantini S, Crooks B, Das A, Dvir R, Farah R, Foulkes WD, Frenkel Z, Gallinger B, Gardner S, Gass D, Ghalibafian M, Gilpin C, Goldberg Y, Goudie C, Hamid SA, Hampel H, Hansford JR, Harlos C, Hijiya N, Hsu S, Kamihara J, Kebudi R, Knipstein J, Koschmann C, Kratz C, Larouche V, Lassaletta A, Lindhorst S, Ling SC, Link MP, Loret De Mola R, Luiten R, Lurye M, Maciaszek JL, MagimairajanIssai V, Maher OM, Massimino M, McGee RB, Mushtaq N, Mason G, Newmark M, Nicholas G, Nichols KE, Nicolaides T, Opocher E, Osborn M, Oshrine B, Pearlman R, Pettee D, Rapp J, Rashid M, Reddy A, Reichman L, Remke M, Robbins G, Roy S, Sabel M, Samuel D, Scheers I, Schneider KW, Sen S, Stearns D, Sumerauer D, Swallow C, Taylor L, Thomas G, Toledano H, Tomboc P, Van Damme A, Winer I, Yalon M, Yen LY, Zapotocky M, Zelcer S, Ziegler DS, et alDurno C, Ercan AB, Bianchi V, Edwards M, Aronson M, Galati M, Atenafu EG, Abebe-Campino G, Al-Battashi A, Alharbi M, Azad VF, Baris HN, Basel D, Bedgood R, Bendel A, Ben-Shachar S, Blumenthal DT, Blundell M, Bornhorst M, Bronsema A, Cairney E, Rhode S, Caspi S, Chamdin A, Chiaravalli S, Constantini S, Crooks B, Das A, Dvir R, Farah R, Foulkes WD, Frenkel Z, Gallinger B, Gardner S, Gass D, Ghalibafian M, Gilpin C, Goldberg Y, Goudie C, Hamid SA, Hampel H, Hansford JR, Harlos C, Hijiya N, Hsu S, Kamihara J, Kebudi R, Knipstein J, Koschmann C, Kratz C, Larouche V, Lassaletta A, Lindhorst S, Ling SC, Link MP, Loret De Mola R, Luiten R, Lurye M, Maciaszek JL, MagimairajanIssai V, Maher OM, Massimino M, McGee RB, Mushtaq N, Mason G, Newmark M, Nicholas G, Nichols KE, Nicolaides T, Opocher E, Osborn M, Oshrine B, Pearlman R, Pettee D, Rapp J, Rashid M, Reddy A, Reichman L, Remke M, Robbins G, Roy S, Sabel M, Samuel D, Scheers I, Schneider KW, Sen S, Stearns D, Sumerauer D, Swallow C, Taylor L, Thomas G, Toledano H, Tomboc P, Van Damme A, Winer I, Yalon M, Yen LY, Zapotocky M, Zelcer S, Ziegler DS, Zimmermann S, Hawkins C, Malkin D, Bouffet E, Villani A, Tabori U. Survival Benefit for Individuals With Constitutional Mismatch Repair Deficiency Undergoing Surveillance. J Clin Oncol 2021; 39:2779-2790. [PMID: 33945292 PMCID: PMC8407605 DOI: 10.1200/jco.20.02636] [Show More Authors] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Constitutional mismatch repair deficiency syndrome (CMMRD) is a lethal cancer predisposition syndrome characterized by early-onset synchronous and metachronous multiorgan tumors. We designed a surveillance protocol for early tumor detection in these individuals.
Collapse
Affiliation(s)
- Carol Durno
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada.,Mount Sinai Hospital, The Familial Gastrointestinal Cancer Registry at the Zane Cohen Centre for Digestive Disease, Toronto, ON, Canada
| | - Ayse Bahar Ercan
- The Hospital for Sick Children, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada.,University of Toronto, Institute of Medical Science, Toronto, ON, Canada
| | - Vanessa Bianchi
- The Hospital for Sick Children, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
| | - Melissa Edwards
- The Hospital for Sick Children, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
| | - Melyssa Aronson
- Mount Sinai Hospital, The Familial Gastrointestinal Cancer Registry at the Zane Cohen Centre for Digestive Disease, Toronto, ON, Canada
| | - Melissa Galati
- The Hospital for Sick Children, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada.,University of Toronto, Institute of Medical Science, Toronto, ON, Canada
| | - Eshetu G Atenafu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Gadi Abebe-Campino
- Department of Pediatric Hematology-Oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Abeer Al-Battashi
- Ministry of Health Oman, Child Health Specialist Muscat, Muscat, Oman
| | - Musa Alharbi
- Department of Pediatric Hematology Oncology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Vahid Fallah Azad
- MAHAK Pediatric Cancer Treatment and Research Center (MPCTRC), Tehran, Iran
| | - Hagit N Baris
- Rambam Health Care Campus, The Genetics Institute, Haifa, Israel
| | - Donald Basel
- Medical College of Wisconsin, Pediatrics, Milwaukee, WI
| | | | - Anne Bendel
- Department of Pediatric Hematology-Oncology, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
| | - Shay Ben-Shachar
- Tel Aviv Sourasky Medical Center, Genetic Institute, Tel Aviv, Israel
| | - Deborah T Blumenthal
- Oncology Division, Tel Aviv University Sackler Faculty of Medicine, Tel Aviv, Israel
| | | | - Miriam Bornhorst
- Children's National Medical Center, Brain Tumor Institute, Washington, DC
| | - Annika Bronsema
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elizabeth Cairney
- Department of Pediatrics, London Health Sciences Centre, London, ON, Canada
| | - Sara Rhode
- Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Shani Caspi
- Sheba Medical Center, Cancer Research Center, Tel Hashomer, Israel
| | - Aghiad Chamdin
- Michigan State University, College of Human Medicine, Center for Bleeding and Clotting Disorders, East Lansing, MI
| | - Stefano Chiaravalli
- Pediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Bruce Crooks
- Division of Hematology-Oncology, IWK Health Centre, Halifax, NS, Canada
| | - Anirban Das
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rina Dvir
- Department of Pediatric Hemato-Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Roula Farah
- Lebanese American University Medical Center-Rizk, Beirut, Lebanon
| | - William D Foulkes
- Deparments of Oncology and Human Genetics, McGill University Health Centre, Cancer Genetics Program, Montreal, QC, Canada
| | | | - Bailey Gallinger
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sharon Gardner
