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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [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: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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2
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Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024:10.1007/s11357-024-01113-3. [PMID: 38488948 DOI: 10.1007/s11357-024-01113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Kusumaningrum AE, Makaba S, Ali E, Singh M, Fenjan MN, Rasulova I, Misra N, Al-Musawi SG, Alsalamy A. A perspective on emerging therapies in metastatic colorectal cancer: Focusing on molecular medicine and drug resistance. Cell Biochem Funct 2024; 42:e3906. [PMID: 38269502 DOI: 10.1002/cbf.3906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/23/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024]
Abstract
The majority of cancer cases are colorectal cancer, which is also the second largest cause of cancer-related deaths worldwide. Metastasis is the leading cause of death for patients with colorectal cancer. Metastatic colorectal cancer incidence are on the rise due to a tiny percentage of tumors developing resistant to medicines despite advances in treatment tactics. Cutting-edge targeted medications are now the go-to option for customized and all-encompassing CRC care. Specifically, multitarget kinase inhibitors, antivascular endothelial growth factors, and epidermal growth factor receptors are widely used in clinical practice for CRC-targeted treatments. Rare targets in metastatic colorectal cancer are becoming more well-known due to developments in precision diagnostics and the extensive use of second-generation sequencing technology. These targets include the KRAS mutation, the BRAF V600E mutation, the HER2 overexpression/amplification, and the MSI-H/dMMR. Incorporating certain medications into clinical trials has significantly increased patient survival rates, opening new avenues and bringing fresh viewpoints for treating metastatic colorectal cancer. These focused therapies change how cancer is treated, giving patients new hope and better results. These markers can significantly transform and individualize therapy regimens. They could open the door to precisely customized and more effective medicines, improving patient outcomes and quality of life. The fast-growing body of knowledge regarding the molecular biology of colorectal cancer and the latest developments in gene sequencing and molecular diagnostics are directly responsible for this advancement.
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Affiliation(s)
| | - Sarce Makaba
- Researcher and lecturer, Universitas Cenderawasih Jayapura, Jayapura, Indonesia
| | - Eyhab Ali
- College of Pharmacy, Al-Zahraa University for Women, Karbala, Iraq
| | - Mandeep Singh
- Directorate of Sports and Physical Education, University of Jammu, Jammu, India
| | - Mohammed N Fenjan
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Iraq
| | - Irodakhon Rasulova
- School of Humanities, Natural & Social Sciences, New Uzbekistan University, Tashkent, Uzbekistan
- Department of Public Health, Samarkand State Medical University, Samarkand, Uzbekistan
| | - Neeti Misra
- Department of Management, Uttaranchal Institute of Management, Uttaranchal University, Dehradun, India
| | - Sada G Al-Musawi
- College of Pharmacy, National University of Science and Technology, Dhi Qar, Iraq
| | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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4
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Zhou Y, Mouw KW. DNA repair deficiency and the immune microenvironment: A pathways perspective. DNA Repair (Amst) 2024; 133:103594. [PMID: 37980867 PMCID: PMC10841828 DOI: 10.1016/j.dnarep.2023.103594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
Timely and accurate repair of DNA damage is required for genomic stability, but DNA repair pathways are often lost or altered in tumors. In addition to directly impacting tumor cell response to DNA damage, DNA repair deficiency can also alter the immune microenvironment via changes in innate and adaptive immune signaling. In some settings, these changes can lead to increased sensitivity to immune checkpoint inhibitors (ICIs). In this review, we discuss the impact of specific DNA repair pathway dysfunction on immune contexture and ICI response in solid tumors.
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Affiliation(s)
- Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Brigham & Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Bruchim I, Capasso I, Polonsky A, Meisel S, Salutari V, Werner H, Lorusso D, Scambia G, Fanfani F. New therapeutic targets for endometrial cancer: a glimpse into the preclinical sphere. Expert Opin Ther Targets 2024; 28:29-43. [PMID: 38327111 DOI: 10.1080/14728222.2024.2316739] [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: 08/30/2023] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
INTRODUCTION Endometrial cancer (EC) is the only gynecologic malignancy showing increasing trends in incidence and mortality. While standard treatment has been effective primarily for early-stage EC, precision medicine with tailored therapy has revolutionized the management of this disease. Genome sequencing analyses have identified four sub-types of EC. Treatments for primary and metastatic disease can now be tailored more accurately to achieve better oncologic results. AREAS COVERED This review provides an overview of the most relevant and updated evidence in the literature regarding EC molecular analysis and its role in risk classification, prognostication, and guidance for tailored and target therapies in early and advanced/metastatic stages. In addition, it provides updated information on optimal surgical management based on molecular classification and highlights key advances and future strategies. EXPERT OPINION EC molecular analysis yields the potential of tailoring adjuvant treatment by escalating or deescalating therapy, as shown for POLE-mutated and p53-mutated tumors. Moreover, the expression of specific molecular signatures offers the possibility to employ novel target therapies, such as immune-checkpoint inhibitors that have demonstrated a significant benefit on prognosis. New treatment guidelines are still being established, and ongoing studies are exploring the potential prognostic role of further sub-stratifications of the four molecular classes and treatment options.