- Department of Pediatric Hematology-Oncology, NYU Langone Health, New York, NY
| | - David Gass
- Department of Pediatric Hematology and Oncology, Atrium Health, Charlotte, NC
| | - Mithra Ghalibafian
- MAHAK Pediatric Cancer Treatment and Research Center (MPCTRC), Tehran, Iran
| | - Catherine Gilpin
- Children's Hospital of Eastern Ontario, Genetics, Ottawa, ON, Canada
| | - Yael Goldberg
- Department of Oncology, Hadassah Medical Center, Jerusalem, Israel
| | - Catherine Goudie
- Division of Oncology, McGill University Health Centre, Montreal, QC, Canada
| | | | - Heather Hampel
- The Ohio State University Comprehensive Cancer Center, Internal Medicine, Columbus, OH
| | - Jordan R Hansford
- The Royal Children's Hospital Melbourne, Children's Cancer Centre, Parkville, Victoria, Australia
| | - Craig Harlos
- Department of Medical Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Nobuko Hijiya
- Pediatric Hematology Oncology and Stem Cell Transplant, Columbia University Irving Medical Center, New York, NY
| | - Saunders Hsu
- Department of Pediatric Hematology-Oncology, Sutter Health, Sacramento, CA
| | - Junne Kamihara
- Dana-Farber Children's Hospital Cancer Center, Pediatric Oncology, Boston, MA
| | - Rejin Kebudi
- Department of Pediatric Hematology-Oncology, Istanbul University, Fatih, Istanbul, Turkey
| | - Jeffrey Knipstein
- Department of Pediatric Neurology, Medical College of Wisconsin, Milwaukee, WI
| | - Carl Koschmann
- Department of Pediatric Hematology-Oncology, University of Michigan Medical School, Ann Arbor, MI
| | - Christian Kratz
- Department of Pediatric Haematology and Oncology, Hospital of the Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Valerie Larouche
- Department of Hematology-Oncology, CHU de Quebec-Universite Laval, Quebec, QC, Canada
| | - Alvaro Lassaletta
- Department of Pediatric Hematology-Oncology, Hospital Infantil Universitario Nino Jesus, Madrid, Spain
| | - Scott Lindhorst
- Department of Hematology-Medical Oncology, Medical University of South Carolina, Charleston, SC
| | - Simon C Ling
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael P Link
- Department of Pediatrics, Stanford Medicine, Stanford, CA
| | | | - Rebecca Luiten
- Department of Clinical Cancer Genetics, Banner MD Anderson Cancer Center, Gilbert, AZ
| | - Michal Lurye
- Sheba Medical Center at Tel Hashomer, Tel Hashomer, Israel
| | | | | | - Ossama M Maher
- Department of Pediatric Hematology-Oncology, Nicklaus Children's Hospital, Miami, FL
| | - Maura Massimino
- Pediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Lombardia, Italy
| | - Rose B McGee
- Saint Jude Children's Research Hospital, Memphis, TN
| | | | - Gary Mason
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA
| | - Monica Newmark
- Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL
| | - Garth Nicholas
- Division of Medical Oncology, University of Ottawa, Ottawa, ON, Canada
| | - Kim E Nichols
- Department of Oncology, Saint Jude Children's Research Hospital, Memphis, TN
| | - Theodore Nicolaides
- Department of Pediatric Hematology-Oncology, NYU Langone Health, New York, NY
| | - Enrico Opocher
- Department of Pediatrics, University of Padua, Padova, Veneto, Italy
| | - Michael Osborn
- Paediatric Haematology, Womens and Childrens Hospital (WCH), North Adelaide, South Australia, Australia
| | - Benjamin Oshrine
- Johns Hopkins All Children's Hospital, Cancer and Blood Disorders Institute, Saint Petersburg, FL
| | - Rachel Pearlman
- Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | - Jan Rapp
- West Virginia University Cancer Institute, Morgantown, WV
| | | | - Alyssa Reddy
- University of California San Francisco, San Francisco, CA
| | - Lara Reichman
- McGill University Health Centre, Montreal, QC, Canada
| | - Marc Remke
- University Hospital Dusseldorf, Dusseldorf, Nordrhein-Westfalen, Germany
| | - Gabriel Robbins
- Department of Pediatric Hematology-Oncology, NYU Langone Health, New York, NY
| | | | - Magnus Sabel
- Department of Pediatrics, University of Gothenburg Sahlgrenska Academy, Goteborg, Sweden
| | | | - Isabelle Scheers
- Universite Catholique de Louvain La Faculte de Medecine, Bruxelles, Belgium
| | - Kami Wolfe Schneider
- Department of Pediatric Hematology-Oncology, Children's Hospital Colorado, Aurora, CO
| | - Santanu Sen
- Department of Pediatrics, Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, Maharashtra, India
| | - Duncan Stearns
- UH Rainbow Babies and Children's Hospital Division of Pediatrics, Pediatric Neuro-oncology, Cleveland, OH
| | - David Sumerauer
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czechia
| | - Carol Swallow
- Department of Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - Leslie Taylor
- Saint Jude Children's Research Hospital, Memphis, TN
| | | | - Helen Toledano
- Department of Pediatric Hematology Oncology, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Patrick Tomboc
- Department of Pediatrics, West Virginia University, Morgantown, WV
| | - An Van Damme
- Department of Pediatric Hematology and Oncology, Universite Catholique de Louvain, Louvain-la-Neuve, Walloon Brabant, Belgium
| | | | - Michal Yalon
- Department of Pediatric Hematology-Oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Lee Yi Yen
- Department of Neurosurgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | - Shayna Zelcer
- Department of Pediatrics, London Health Sciences Centre, London, ON, Canada
| | - David S Ziegler
- Sydney Children's Hospital Randwick, Kids Cancer Centre, Randwick, New South Wales, Australia
| | - Stefanie Zimmermann
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Cynthia Hawkins
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - David Malkin
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eric Bouffet
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anita Villani
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Uri Tabori
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| |
Collapse
|
31
|
Feldman T, Bercovich A, Moskovitz Y, Chapal-Ilani N, Mitchell A, Medeiros JJF, Biezuner T, Kaushansky N, Minden MD, Gupta V, Milyavsky M, Livneh Z, Tanay A, Shlush LI. Recurrent deletions in clonal hematopoiesis are driven by microhomology-mediated end joining. Nat Commun 2021; 12:2455. [PMID: 33911081 PMCID: PMC8080710 DOI: 10.1038/s41467-021-22803-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 03/29/2021] [Indexed: 01/19/2023] Open
Abstract
The mutational mechanisms underlying recurrent deletions in clonal hematopoiesis are not entirely clear. In the current study we inspect the genomic regions around recurrent deletions in myeloid malignancies, and identify microhomology-based signatures in CALR, ASXL1 and SRSF2 loci. We demonstrate that these deletions are the result of double stand break repair by a PARP1 dependent microhomology-mediated end joining (MMEJ) pathway. Importantly, we provide evidence that these recurrent deletions originate in pre-leukemic stem cells. While DNA polymerase theta (POLQ) is considered a key component in MMEJ repair, we provide evidence that pre-leukemic MMEJ (preL-MMEJ) deletions can be generated in POLQ knockout cells. In contrast, aphidicolin (an inhibitor of replicative polymerases and replication) treatment resulted in a significant reduction in preL-MMEJ. Altogether, our data indicate an association between POLQ independent MMEJ and clonal hematopoiesis and elucidate mutational mechanisms involved in the very first steps of leukemia evolution.
Collapse
Affiliation(s)
- Tzah Feldman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoni Moskovitz
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Chapal-Ilani
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
| | - Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tamir Biezuner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathali Kaushansky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - Vikas Gupta
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | - Michael Milyavsky
- Department of Pathology, Tel-Aviv University, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada.
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel.
| |
Collapse
|
32
|
Yang C, Tian C, Hoffman TE, Jacobsen NK, Spencer SL. Melanoma subpopulations that rapidly escape MAPK pathway inhibition incur DNA damage and rely on stress signalling. Nat Commun 2021; 12:1747. [PMID: 33741929 PMCID: PMC7979728 DOI: 10.1038/s41467-021-21549-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Despite the increasing number of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the responses of thousands of single melanoma cells to BRAF inhibitors and show that a subset of cells escapes drug via non-genetic mechanisms within the first three days of treatment. Cells that escape drug rely on ATF4 stress signalling to cycle periodically in drug, experience DNA replication defects leading to DNA damage, and yet out-proliferate other cells over extended treatment. Together, our work reveals just how rapidly melanoma cells can adapt to drug treatment, generating a mutagenesis-prone subpopulation that expands over time.
Collapse
Affiliation(s)
- Chen Yang
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Chengzhe Tian
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Timothy E Hoffman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Nicole K Jacobsen
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
| |
Collapse
|
33
|
Gong M, Song E, Huang G, Ni W, Dong W, Yuan R. Enhanced Expression of CNTD2/CCNP Predicts Poor Prognosis in Bladder Cancer Based on the GSE13507. Front Genet 2021; 12:579900. [PMID: 33613629 PMCID: PMC7886781 DOI: 10.3389/fgene.2021.579900] [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: 07/14/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
Bladder cancer is one of the most common urogenital malignancies in the world, and there are no adequate prognostic indicators. CNTD2 is one of the atypical cyclins, which may be related to the cell cycle and even the development of cancers. Early studies have shown that CNTD2 is closely related to the occurrence and development of many malignant tumors. However, the mechanism of CNTD2 in bladder cancer has not been reported. In our research, we explored the different expressions of CNTD2 between 411 bladder cancers and 19 normal bladder tissues based on the TCGA dataset. CNTD2-related signaling pathways were identified through the GSEA. We analyzed the associations of CNTD2 expression and bladder cancer progression and survival using GSE13507. Compared with 19 cases of normal bladder tissue, CNTD2 gene expression was increased in 411 cases of bladder cancer. The high expression of CNTD2 strongly correlated with grade (P < 0.0001), T classification (P = 0.0001), N classification (P = 0.00011), M classification (P = 0.044), age (P = 0.027), and gender (P = 0.0012). Bladder cancer patients with high CNTD2 expression had shorter overall survival (P < 0.001). In the meantime, univariate and multivariate analyses showed that the increased expression of CNTD2 was an independent factor for poor prognosis in bladder cancer patients (P < 0.001 and P < 0.001, respectively). CNTD2 expression is closely related to bladder cancer progression, and the high expression of CNTD2 may be an adverse biomarker in bladder cancer patients.