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Affiliation(s)
- Ilan Bruchim
- Gynecology and Gynecologic Oncology Department, Hillel Yaffe Medical Center, Hadera, Israel
- Gynecology Laboratory, Department of Obstetrics and Gynecology, Hillel Yaffe Medical Center, Hadera, Israel
- The Technion, Institute of Technology, Haifa, Israel
| | - Ilaria Capasso
- Gynecologic Oncology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ariel Polonsky
- Gynecology and Gynecologic Oncology Department, Hillel Yaffe Medical Center, Hadera, Israel
- Gynecology Laboratory, Department of Obstetrics and Gynecology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Shilhav Meisel
- Gynecology Laboratory, Department of Obstetrics and Gynecology, Hillel Yaffe Medical Center, Hadera, Israel
- The Technion, Institute of Technology, Haifa, Israel
| | - Vanda Salutari
- Gynecologic Oncology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Haim Werner
- The Technion, Institute of Technology, Haifa, Israel
- Department of Human Molecular Genetics and Biochemistry, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Domenica Lorusso
- Università Cattolica del Sacro Cuore, Rome, Italy
- Scientific Directorate, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Gynecologic Oncology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Fanfani
- Gynecologic Oncology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
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Tan IL, Perez AR, Lew RJ, Sun X, Baldwin A, Zhu YK, Shah MM, Berger MS, Doudna JA, Fellmann C. Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis. Cell Rep 2023; 42:113339. [PMID: 37917583 PMCID: PMC10725516 DOI: 10.1016/j.celrep.2023.113339] [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: 08/25/2022] [Revised: 07/25/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Glioblastoma (GBM) is the most common lethal primary brain cancer in adults. Despite treatment regimens including surgical resection, radiotherapy, and temozolomide (TMZ) chemotherapy, growth of residual tumor leads to therapy resistance and death. At recurrence, a quarter to a third of all gliomas have hypermutated genomes, with mutational burdens orders of magnitude greater than in normal tissue. Here, we quantified the mutational landscape progression in a patient's primary and recurrent GBM, and we uncovered Cas9-targetable repeat elements. We show that CRISPR-mediated targeting of highly repetitive loci enables rapid elimination of GBM cells, an approach we term "genome shredding." Importantly, in the patient's recurrent GBM, we identified unique repeat sequences with TMZ mutational signature and demonstrated that their CRISPR targeting enables cancer-specific cell ablation. "Cancer shredding" leverages the non-coding genome and therapy-induced mutational signatures for targeted GBM cell depletion and provides an innovative paradigm to develop treatments for hypermutated glioma.
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Affiliation(s)
- I-Li Tan
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexendar R Perez
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94131, USA; Silico Therapeutics, San Francisco, CA 94131, USA
| | - Rachel J Lew
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Xiaoyu Sun
- Silico Therapeutics, San Francisco, CA 94131, USA
| | - Alisha Baldwin
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yong K Zhu
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mihir M Shah
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94131, USA
| | - Jennifer A Doudna
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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7
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Salari K, Sundi D, Lee JJ, Wu S, Wu CL, DiFiore G, Yan QR, Pienkny A, Lee CK, Oberlin D, Barme G, Piser J, Kahn R, Collins E, Phillips KG, Caruso VM, Goudarzi M, Garcia-Ransom M, Lentz PS, Evans-Holm ME, MacBride AR, Fischer DS, Haddadzadeh IJ, Mazzarella BC, Gray JW, Koppie TM, Bicocca VT, Levin TG, Lotan Y, Feldman AS. Development and Multicenter Case-Control Validation of Urinary Comprehensive Genomic Profiling for Urothelial Carcinoma Diagnosis, Surveillance, and Risk-Prediction. Clin Cancer Res 2023; 29:3668-3680. [PMID: 37439796 PMCID: PMC10502470 DOI: 10.1158/1078-0432.ccr-23-0570] [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: 03/01/2023] [Revised: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE Urinary comprehensive genomic profiling (uCGP) uses next-generation sequencing to identify mutations associated with urothelial carcinoma and has the potential to improve patient outcomes by noninvasively diagnosing disease, predicting grade and stage, and estimating recurrence risk. EXPERIMENTAL DESIGN This is a multicenter case-control study using banked urine specimens collected from patients undergoing initial diagnosis/hematuria workup or urothelial carcinoma surveillance. A total of 581 samples were analyzed by uCGP: 333 for disease classification and grading algorithm development, and 248 for blinded validation. uCGP testing was done using the UroAmp platform, which identifies five classes of mutation: single-nucleotide variants, copy-number variants, small insertion-deletions, copy-neutral loss of heterozygosity, and aneuploidy. UroAmp algorithms predicting urothelial carcinoma tumor presence, grade, and recurrence risk were compared with cytology, cystoscopy, and pathology. RESULTS uCGP algorithms had a validation sensitivity/specificity of 95%/90% for initial cancer diagnosis in patients with hematuria and demonstrated a negative predictive value (NPV) of 99%. A positive diagnostic likelihood ratio (DLR) of 9.2 and a negative DLR of 0.05 demonstrate the ability to risk-stratify patients presenting with hematuria. In surveillance patients, binary urothelial carcinoma classification demonstrated an NPV of 91%. uCGP recurrence-risk prediction significantly prognosticated future recurrence (hazard ratio, 6.2), whereas clinical risk factors did not. uCGP demonstrated positive predictive value (PPV) comparable with cytology (45% vs. 42%) with much higher sensitivity (79% vs. 25%). Finally, molecular grade predictions had a PPV of 88% and a specificity of 95%. CONCLUSIONS uCGP enables noninvasive, accurate urothelial carcinoma diagnosis and risk stratification in both hematuria and urothelial carcinoma surveillance patients.
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Affiliation(s)
- Keyan Salari
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Debasish Sundi
- Department of Urology, The Ohio State University Comprehensive Cancer Center & Pelotonia Institute for Immuno-Oncology, Columbus, Ohio
| | - Jason J. Lee
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Gabrielle DiFiore
- Department of Urology, The Ohio State University Comprehensive Cancer Center & Pelotonia Institute for Immuno-Oncology, Columbus, Ohio
| | - Q. Robert Yan
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Andrew Pienkny
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Chi K. Lee
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Daniel Oberlin
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Greg Barme
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Joel Piser
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Robert Kahn
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | - Edward Collins
- Golden Gate Urology, Oakland, Berkeley and San Francisco, California
| | | | | | | | | | | | | | | | | | | | | | - Joe W. Gray
- Oregon Health & Science University, Portland, Oregon
| | - Theresa M. Koppie
- Oregon Health & Science University, Portland, Oregon
- Willamette Urology, Salem, Oregon
| | | | | | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center Dallas, Dallas, Texas
| | - Adam S. Feldman
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
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Pan J, Lan Q, Li S. Identification of RNF150 as the hub gene associated with microsatellite instability in gastric cancer. Sci Rep 2023; 13:12495. [PMID: 37528105 PMCID: PMC10393951 DOI: 10.1038/s41598-023-39255-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/22/2023] [Indexed: 08/03/2023] Open
Abstract
Gastric cancer (GC) is a common digestive tract malignancy with the sixth global incidence and third cancer-related deaths, respectively. Microsatellite instability (MSI), accounting for one of the molecular subtypes of GC, plays an important role in GC and is affected by a sophisticated network of gene interactions. In this study, we aimed to explore the expression pattern and clinical performance of MSI related gene in GC patients. Weighted gene co-expression network analysis (WGCNA) was exploited to single out the vital module and core genes in TCGA database. We applied the protein-protein interaction (PPI) and survival analysis to propose and confirm RNF150 as the hub gene in GC. Finally, we utilized immunohistochemistry (IHC) and reverse transcription-polymerase chain reaction (RT-PCR) to explore the expression pattern of RNF150 in GC patients. With the highest weight correlation and standard correlation, RNF150 was selected as the hub gene for following validation. In validation, data obtained from the test sets showed a lower expression of RNF150 in MSI GC compared to microsatellite stability (MSS) GC. Moreover, survival analysis shows that MSI GC patients with a lower RNF150 expression level displayed the longer OS time. Compared to the expression in normal gastric tissues, the protein level of RNF150 was virtually up-regulated in ten cases of GC tissues. Furthermore, RNF150 protein level was decreased in MSI GC samples compared to MSS GC samples. When validated the mRNA expression with RT-PCR in fresh GC tissues, we also found the similar trend. RNF150 was identified as a novel MSI-related gene in GC. It is expected to be an auspicious prognostic biomarker for GC patients.