Collapse
Affiliation(s)
- Mancheng Gong
- Department of Urology, The People's Hospital of Zhongshan, Zhongshan, China
| | - Erlin Song
- Department of Urology, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guiying Huang
- Department of Urology, The People's Hospital of Zhongshan, Zhongshan, China
| | - Wenjun Ni
- Department of Urology, The People's Hospital of Zhuhai, Zhuhai, China
| | - Wenjing Dong
- Department of Oncology, The People's Hospital of Zhongshan, Zhongshan, China
| | - Runqiang Yuan
- Department of Urology, The People's Hospital of Zhongshan, Zhongshan, China
| |
Collapse
|
34
|
Chitwood DG, Wang Q, Elliott K, Bullock A, Jordana D, Li Z, Wu C, Harcum SW, Saski CA. Characterization of metabolic responses, genetic variations, and microsatellite instability in ammonia-stressed CHO cells grown in fed-batch cultures. BMC Biotechnol 2021; 21:4. [PMID: 33419422 PMCID: PMC7791692 DOI: 10.1186/s12896-020-00667-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND As bioprocess intensification has increased over the last 30 years, yields from mammalian cell processes have increased from 10's of milligrams to over 10's of grams per liter. Most of these gains in productivity can be attributed to increasing cell densities within bioreactors. As such, strategies have been developed to minimize accumulation of metabolic wastes, such as lactate and ammonia. Unfortunately, neither cell growth nor biopharmaceutical production can occur without some waste metabolite accumulation. Inevitably, metabolic waste accumulation leads to decline and termination of the culture. While it is understood that the accumulation of these unwanted compounds imparts a suboptimal culture environment, little is known about the genotoxic properties of these compounds that may lead to global genome instability. In this study, we examined the effects of high and moderate extracellular ammonia on the physiology and genomic integrity of Chinese hamster ovary (CHO) cells. RESULTS Through whole genome sequencing, we discovered 2394 variant sites within functional genes comprised of both single nucleotide polymorphisms and insertion/deletion mutations as a result of ammonia stress with high or moderate impact on functional genes. Furthermore, several of these de novo mutations were found in genes whose functions are to maintain genome stability, such as Tp53, Tnfsf11, Brca1, as well as Nfkb1. Furthermore, we characterized microsatellite content of the cultures using the CriGri-PICR Chinese hamster genome assembly and discovered an abundance of microsatellite loci that are not replicated faithfully in the ammonia-stressed cultures. Unfaithful replication of these loci is a signature of microsatellite instability. With rigorous filtering, we found 124 candidate microsatellite loci that may be suitable for further investigation to determine whether these loci may be reliable biomarkers to predict genome instability in CHO cultures. CONCLUSION This study advances our knowledge with regards to the effects of ammonia accumulation on CHO cell culture performance by identifying ammonia-sensitive genes linked to genome stability and lays the foundation for the development of a new diagnostic tool for assessing genome stability.
Collapse
Affiliation(s)
- Dylan G Chitwood
- Department of Bioengineering, College of Engineering, Computing and Applied Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Qinghua Wang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Kathryn Elliott
- Department of Bioengineering, College of Engineering, Computing and Applied Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Aiyana Bullock
- Department of Biological Sciences, College of Agriculture, Science & Technology, Delaware State University, Dover, DE, 19901, USA
| | - Dwon Jordana
- Department of Biological Sciences, Grambling State University, Grambling, LA, 71245, USA
| | - Zhigang Li
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Cathy Wu
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Sarah W Harcum
- Department of Bioengineering, College of Engineering, Computing and Applied Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA.
| |
Collapse
|
35
|
Casey L, Singh N. POLE, MMR, and MSI Testing in Endometrial Cancer: Proceedings of the ISGyP Companion Society Session at the USCAP 2020 Annual Meeting. Int J Gynecol Pathol 2021; 40:5-16. [PMID: 33290350 DOI: 10.1097/pgp.0000000000000710] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Subclassification of endometrial carcinoma (EC) based on morphologic features alone has been shown to have suboptimal reproducibility, both in regard to biopsy versus hysterectomy findings, as well as interobserver agreement. This restricts the role of morphologic classification of EC as a tool for risk prediction and therefore treatment planning. A diagnostic algorithm based on The Cancer Genome Atlas (TCGA) classification of EC holds promise for improving accuracy in risk prediction. This classifies EC into 4 groups: those harbouring mutations in the exonuclease domain of DNA polymerase epsilon, POLE (POLEmut), those showing a mismatch repair defect, those showing mutations in TP53 (p53abn) and a heterogenous group showing none of these 3 abnormalities (currently termed no specific molecular profile). These groups can be accurately and reproducibly diagnosed on biopsy samples using a limited panel of tests, namely immunohistochemistry for mismatch repair proteins and p53, and testing for POLE exonuclease domain pathogenic variants. In this article we briefly review the biology, testing and interpretation of POLE and mismatch repair defects in EC.
Collapse
Affiliation(s)
- Laura Casey
- Department of Cellular Pathology, Barts Health NHS Trust, London, UK
| | | |
Collapse
|
36
|
Pavlov YI, Zhuk AS, Stepchenkova EI. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer. Cancers (Basel) 2020; 12:E3489. [PMID: 33255191 PMCID: PMC7760166 DOI: 10.3390/cancers12123489] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named "division of labor," remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants' effects on cancer.