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Affiliation(s)
- Jun Pan
- Department of Gastroenterology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Qingzhi Lan
- Department of Pathology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, China
| | - Shengbao Li
- Department of Gastroenterology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
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Concannon K, Morris BB, Gay CM, Byers LA. Combining targeted DNA repair inhibition and immune-oncology approaches for enhanced tumor control. Mol Cell 2023; 83:660-680. [PMID: 36669489 PMCID: PMC9992136 DOI: 10.1016/j.molcel.2022.12.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/08/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Targeted therapy and immunotherapy have revolutionized cancer treatment. However, the ability of cancer to evade the immune system remains a major barrier for effective treatment. Related to this, several targeted DNA-damage response inhibitors (DDRis) are being tested in the clinic and have been shown to potentiate anti-tumor immune responses. Seminal studies have shown that these agents are highly effective in a pan-cancer class of tumors with genetic defects in key DNA repair genes such as BRCA1/2, BRCA-related genes, ataxia telangiectasia mutated (ATM), and others. Here, we review the molecular consequences of targeted DDR inhibition, from tumor cell death to increased engagement of the anti-tumor immune response. Additionally, we discuss mechanistic and clinical rationale for pairing targeted DDRis with immunotherapy for enhanced tumor control. We also review biomarkers for patient selection and promising new immunotherapy approaches poised to form the foundation of next-generation DDRi and immunotherapy combinations.
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Affiliation(s)
- Kyle Concannon
- Department of Hematology/Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin B Morris
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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10
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Challenges and Therapeutic Opportunities in the dMMR/MSI-H Colorectal Cancer Landscape. Cancers (Basel) 2023; 15:cancers15041022. [PMID: 36831367 PMCID: PMC9954007 DOI: 10.3390/cancers15041022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
About 5 to 15% of all colorectal cancers harbor mismatch repair deficient/microsatellite instability-high status (dMMR/MSI-H) that associates with high tumor mutation burden and increased immunogenicity. As a result, and in contrast to other colorectal cancer phenotypes, a significant subset of dMMR/MSI-H cancer patients strongly benefit from immunotherapy. Yet, a large proportion of these tumors remain unresponsive to any immuno-modulating treatment. For this reason, current efforts are focused on the characterization of resistance mechanisms and the identification of predictive biomarkers to guide therapeutic decision-making. Here, we provide an overview on the new advances related to the diagnosis and definition of dMMR/MSI-H status and focus on the distinct clinical, functional, and molecular cues that associate with dMMR/MSI-H colorectal cancer. We review the development of novel predictive factors of response or resistance to immunotherapy and their potential application in the clinical setting. Finally, we discuss current and emerging strategies applied to the treatment of localized and metastatic dMMR/MSI-H colorectal tumors in the neoadjuvant and adjuvant setting.
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11
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Kullmann F, Strissel PL, Strick R, Stoehr R, Eckstein M, Bertz S, Wullich B, Sikic D, Wach S, Taubert H, Olbert P, Heers H, Lara MF, Macias ML, Matas-Rico E, Lozano MJ, Prieto D, Hierro I, van Doeveren T, Bieche I, Masliah-Planchon J, Beaurepere R, Boormans JL, Allory Y, Herrera-Imbroda B, Hartmann A, Weyerer V. Frequency of microsatellite instability (MSI) in upper tract urothelial carcinoma: comparison of the Bethesda panel and the Idylla MSI assay in a consecutively collected, multi-institutional cohort. J Clin Pathol 2023; 76:126-132. [PMID: 34583948 PMCID: PMC9887356 DOI: 10.1136/jclinpath-2021-207855] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/06/2021] [Indexed: 02/03/2023]
Abstract
AIMS Upper tract urothelial carcinoma (UTUC) is a rare malignancy with a poor prognosis which occurs sporadically or in few cases results from a genetic disorder called Lynch syndrome. Recently, examination of microsatellite instability (MSI) has gained importance as a biomarker: MSI tumours are associated with a better response to immunomodulative therapies. Limited data are known about the prevalence of MSI in UTUC. New detection methods using the fully automated Idylla MSI Assay facilitate analysis of increased patient numbers. METHODS We investigated the frequency of MSI in a multi-institutional cohort of 243 consecutively collected UTUC samples using standard methodology (Bethesda panel), along with immunohistochemistry of mismatch repair (MMR) proteins. The same tumour cohort was retested using the Idylla MSI Assay by Biocartis. RESULTS Using standard methodology, 230/243 tumours were detected as microsatellite stable (MSS), 4/243 tumours as MSI and 9/243 samples as invalid. In comparison, the Idylla MSI Assay identified four additional tumours as MSS, equalling 234/243 tumours; 4/243 were classified as MSI and only 5/243 cases as invalid. At the immunohistochemical level, MSI results were supported in all available cases with a loss in MMR proteins. The overall concordance between the standard and the Idylla MSI Assay was 98.35%. Time to result differed between 3 hours for Idylla MSI Assay and 2 days with the standard methodology. CONCLUSION Our data indicate a low incidence rate of MSI tumours in patients with UTUC. Furthermore, our findings highlight that Idylla MSI Assay can be applied as an alternative method of MSI analysis for UTUC.
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Affiliation(s)
- Friederike Kullmann
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pamela L Strissel
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Reiner Strick
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Robert Stoehr
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Markus Eckstein
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Simone Bertz
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Bernd Wullich
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany,Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Danijel Sikic
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany,Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sven Wach
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany,Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Helge Taubert
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany,Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Hendrik Heers
- Department of Urology and Pediatric Urology, University Hospital Gießen and Marburg, Marburg, Germany
| | - María Fernanda Lara
- Department of Urology, Virgen de la Victoria University Hospital Málaga, Instituto de Investigación Biomédica de Málaga, Málaga, Spain,Genitourinary Cancer Translational Research Group, Instituto de Investigación Biomédica de Málaga, Málaga, Spain
| | - Maria Luisa Macias
- Genitourinary Cancer Translational Research Group, Instituto de Investigación Biomédica de Málaga, Málaga, Spain
| | - Elisa Matas-Rico
- Genitourinary Cancer Translational Research Group, Instituto de Investigación Biomédica de Málaga, Málaga, Spain,Department of Cell Biology, Genetics and Physiology, Málaga University, Málaga, Spain
| | - Maria José Lozano
- Department of Pathology, Faculty of Medicine, Universidad de Málaga, Málaga, Spain,Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Daniel Prieto
- Department of Pathology, Unidad de Gestión Clínica de Patología, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Isabel Hierro
- Department of Pathology, Unidad de Gestión Clínica de Patología, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Thomas van Doeveren
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Ivan Bieche
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | | | - Romane Beaurepere
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Yves Allory
- Department of Pathology, René Huguenin Curie Institute, Saint Cloud, Paris, France
| | - Bernardo Herrera-Imbroda
- Department of Urology, Virgen de la Victoria University Hospital Málaga, Instituto de Investigación Biomédica de Málaga, Málaga, Spain,Genitourinary Cancer Translational Research Group, Instituto de Investigación Biomédica de Málaga, Málaga, Spain
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Veronika Weyerer
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
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12
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Fanaei K, Salahshourifar I, Ameli F, Esfandbod M, Irani S. High Frequency of Microsatellite Instability among Non-Metastatic Gastric Cancer. Int J Hematol Oncol Stem Cell Res 2022; 16:239-249. [PMID: 36883110 PMCID: PMC9985814 DOI: 10.18502/ijhoscr.v16i4.10882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/12/2021] [Indexed: 11/05/2022] Open
Abstract
Background: Microsatellite instability (MSI) is considered a key factor in carcinogenesis and a genetic alteration pattern in many types of cancers such as gastric cancer (GC). Although the role of MSI in colorectal cancer (CRC) is well known, its prognostic impact on GC has not been clearly defined. The assessment of MSI in GC has not been documented in the Iranian population yet. Therefore, this study analyzed the association of MSI status with GC in Iranian patients. Materials and Methods: We compared the frequency of MSI at 5 loci from formalin-fixed paraffin-embedded (FFPE) gastrectomy specimens, between metastatic and non-metastatic cases of GC (N = 60). A panel of five quasi-monomorphic markers and a single dinucleotide marker with linker-based fluorescent primers was used. Results: MSI was observed in 46.6% of cases, including MSI-high (H) (33.3%) and MSI-Low (L) (13.3%). Moreover, the most unstable and stable markers in our study were NR-21 and BAT-26 accordingly. MSI-H and MSI were seen more frequently in non-metastatic tumors (p= 0.028 and p= 0.019, respectively). Conclusion: The current study showed MSI status more frequently in non-metastatic GC which may reflect a good prognostic factor in GC like CRC. Although, larger and more comprehensive studies are needed to confirm this statement. A panel consisting of NR-21, BAT-25, and NR-27 mononucleotide markers appears to be reliable and useful markers for detecting MSI in GC in Iranian patients.
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Affiliation(s)
- Khadijeh Fanaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iman Salahshourifar
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fereshteh Ameli
- Department of Pathology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Esfandbod
- Department of Hematology and Oncology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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13
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Atjimakul T, Wattanapaisal P, Suwiwat S, Wanichsuwan W, Hanprasertpong J. Microsatellite instability and oncological outcomes in Thai patients with endometrial cancer. J OBSTET GYNAECOL 2022; 42:3117-3123. [PMID: 35930016 DOI: 10.1080/01443615.2022.2106557] [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: 01/06/2023]
Abstract
Here, we determined the frequency of microsatellite instability (MSI) and the impact of MSI-high (MSI-H) on clinical outcomes of Thai patients with endometrial cancer (EC). Tissue samples of 110 Thai patients with EC, who had undergone surgical staging, were tested for mismatch repair (MMR) gene deficiency, and the patients were grouped into MSI-H and MSI-stable (MSI-S) groups; 24.5% had MSI-H. Unlike MSI-S group patients, MSI-H group patients had synchronous and metachronous cancer. They showed better 3-year disease-free survival (DFS) than those in the MSI-S group (p=.182; 92.3% vs. 82.6%). The 3-year overall survival was 96.2% in MSI-H and 86.4% in MSI-S groups (p=.163). Multivariate analyses showed lower uterine involvement (p=.004), myometrial invasion ≥50% (p=.032), lymphovascular space invasion (p<.001) and MSI-S (p=.006) as prognostic factors for DFS. Our study showed that the prevalence of MMR gene deficiency in Thai patients with EC is common and associated with better outcomes.Impact StatementWhat is already known on this subject? Microsatellite instability (MSI) occurs in approximately 20-40% of endometrial cancer (EC) cases. MSI analysis in EC can identify patients at higher risk of hereditary nonpolyposis colorectal cancer and those having prognostic factors. Additionally, it is predictive of immune checkpoint inhibitor treatment. However, current evidence shows a correlation between clinicopathological characteristics and EC prognosis. Studies on EC and MSI status effect on survival outcome have yielded inconsistent results regarding the pathological significance of MSI in such malignancies.What do the results of this study add? The prevalence of mismatch repair (MMR) gene deficiency in Thai patients with EC is common (24.5%) and associated with better outcomes.What are the implications of these findings for clinical practice and/or further research? This study highlights the prevalence and impact of MSI on oncological outcomes in patients with EC in a low-incidence country. Future studies should focus on the detection of germline mutation to understand the accurate prevalence of Lynch syndrome in Thai patients with EC.