Collapse
Affiliation(s)
- Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Anna S. Zhuk
- International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia;
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
| |
Collapse
|
37
|
Haratipour P, Minard C, Nakhjiri M, Negahbani A, Chamberlain BT, Osuna J, Upton TG, Zhao M, Kashemirov BA, McKenna CE. Completing the β,γ-CXY-dNTP Stereochemical Probe Toolkit: Synthetic Access to the dCTP Diastereomers and 31P and 19F NMR Correlations with Absolute Configurations. J Org Chem 2020; 85:14592-14609. [PMID: 33125847 DOI: 10.1021/acs.joc.0c01204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside 5'-triphosphate (dNTP) analogues in which the β,γ-oxygen is mimicked by a CXY group (β,γ-CXY-dNTPs) have provided information about DNA polymerase catalysis and fidelity. Definition of CXY stereochemistry is important to elucidate precise binding modes. We previously reported the (R)- and (S)-β,γ-CHX-dGTP diastereomers (X = F, Cl), prepared via P,C-dimorpholinamide CHCl (6a, 6b) and CHF (7a, 7b) bisphosphonates (BPs) equipped with an (R)-mandelic acid as a chiral auxiliary, with final deprotection using H2/Pd. This method also affords the β,γ-CHCl-dTTP (11a, 11b), β,γ-CHF (12a, 12b), and β,γ-CHCl (13a, 13b) dATP diastereomers as documented here, but the reductive deprotection step is not compatible with dCTP or the bromo substituent in β,γ-CHBr-dNTP analogues. To complete assembly of the toolkit, we describe an alternative synthetic strategy featuring ethylbenzylamine or phenylglycine-derived chiral BP synthons incorporating a photolabile protecting group. After acid-catalyzed removal of the (R)-(+)-α-ethylbenzylamine auxiliary, coupling with activated dCMP and photochemical deprotection, the individual diastereomers of β,γ-CHBr- (33a, 33b), β,γ-CHCl- (34a, 34b), β,γ-CHF-dCTP (35a, 35b) were obtained. The β,γ-CH(CH3)-dATPs (44a, 44b) were obtained using a methyl (R)-(-)-phenylglycinate auxiliary. 31P and 19F NMR Δδ values are correlated with CXY stereochemistry and pKa2-4 values for 13 CXY-bisphosphonic acids and imidodiphosphonic acid are tabulated.
Collapse
Affiliation(s)
- Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Amirsoheil Negahbani
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Brian T Chamberlain
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Jorge Osuna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Thomas G Upton
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Michelle Zhao
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| |
Collapse
|
38
|
Siraj AK, Bu R, Arshad M, Iqbal K, Parvathareddy SK, Masoodi T, Ghazwani LO, Al-Sobhi SS, Al-Dayel F, Al-Kuraya KS. POLE and POLD1 pathogenic variants in the proofreading domain in papillary thyroid cancer. Endocr Connect 2020; 9:923-932. [PMID: 32992294 PMCID: PMC7583138 DOI: 10.1530/ec-20-0258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
Thyroid cancer is the most frequent endocrine cancer with an increasing incidence rate worldwide and is the second most common malignancy among females in Saudi Arabia. Papillary thyroid cancer (PTC) is the most common subtype. Germline pathogenic variants in the proofreading domain of the POLE and POLD1 genes predispose to several types of cancers. However, the role of pathogenic variants of these two genes in PTC remains unknown. Capture sequencing, Sanger sequencing and immunohistochemistry were performed on 300 PTC cases from the Middle Eastern region. One germline pathogenic variant each of POLE (1/300, 0.33%) and POLD1 (1/300, 0.33%) genes was identified. Low expression of POLD1 was detected in 46.5% (133/286) of cases and was significantly associated with the follicular variant of PTC (P = 0.0006), distant metastasis (P = 0.0033) and stage IV tumours (P = 0.0081). However, no somatic pathogenic variant was detected in POLE gene. Furthermore, low expression of POLE was noted in 61.7% (175/284) of cases with no significant clinicopathological associations. Our study shows that pathogenic variant in the POLE and POLD1 proofreading domain is a cause of PTC and low expression of POLD1 is associated with poor prognostic markers in the Middle Eastern population. Further studies from different geographic populations are needed to determine the frequency and spectrum of proofreading domain pathogenic variants in POLE and POLD1 genes and in PTC from different ethnicities.
Collapse
Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rong Bu
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maham Arshad
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Tariq Masoodi
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Laila Omar Ghazwani
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saif S Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| |
Collapse
|
39
|
Dörk T, Hillemanns P, Tempfer C, Breu J, Fleisch MC. Genetic Susceptibility to Endometrial Cancer: Risk Factors and Clinical Management. Cancers (Basel) 2020; 12:cancers12092407. [PMID: 32854222 PMCID: PMC7565375 DOI: 10.3390/cancers12092407] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Endometrial cancer (EC) is the most common cancer affecting the female reproductive organs in higher-income states. Apart from reproductive factors and excess weight, genetic predisposition is increasingly recognized as a major factor in endometrial cancer risk. Endometrial cancer is genetically heterogeneous: while a subgroup of patients belongs to cancer predisposition syndromes (most notably the Lynch Syndrome) with high to intermediate lifetime risks, there are also several common genomic polymorphisms contributing to the spectrum of germline predispositions. Germline variants and somatic events may act in concert to modulate the molecular evolution of the tumor, where mismatch-repair deficiency is common in endometrioid endometrial tumors whereas homologous recombinational repair deficiency has been described for non-endometrioid endometrial tumors. In this review, we will survey the currently known genomic predispositions for endometrial cancer and discuss their relevance for clinical management in terms of counseling, screening and novel treatments.