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Affiliation(s)
- Thiti Atjimakul
- Department of Obstetrics and Gynecology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Panote Wattanapaisal
- Department of Obstetrics and Gynecology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Supaporn Suwiwat
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Worrawit Wanichsuwan
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jitti Hanprasertpong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.,Department of Research and Medical Innovation, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
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14
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Pancancer Analysis of Revealed TDO2 as a Biomarker of Prognosis and Immunotherapy. DISEASE MARKERS 2022; 2022:5447017. [PMID: 36118672 PMCID: PMC9481368 DOI: 10.1155/2022/5447017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/27/2022] [Indexed: 12/17/2022]
Abstract
Background Tryptophan 2,3-dioxygenase (TDO) encoded by TDO2, a rate-limiting enzyme in the kynurenine pathway, catabolizes tryptophan to kynurenine, evades immune surveillance, and promotes tumor growth. Although accumulating evidence suggests a crucial role of TDO2 during tumor formation and development, systematic evaluation of TDO2 across human cancers has rarely been reported. Methods To shed more light on the role of TDO2 in human cancer, we explored the expression profiles of TDO2 and identified its prognostic value in pancancer analysis through TCGA, CCLE, and GTEx databases. We further utilized TCGA data to evaluate the association between TDO2 and tumor immunological features, such as mismatch repair (MMR), tumor immune infiltration, immune checkpoint-related genes, tumor mutational burden (TMB), microsatellite instability (MSI), and DNA methyltransferase (DNMT). Results TDO2 exhibited different expression levels in various cancer cell lines. Frequently, TDO2 was detected to be highly expressed in the majority of cancers. In addition, high TDO2 expression was correlated with an unfavorable prognosis for patients in KIRP, LGG, TGCT, and UVM. Moreover, high TDO2 expression level positively correlated with higher immune infiltration, especially dendritic cells. Additionally, there is a close relationship between TDO2 and immune checkpoint-related gene markers, such as LAIR1, CD276, NRP1, CD80, and CD86. Finally, correlation analysis has demonstrated a high-correlation between TDO2 and TMB, MSI, MMR, and DNMT of multiple cancer types. Conclusion Therefore, our results suggest that TDO2 can function as a potential prognostic biomarker due to its role in tumor immunity regulation.
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15
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Alim I, Loke J, Yam S, Templeton AS, Newcomb P, Lindor NM, Pai RK, Jenkins MA, Buchanan DD, Gallinger S, Klugman S, Ostrer H. Cancer Risk C (CR-C), a functional genomics test is a sensitive and rapid test for germline mismatch repair deficiency. Genet Med 2022; 24:1821-1830. [PMID: 35616648 PMCID: PMC10072225 DOI: 10.1016/j.gim.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Heritable pathogenic variants in the DNA mismatch repair (MMR) pathway cause Lynch syndrome, a condition that significantly increases risk of colorectal and other cancers. At least half of individuals tested using gene panel sequencing have a variant of uncertain significance or no variant identified leading to no diagnosis. To fill this diagnostic gap, we developed Cancer Risk C (CR-C), a flow variant assay test. METHODS In response to treatment with an alkylating agent, individual assays of the nuclear translocation of MLH1, MSH2, BARD1, PMS2, and BRCA2 proteins and the nuclear phosphorylation of the ATM and ATR proteins distinguished pathogenic/likely pathogenic (P/LP) from benign/likely benign variants in MMR genes. RESULTS A risk classification score based on MLH1, MSH2, and ATR assays was 100% sensitive and 98% specific. Causality of MMR P/LP variants was shown through gene editing and rescue. In individuals with suspected Lynch syndrome but no P/LP, CR-C identified most (73%) as having germline MMR defects. Direct comparison of CR-C on matched blood samples and lymphoblastoid cell lines yielded comparable results (r2 > 0.9). CONCLUSION For identifying germline MMR defects, CR-C provides augmentation to traditional panel sequencing through greater accuracy, shorter turnaround time (48 hours), and performance on blood with minimal sample handling.
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Affiliation(s)
| | - Johnny Loke
- Morgan & Mendel Genomics, Inc, Bronx, NY; Albert Einstein College of Medicine, Bronx, NY
| | - Sarah Yam
- Morgan & Mendel Genomics, Inc, Bronx, NY
| | | | | | | | | | - Mark A Jenkins
- The University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Susan Klugman
- Albert Einstein College of Medicine, Bronx, NY; Montefiore Medical Center, Bronx, NY
| | - Harry Ostrer
- Morgan & Mendel Genomics, Inc, Bronx, NY; Albert Einstein College of Medicine, Bronx, NY; Montefiore Medical Center, Bronx, NY.
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16
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STR Profiling Reveals Tumor Genome Instability in Primary Mediastinal B-Cell Lymphoma. Curr Oncol 2022; 29:3449-3459. [PMID: 35621668 PMCID: PMC9139229 DOI: 10.3390/curroncol29050278] [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: 03/31/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/27/2022] Open
Abstract
Primary mediastinal B-cell lymphoma (PMBCL) is the only non-Hodgkin’s lymphoma variant responding to immune checkpoint inhibitor (ICI) therapy, approximately in half of the cases; however, no molecular markers predicting a response to ICI therapy in PMBCL have been described so far. In this study, we assessed the incidence of the loss of heterozygosity (LOH), elevated microsatellite alteration at selected tetranucleotides (EMAST), and microsatellite instability (MSI) in the tumor genomes of 72 patients with PMBCL undergoing high-dose chemotherapy treatment at the National Research Center for Hematology (Moscow, Russia). Tumor DNA was isolated from biopsy samples taken at diagnosis. Control DNA was isolated from the blood of patients in complete remission or from buccal epithelium. STR-profiles for LOH and EMAST were assessed by PCR with COrDIS Plus multiplex kit (Gordiz Ltd., Moscow, Russia). LOH was detected in 37 of 72 patients (51.4%). EMAST was found in 40 patients (55.5%); 24 had a combination of EMAST with LOH. MSI-high was not found, while MSI-low was detected only in one patient. The association of certain genetic lesions with the clinical outcome in patients receiving treatment according to the standard clinical protocol R-Da-EPOCH-21 has been estimated (58 patients out of 72) and no associations with the worst overall or event-free survival were found.
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17
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Wyvekens N, Tsai HK, Sholl LM, Tucci J, Giannico GA, Gordetsky JB, Hirsch MS, Barletta JA, Acosta AM. Histopathologic and Genetic Features of Mismatch Repair-Deficient High-Grade Prostate Cancer. Histopathology 2022; 80:1050-1060. [PMID: 35395112 DOI: 10.1111/his.14645] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
AIMS Mismatch repair (MMR) deficiency is commonly caused by functional inactivation of MLH1, PMS2, MSH2 or MSH6. The morphologic and molecular correlates of MMR deficiency have been extensively characterized in certain tumor types such as colorectal and endometrial adenocarcinoma. In contrast, the histologic and molecular features of MMR-deficient prostate cancer remain incompletely described. In this study, we evaluated 19 MMR-deficient prostate cancers, including 11 cases without prior systemic treatment. METHODS AND RESULTS All treatment-naïve cases (11/11, 100%) were Grade Group 4-5 and had predominant cribriform and/or solid growth patterns. Solid components (any amount) and tumor infiltrating lymphocytes were seen in 7/11 (64%) of these cases each. In 68 MMR-proficient Grade Group 5 prostate cancers, predominant cribriform or solid growth patterns, solid components (any amount) and tumor infiltrating lymphocytes were seen at significantly lower frequencies (31/68, 46%; 9/68, 13% and 6/62, 9%, respectively; p<0.001 for all comparisons). Molecular evaluation of 19 cases demonstrated that MMR-deficiency was secondary to functional loss of MSH2/MSH6 and MLH1/PMS2 in 15 cases (79%) and 4 cases (21%), respectively. Definite or likely germline mutations were present in 4 cases (4/19, 21%). TMPRSS2::ERG rearrangements were identified in 2 cases (2/19, 11%). Recurrent cancer-relevant somatic mutations included (but were not limited to) ATM, TP53, FOXA1, RB1, BRCA2 and PTEN. CONCLUSIONS MMR deficiency was most commonly secondary to inactivation of MSH2/MSH6 in this study. Importantly, MMR-deficient high-grade prostatic adenocarcinomas had morphologic features that might be useful to identify selected cases for MMR IHC.
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Affiliation(s)
- Nicolas Wyvekens
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan Tucci
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Giovanna A Giannico
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer B Gordetsky
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Justine A Barletta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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18
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Liu J, Cui G, Ye J, Wang Y, Wang C, Bai J. Comprehensive Analysis of the Prognostic Signature of Mutation-Derived Genome Instability-Related lncRNAs for Patients With Endometrial Cancer. Front Cell Dev Biol 2022; 10:753957. [PMID: 35433686 PMCID: PMC9012522 DOI: 10.3389/fcell.2022.753957] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/21/2022] [Indexed: 01/18/2023] Open
Abstract
Background: Emerging evidence shows that genome instability-related long non-coding RNAs (lncRNAs) contribute to tumor–cell proliferation, differentiation, and metastasis. However, the biological functions and molecular mechanisms of genome instability-related lncRNAs in endometrial cancer (EC) are underexplored.Methods: EC RNA sequencing and corresponding clinical data obtained from The Cancer Genome Atlas (TCGA) database were used to screen prognostic lncRNAs associated with genomic instability via univariate and multivariate Cox regression analysis. The genomic instability-related lncRNA signature (GILncSig) was developed to assess the prognostic risk of high- and low-risk groups. The prediction performance was analyzed using receiver operating characteristic (ROC) curves. The immune status and mutational loading of different risk groups were compared. The Genomics of Drug Sensitivity in Cancer (GDSC) and the CellMiner database were used to elucidate the relationship between the correlation of prognostic lncRNAs and drug sensitivity. Finally, we used quantitative real-time PCR (qRT-PCR) to detect the expression levels of genomic instability-related lncRNAs in clinical samples.Results: GILncSig was built using five lncRNAs (AC007389.3, PIK3CD-AS2, LINC01224, AC129507.4, and GLIS3-AS1) associated with genomic instability, and their expression levels were verified using qRT-PCR. Further analysis revealed that risk score was negatively correlated with prognosis, and the ROC curve demonstrated the higher accuracy of GILncSig. Patients with a lower risk score had higher immune cell infiltration, a higher immune score, lower tumor purity, higher immunophenoscores (IPSs), lower mismatch repair protein expression, higher microsatellite instability (MSI), and a higher tumor mutation burden (TMB). Furthermore, the level of expression of prognostic lncRNAs was significantly related to the sensitivity of cancer cells to anti-tumor drugs.Conclusion: A novel signature composed of five prognostic lncRNAs associated with genome instability can be used to predict prognosis, influence immune status, and chemotherapeutic drug sensitivity in EC.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Ye
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yutong Wang
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Can Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianling Bai
- Department of Biostatistics, School of Public Heath, Nanjing Medical University, Nanjing, China
- *Correspondence: Jianling Bai,
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19
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Dedeurwaerdere F, Claes KB, Van Dorpe J, Rottiers I, Van der Meulen J, Breyne J, Swaerts K, Martens G. Comparison of microsatellite instability detection by immunohistochemistry and molecular techniques in colorectal and endometrial cancer. Sci Rep 2021; 11:12880. [PMID: 34145315 PMCID: PMC8213758 DOI: 10.1038/s41598-021-91974-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/20/2021] [Indexed: 02/08/2023] Open
Abstract
DNA mismatch repair deficiency (dMMR) testing is crucial for diagnosing Lynch syndrome and detection of microsatellite unstable (MSI) tumors eligible for immunotherapy. The aim of this study was to compare the relative diagnostic performance of three molecular MSI assays: polymerase chain reaction (PCR), MSI testing by Idylla and next-generation-sequencing (NGS) on 49 tumor samples (28 colorectal and 21 endometrial adenocarcinomas) versus immunohistochemistry (IHC). Discrepancies were investigated by MLH1 methylation analysis and integrated with germline results if available. Overall, the molecular assays achieved equivalent diagnostic performance for MSI detection with area under the ROC curves (AUC) of respectively 0.91 for Idylla and PCR, and 0.93 for NGS. In colorectal cancers with tumor cell percentages ≥ 30% all three molecular assays achieved 100% sensitivity and specificity (AUC = 1) versus IHC. Also, in endometrial cancers, all three molecular assays showed equivalent diagnostic performance, albeit at a clearly lower sensitivity ranging from 58% for Idylla to 75% for NGS, corresponding to negative predictive values from 78 to 86%. PCR, Idylla and NGS show similar diagnostic performance for dMMR detection in colorectal and endometrial cancers. Molecular MSI analysis has lower sensitivity for dMMR detection in endometrial cancer indicating that combined use of both IHC and molecular methods is recommended.Clinical Trial Number/IRB: B1172020000040, Ethical Committee, AZ Delta General Hospital.