Collapse
Affiliation(s)
- Thilo Dörk
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, 30625 Hannover, Germany;
- Correspondence:
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, 30625 Hannover, Germany;
| | - Clemens Tempfer
- Department of Gynaecology, Marien-Hospital, Ruhr University of Bochum, 44625 Herne, Germany;
| | - Julius Breu
- Department of Gynecology and Obstetrics, University of Witten/Herdecke, 42283 Wuppertal, Germany; (J.B.); (M.C.F.)
| | - Markus C. Fleisch
- Department of Gynecology and Obstetrics, University of Witten/Herdecke, 42283 Wuppertal, Germany; (J.B.); (M.C.F.)
| |
Collapse
|
40
|
Hodel KP, Sun MJS, Ungerleider N, Park VS, Williams LG, Bauer DL, Immethun VE, Wang J, Suo Z, Lu H, McLachlan JB, Pursell ZF. POLE Mutation Spectra Are Shaped by the Mutant Allele Identity, Its Abundance, and Mismatch Repair Status. Mol Cell 2020; 78:1166-1177.e6. [PMID: 32497495 PMCID: PMC8177757 DOI: 10.1016/j.molcel.2020.05.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Human tumors with exonuclease domain mutations in the gene encoding DNA polymerase ε (POLE) have incredibly high mutation burdens. These errors arise in four unique mutation signatures occurring in different relative amounts, the etiologies of which remain poorly understood. We used CRISPR-Cas9 to engineer human cell lines expressing POLE tumor variants, with and without mismatch repair (MMR). Whole-exome sequencing of these cells after defined numbers of population doublings permitted analysis of nascent mutation accumulation. Unlike an exonuclease active site mutant that we previously characterized, POLE cancer mutants readily drive signature mutagenesis in the presence of functional MMR. Comparison of cell line and human patient data suggests that the relative abundance of mutation signatures partitions POLE tumors into distinct subgroups dependent on the nature of the POLE allele, its expression level, and MMR status. These results suggest that different POLE mutants have previously unappreciated differences in replication fidelity and mutagenesis.
Collapse
Affiliation(s)
- Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Meijuan J S Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Leonard G Williams
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; BioInnovation Program, Tulane University, New Orleans, LA 70112, USA
| | - David L Bauer
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Victoria E Immethun
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jieqiong Wang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zucai Suo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - James B McLachlan
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA.
| |
Collapse
|
41
|
Wing-Cheuk Wong R, Palicelli A, Hoang L, Singh N. Interpretation of p16, p53 and mismatch repair protein immunohistochemistry in gynaecological neoplasia. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.mpdhp.2020.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
42
|
Min KW, Kim WS, Kim DH, Son BK, Oh YH, Kwon MJ, Lee HS, Lee SE, Kim IA, Moon JY, Kim KY, Park JH. High polymerase ε expression associated with increased CD8+T cells improves survival in patients with non-small cell lung cancer. PLoS One 2020; 15:e0233066. [PMID: 32433714 PMCID: PMC7239475 DOI: 10.1371/journal.pone.0233066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/27/2020] [Indexed: 11/18/2022] Open
Abstract
DNA replicase polymerase ε (POLE) is critical in proofreading and correcting errors of DNA replication. Low POLE expression plays a pivotal role in accumulation of mutations and onset of cancer, contributing to development and growth of tumor cells. The aim of this study is to reveal the survival, alternative genes and antitumoral immune activities in non-small cell lung cancer (NSCLC) patients with low POLE expression and provide treatment strategies that can increase their survival rates. This study investigated the clinicopathologic parameters, various tumor-infiltrating lymphocytes (TILs), endogenous retrovirus, molecular interactions and in vitro drug screen according to POLE mutation/expression in 168 and 1,019 NSCLC patients from the Konkuk University Medical Center (KUMC) and the Cancer Genome Atlas, respectively. We identified mutations of 75 genes in the sequencing panels, with POLE frame shift p.V1446fs being the most frequent (56.8%) in KUMC based on 170 targeted sequencing panels. Mutant and high expression of POLE correlated with favorable prognosis with increased TILs and tumor mutation burden, compared with wild type and low expression of POLE. We found specific molecular interactions associated with cell cycle and antigen presentation. An in vitro drug screen identified dasatinib that inhibited growth of the NSCLC cell line with low POLE expression. POLE could contribute to the future development of anticancer drugs for patients with NSCLC.
Collapse
Affiliation(s)
- Kyueng-Whan Min
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Wan-Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
- * E-mail:
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Byoung Kwan Son
- Department of Internal Medicine, Eulji Hospital, Eulji University School of Medicine, Seoul, Republic of Korea
| | - Young Ha Oh
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Gyeonggi-do, Republic of Korea
| | - Hye Seung Lee
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - In Ae Kim
- Department of Internal Medicine, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Ji-Yong Moon
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | | | | |
Collapse
|
43
|
Lorca V, Garre P. Current status of the genetic susceptibility in attenuated adenomatous polyposis. World J Gastrointest Oncol 2019; 11:1101-1114. [PMID: 31908716 PMCID: PMC6937445 DOI: 10.4251/wjgo.v11.i12.1101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Adenomatous polyposis (AP) is classified according to cumulative adenoma number in classical AP (CAP) and attenuated AP (AAP). Genetic susceptibility is the major risk factor in CAP due to mutations in the known high predisposition genes APC and MUTYH. However, the contribution of genetic susceptibility to AAP is lower and less understood. New predisposition genes have been recently proposed, and some of them have been validated, but their scarcity hinders accurate risk estimations and prevalence calculations. AAP is a heterogeneous condition in terms of severity, clinical features and heritability. Therefore, clinicians do not have strong discriminating criteria for the recommendation of the genetic study of known predisposition genes, and the detection rate is low. Elucidation and knowledge of new AAP high predisposition genes are of great importance to offer accurate genetic counseling to the patient and family members. This review aims to update the genetic knowledge of AAP, and to expound the difficulties involved in the genetic analysis of a highly heterogeneous condition such as AAP.
Collapse
Affiliation(s)
- Víctor Lorca
- Laboratorio de Oncología Molecular, Grupo de Investigación Clínica y Traslacional en Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Servicio de Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| |
Collapse
|
44
|
Christofi T, Baritaki S, Falzone L, Libra M, Zaravinos A. Current Perspectives in Cancer Immunotherapy. Cancers (Basel) 2019; 11:1472. [PMID: 31575023 PMCID: PMC6826426 DOI: 10.3390/cancers11101472] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Different immunotherapeutic approaches have proved to be of significant clinical value to many patients with different types of advanced cancer. However, we need more precise immunotherapies and predictive biomarkers to increase the successful response rates. The advent of next generation sequencing technologies and their applications in immuno-oncology has helped us tremendously towards this aim. We are now moving towards the realization of personalized medicine, thus, significantly increasing our expectations for a more successful management of the disease. Here, we discuss the current immunotherapeutic approaches against cancer, including immune checkpoint blockade with an emphasis on anti-PD-L1 and anti-CTLA-4 monoclonal antibodies. We also analyze a growing list of other co-inhibitory and co-stimulatory markers and emphasize the mechanism of action of the principal pathway for each of these, as well as on drugs that either have been FDA-approved or are under clinical investigation. We further discuss recent advances in other immunotherapies, including cytokine therapy, adoptive cell transfer therapy and therapeutic vaccines. We finally discuss the modulation of gut microbiota composition and response to immunotherapy, as well as how tumor-intrinsic factors and immunological processes influence the mutational and epigenetic landscape of progressing tumors and response to immunotherapy but also how immunotherapeutic intervention influences the landscape of cancer neoepitopes and tumor immunoediting.
Collapse
Affiliation(s)
- Theodoulakis Christofi
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus.
| | - Stavroula Baritaki
- Division of Surgery, School of Medicine, University of Crete, P.O. Box 2208, Voutes, 71003 Heraklion, Crete, Greece.
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, Oncologic, Clinic and General Pathology Section, University of Catania, 95123 Catania, Italy.
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, Oncologic, Clinic and General Pathology Section, University of Catania, 95123 Catania, Italy.
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Napoli, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| |
Collapse
|
45
|
Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform 2019; 19:1085-1101. [PMID: 28498882 DOI: 10.1093/bib/bbx049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 12/22/2022] Open
Abstract
Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the 'Emperor of Maladies'. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts. Over the past decade, a surge in available sequencing technologies has allowed the sequencing of whole genomes from liquid malignancies and solid tumors belonging to different types and stages of cancer, giving birth to the new field of cancer genomics. One of the most striking discoveries has been that cancer genomes are highly enriched with mutations of specific kinds. It has been suggested that these mutations can be classified into 'families' based on their mutational signatures. A mutational signature may be regarded as a type of base substitution (e.g. C:G to T:A) within a particular context of neighboring nucleotide sequence (the bases upstream and/or downstream of the mutation). These mutational signatures, supplemented by mutable motifs (a wider mutational context), promise to help us to understand the nature of the mutational processes that operate during tumor evolution because they represent the footprints of interactions between DNA, mutagens and the enzymes of the repair/replication/modification pathways.
Collapse
Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Youri I Pavlov
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, USA
| | | | | | - Artem G Lada
- Department Microbiology and Molecular Genetics, University of California, Davis, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Institutes of Health, USA
| | | |
Collapse
|
46
|
Abstract
The Elg1protein forms an RFC-like complex in charge of unloading PCNA from chromatin during DNA replication and repair. Mutations in the ELG1 gene caused genomic instability in all organisms tested and cancer in mammals. Here we show that Elg1 plays a role in the induction of the DNA damage checkpoint, a cellular response to DNA damage. We show that this defect is due to a defect in the signal amplification process during induction. Thus, cells coordinate the cell's response and the PCNA unloading through the activity of Elg1. The PCNA (proliferating cell nuclear antigen) ring plays central roles during DNA replication and repair. The yeast Elg1 RFC-like complex (RLC) is the principal unloader of chromatin-bound PCNA and thus plays a central role in maintaining genome stability. Here we identify a role for Elg1 in the unloading of PCNA during DNA damage. Using DNA damage checkpoint (DC)-inducible and replication checkpoint (RC)-inducible strains, we show that Elg1 is essential for eliciting the signal in the DC branch. In the absence of Elg1 activity, the Rad9 (53BP1) and Dpb11 (TopBP1) adaptor proteins are recruited but fail to be phosphorylated by Mec1 (ATR), resulting in a lack of checkpoint activation. The chromatin immunoprecipitation of PCNA at the Lac operator sites reveals that accumulated local PCNA influences the checkpoint activation process in elg1 mutants. Our data suggest that Elg1 participates in a mechanism that may coordinate PCNA unloading during DNA repair with DNA damage checkpoint induction.