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Affiliation(s)
| | - Kathleen Bm Claes
- Center for Medical Genetics, Ghent University Hospital, Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Gent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | | | - Joni Van der Meulen
- Center for Medical Genetics, Ghent University Hospital, Gent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
- Molecular Diagnostics, Ghent University Hospital, Gent, Belgium
| | - Joke Breyne
- Department of Laboratory Medicine, Department of Laboratory Medicine, AZ Delta General Hospital, AZ Delta General Hospital, Deltalaan 1, 8800, Roeselare, Belgium
| | - Koen Swaerts
- Department of Laboratory Medicine, Department of Laboratory Medicine, AZ Delta General Hospital, AZ Delta General Hospital, Deltalaan 1, 8800, Roeselare, Belgium
| | - Geert Martens
- Department of Laboratory Medicine, Department of Laboratory Medicine, AZ Delta General Hospital, AZ Delta General Hospital, Deltalaan 1, 8800, Roeselare, Belgium.
- Department of Biomolecular Medicine, Ghent University, Gent, Belgium.
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20
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Palmieri G, Rozzo CM, Colombino M, Casula M, Sini MC, Manca A, Pisano M, Doneddu V, Paliogiannis P, Cossu A. Are Molecular Alterations Linked to Genetic Instability Worth to Be Included as Biomarkers for Directing or Excluding Melanoma Patients to Immunotherapy? Front Oncol 2021; 11:666624. [PMID: 34026645 PMCID: PMC8132875 DOI: 10.3389/fonc.2021.666624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
The improvement of the immunotherapeutic potential in most human cancers, including melanoma, requires the identification of increasingly detailed molecular features underlying the tumor immune responsiveness and acting as disease-associated biomarkers. In recent past years, the complexity of the immune landscape in cancer tissues is being steadily unveiled with a progressive better understanding of the plethora of actors playing in such a scenario, resulting in histopathology diversification, distinct molecular subtypes, and biological heterogeneity. Actually, it is widely recognized that the intracellular patterns of alterations in driver genes and loci may also concur to interfere with the homeostasis of the tumor microenvironment components, deeply affecting the immune response against the tumor. Among others, the different events linked to genetic instability—aneuploidy/somatic copy number alteration (SCNA) or microsatellite instability (MSI)—may exhibit opposite behaviors in terms of immune exclusion or responsiveness. In this review, we focused on both prevalence and impact of such different types of genetic instability in melanoma in order to evaluate whether their use as biomarkers in an integrated analysis of the molecular profile of such a malignancy may allow defining any potential predictive value for response/resistance to immunotherapy.
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Affiliation(s)
- Giuseppe Palmieri
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Carla Maria Rozzo
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Milena Casula
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Antonella Manca
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Marina Pisano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Valentina Doneddu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
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21
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Dai Y, Wang J, Zhao L, Wang Z, Wang J. Tumor Molecular Features Predict Endometrial Cancer Patients' Survival After Open or Minimally Invasive Surgeries. Front Oncol 2021; 11:634857. [PMID: 33718224 PMCID: PMC7952993 DOI: 10.3389/fonc.2021.634857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 01/22/2023] Open
Abstract
Background The Cancer Genome Atlas (TCGA) project shed light on the vital role of tumor molecular features in predicting endometrial cancer patients’ prognosis. This study aims to investigate the survival impact of surgical approaches on patients with different genetic alterations. Methods 473 endometrial cancer patients from TCGA database were selected. To analyze the prognostic impact of surgical approach, survival analyses were conducted in patients with different molecular features. Finally, a simplified molecular stratification model was established to select patients suitable for open or minimally invasive surgery (MIS). Results In our cohort, 291 patients received open surgery and 182 received MIS. Molecular features influenced patients’ survival after different surgical approaches. Based on survival analyses, three molecular subtypes were generated, with subtype 1 harboring POLE mutation (POLEmt), microsatellite-instability high (MSI-H), homologous recombination repair (HRR) pathway mutation or MUC16 mutation (MUC16mt); subtype 3 carrying TP53 mutation; and subtype 2 without specific molecular feature. The survival influence of molecular subtypes depended on surgical approaches. In the open surgery cohort, three subtypes showed similar survival outcome, while in the MIS cohort, prognosis varied significantly among three subtypes, with subtype 1 the best and subtype 3 the worst. In stepwise Cox regression, molecular subtype was an independent predictor of recurrence-free survival in patients receiving MIS (p < 0.001). Conclusion The molecular features of endometrial cancer are associated with patients’ prognosis after different surgical approaches. MIS should be recommended in patients with POLEmt, MSI-H, HRR pathway mutation or MUC16mt, while for patients with TP53 mutation, open surgery is better concerning oncological safety.
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Affiliation(s)
- Yibo Dai
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Jingyuan Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Luyang Zhao
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Zhiqi Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
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22
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Lee Y, Lee JA, Park HE, Han H, Kim Y, Bae JM, Kim JH, Cho NY, Kim HP, Kim TY, Kang GH. Targeted next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas. PLoS One 2021; 16:e0246356. [PMID: 33524032 PMCID: PMC7850495 DOI: 10.1371/journal.pone.0246356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/18/2021] [Indexed: 01/02/2023] Open
Abstract
In the present study, we developed a computational method and panel markers to assess microsatellite instability (MSI) using a targeted next-generation sequencing (NGS) platform and compared the performance of our computational method, mSILICO, with that of mSINGS to detect MSI in CRCs. We evaluated 13 CRC cell lines, 84 fresh and 119 formalin-fixed CRC tissues (including 61 MSI-high CRCs and 155 microsatellite-stable CRCs) and tested the classification performance of the two methods on 23, 230, and 3,154 microsatellite markers. For the fresh tissue and cell line samples, mSILICO showed a sensitivity of 100% and a specificity of 100%, regardless of the number of panel markers, whereas for the formalin-fixed tissue samples, mSILICO exhibited a sensitivity of up to 100% and a specificity of up to 100% with three differently sized panels ranging from 23 to 3154. These results were similar to those of mSINGS. With the application of mSILICO, the small panel of 23 markers had a sensitivity of ≥95% and a specificity of 100% in cell lines/fresh tissues and formalin-fixed tissues of CRC. In conclusion, we developed a new computational method and microsatellite marker panels for the determination of MSI that does not require paired normal tissues. A small panel could be integrated into the targeted NGS panel for the concurrent analysis of single nucleotide variations and MSI.