Collapse
|
47
|
Hamid A, Petreaca B, Petreaca R. Frequent homozygous deletions of the CDKN2A locus in somatic cancer tissues. Mutat Res 2019; 815:30-40. [PMID: 31096160 DOI: 10.1016/j.mrfmmm.2019.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 02/07/2023]
Abstract
Here we present and describe data on homozygous deletions (HD) of human CDKN2 A and neighboring regions on the p arm of Chromosome 9 from cancer genome sequences deposited on the online Catalogue of Somatic Mutations in Cancer (COSMIC) database. Although CDKN2 A HDs have been previously described in many cancers, this is a pan-cancer report of these aberrations with the aim to map the distribution of the breakpoints. We find that HDs of this locus have a median range of 1,255,650bps. When the deletion breakpoints were mapped on both the telomere and centromere proximal sides of CDKN2A, most of the telomere proximal breakpoints concentrate to a narrow region of the chromosome which includes the gene MTAP.. The centromere proximal breakpoints of the deletions are distributed over a wider chromosomal region. Furthermore, gene expression analysis shows that the deletions that include the CDKN2A region also include the MTAP region and this observation is tissue independent. We propose a model that may explain the origin of the telomere proximal CDKN2A breakpoints Finally, we find that HD distributions for at least three other loci, RB1, SMAD4 and PTEN are also not random.
Collapse
Affiliation(s)
- Abdulaziz Hamid
- The Ohio State University, MSE110A, 1464 Mount Vernon Ave, Marion, OH 43302, United States
| | - Beniamin Petreaca
- The Ohio State University, MSE110A, 1464 Mount Vernon Ave, Marion, OH 43302, United States
| | - Ruben Petreaca
- The Ohio State University, MSE110A, 1464 Mount Vernon Ave, Marion, OH 43302, United States.
| |
Collapse
|
48
|
Zhang M, Yang J, Hua W, Li Z, Xu Z, Qian Q. Monitoring checkpoint inhibitors: predictive biomarkers in immunotherapy. Front Med 2019; 13:32-44. [PMID: 30680606 DOI: 10.1007/s11684-018-0678-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022]
Abstract
Immunotherapy has become the fourth cancer therapy after surgery, chemotherapy, and radiotherapy. In particular, immune checkpoint inhibitors are proved to be unprecedentedly in increasing the overall survival rates of patients with refractory cancers, such as advanced melanoma, non-small cell lung cancer, and renal cell carcinoma. However, inhibitor therapies are only effective in a small proportion of patients with problems, such as side effects and high costs. Therefore, doctors urgently need reliable predictive biomarkers for checkpoint inhibitor therapies to choose the optimal therapies. Here, we review the biomarkers that can serve as potential predictors of the outcomes of immune checkpoint inhibitor treatment, including tumor-specific profiles and tumor microenvironment evaluation and other factors.
Collapse
Affiliation(s)
- Min Zhang
- ShangHai Cell Therapy Group Co., Ltd., Shanghai, 201805, China
| | - Jingwen Yang
- ShangHai Cell Therapy Group Co., Ltd., Shanghai, 201805, China
| | - Wenjing Hua
- ShangHai Cell Therapy Group Co., Ltd., Shanghai, 201805, China
| | - Zhong Li
- ShangHai Cell Therapy Group Co., Ltd., Shanghai, 201805, China
| | - Zenghui Xu
- ShangHai Cell Therapy Group Co., Ltd., Shanghai, 201805, China.
| | - Qijun Qian
- ShangHai Cell Therapy Group Co., Ltd., Shanghai, 201805, China.
| |
Collapse
|
49
|
Kang S, Kang MS, Ryu E, Myung K. Eukaryotic DNA replication: Orchestrated action of multi-subunit protein complexes. Mutat Res 2018; 809:58-69. [PMID: 28501329 DOI: 10.1016/j.mrfmmm.2017.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/13/2017] [Accepted: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Genome duplication is an essential process to preserve genetic information between generations. The eukaryotic cell cycle is composed of functionally distinct phases: G1, S, G2, and M. One of the key replicative proteins that participate at every stage of DNA replication is the Mcm2-7 complex, a replicative helicase. In the G1 phase, inactive Mcm2-7 complexes are loaded on the replication origins by replication-initiator proteins, ORC and Cdc6. Two kinases, S-CDK and DDK, convert the inactive origin-loaded Mcm2-7 complex to an active helicase, the CMG complex in the S phase. The activated CMG complex begins DNA unwinding and recruits enzymes essential for DNA synthesis to assemble a replisome at the replication fork. After completion of DNA synthesis, the inactive CMG complex on the replicated DNA is removed from chromatin to terminate DNA replication. In this review, we will discuss the structure, function, and regulation of the molecular machines involved in each step of DNA replication.
Collapse
Affiliation(s)
- Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; School of Life Sciences, Ulsan National Institute for Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; School of Life Sciences, Ulsan National Institute for Science and Technology, Ulsan 44919, Republic of Korea
| |
Collapse
|
50
|
Family A and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions. BIOLOGY 2018; 7:biology7010005. [PMID: 29301327 PMCID: PMC5872031 DOI: 10.3390/biology7010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/14/2017] [Accepted: 12/29/2017] [Indexed: 02/07/2023]
Abstract
DNA polymerases are essential for genome replication, DNA repair and translesion DNA synthesis (TLS). Broadly, these enzymes belong to two groups: replicative and non-replicative DNA polymerases. A considerable body of data suggests that both groups of DNA polymerases are associated with cancer. Many mutations in cancer cells are either the result of error-prone DNA synthesis by non-replicative polymerases, or the inability of replicative DNA polymerases to proofread mismatched nucleotides due to mutations in 3'-5' exonuclease activity. Moreover, non-replicative, TLS-capable DNA polymerases can negatively impact cancer treatment by synthesizing DNA past lesions generated from treatments such as cisplatin, oxaliplatin, etoposide, bleomycin, and radiotherapy. Hence, the inhibition of DNA polymerases in tumor cells has the potential to enhance treatment outcomes. Here, we review the association of DNA polymerases in cancer from the A and B families, which participate in lesion bypass, and conduct gene replication. We also discuss possible therapeutic interventions that could be used to maneuver the role of these enzymes in tumorigenesis.
Collapse
|