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Affiliation(s)
| | - Ji Ae Lee
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Eun Park
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | | | | | - Jeong Mo Bae
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hwang-Phill Kim
- Laboratory of Cancer Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Laboratory of Cancer Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- * E-mail:
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23
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Velasco A, Tokat F, Bonde J, Trim N, Bauer E, Meeney A, de Leng W, Chong G, Dalstein V, Kis LL, Lorentzen JA, Tomić S, Thwaites K, Putzová M, Birnbaum A, Qazi R, Primmer V, Dockhorn-Dworniczak B, Hernández-Losa J, Soares FA, Gertler AA, Kalman M, Wong C, Carraro DM, Sousa AC, Reis RM, Fox SB, Fassan M, Brevet M, Merkelbach-Bruse S, Colling R, Soilleux E, Teo RYW, D'Haene N, Nolet S, Ristimäki A, Väisänen T, Chapusot C, Soruri A, Unger T, Wecgowiec J, Biscuola M, Frattini M, Long A, Campregher PV, Matias-Guiu X. Multi-center real-world comparison of the fully automated Idylla™ microsatellite instability assay with routine molecular methods and immunohistochemistry on formalin-fixed paraffin-embedded tissue of colorectal cancer. Virchows Arch 2020; 478:851-863. [PMID: 33170334 PMCID: PMC8099763 DOI: 10.1007/s00428-020-02962-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/14/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Microsatellite instability (MSI) is present in 15–20% of primary colorectal cancers. MSI status is assessed to detect Lynch syndrome, guide adjuvant chemotherapy, determine prognosis, and use as a companion test for checkpoint blockade inhibitors. Traditionally, MSI status is determined by immunohistochemistry or molecular methods. The Idylla™ MSI Assay is a fully automated molecular method (including automated result interpretation), using seven novel MSI biomarkers (ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, SULF2) and not requiring matched normal tissue. In this real-world global study, 44 clinical centers performed Idylla™ testing on a total of 1301 archived colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissue sections and compared Idylla™ results against available results from routine diagnostic testing in those sites. MSI mutations detected with the Idylla™ MSI Assay were equally distributed over the seven biomarkers, and 84.48% of the MSI-high samples had ≥ 5 mutated biomarkers, while 98.25% of the microsatellite-stable samples had zero mutated biomarkers. The concordance level between the Idylla™ MSI Assay and immunohistochemistry was 96.39% (988/1025); 17/37 discordant samples were found to be concordant when a third method was used. Compared with routine molecular methods, the concordance level was 98.01% (789/805); third-method analysis found concordance for 8/16 discordant samples. The failure rate of the Idylla™ MSI Assay (0.23%; 3/1301) was lower than that of referenced immunohistochemistry (4.37%; 47/1075) or molecular assays (0.86%; 7/812). In conclusion, lower failure rates and high concordance levels were found between the Idylla™ MSI Assay and routine tests.
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Affiliation(s)
- Ana Velasco
- Departments of Pathology and Molecular Genetics, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida, IRBLLEIDA, IDIBELL, CIBERONC, Av. Alcalde Rovira Roure, 80 25198, Lleida, Spain.
| | - Fatma Tokat
- Department of Pathology, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, afs. 134, Hvidovre Hospital, Hvidovre, Denmark
| | - Nicola Trim
- Molecular Pathology Diagnostic Service, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Elisabeth Bauer
- Städtisches Klinikum Karlsruhe gGmbH, Institut für Pathologie, Karlsruhe, Germany
| | - Adam Meeney
- Ophthalmic Pathology Laboratory Histopathology, Royal Hallamshire Hospital, Glossop Road, Sheffield, UK
| | - Wendy de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - George Chong
- Molecular Pathology Centre, Jewish General Hospital-McGill University, Montreal, Quebec, Canada
| | - Véronique Dalstein
- Laboratoire de Biopathologie, Unité INSERM UMR-S 1250, CHU Reims, Reims, France
| | - Lorand L Kis
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Jon A Lorentzen
- Molecular Pathology Unit, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Snjezana Tomić
- Department of Pathology, Forensic Medicine and Cytology, University Hospital Split, Split, Croatia
| | - Keeley Thwaites
- Histopathology Department, Barking, Havering and Redbridge University Hospitals NHS Trust, Queen's Hospital, Romford, UK
| | - Martina Putzová
- Bioptická laboratoř s.r.o., Laboratory of Molecular Genetics, Plzeň, Czech Republic.,ÚBLG FN Motol, Praha, Czech Republic.,LF UK, Plzeň, Czech Republic
| | | | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Johr Town, Lahore, Pakistan
| | - Vanessa Primmer
- Pathologisch-Bakteriologisches Institut Kaiser-Franz-Josef-Spital, Vienna, Austria
| | | | - Javier Hernández-Losa
- Department of Pathology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | | | - Asaf A Gertler
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Michal Kalman
- Department of Pathologic Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic.,Martin's Biopsy Center Ltd., Martin, Slovak Republic
| | - Chris Wong
- Hong Kong Molecular Pathology Diagnostic Centre, Hong Kong Special Administrative Region of the People's Republic of China, Hong Kong, People's Republic of China
| | - Dirce M Carraro
- Genomics and Molecular Biology Group, International Research Center/CIPE, A. C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Ana C Sousa
- GenoMed, Diagnósticos de Medicina Molecular, SA, Lisbon, Portugal
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre and University of Melbourne, Vic, Australia
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Marie Brevet
- Department of Pathology, Hospices Civils de Lyon, Université Lyon 1, Bron, France & Cypath, Villeurbanne, France
| | | | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Ryan Yee Wei Teo
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Serge Nolet
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, Québec, Canada
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Timo Väisänen
- Oulu University Hospital and Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland
| | | | - Afsaneh Soruri
- Institut für Pathologie und Molekularpathologie, Pforzheim, Germany
| | - Tina Unger
- Institut für Pathologie, University of Leipzig, Leipzig, Germany
| | - Johanna Wecgowiec
- Institut für Pathologie, Evangelisches Krankenhaus BETHESDA Zu Duisburg GmbH, Duisburg, Germany
| | - Michele Biscuola
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Anna Long
- Cellular Pathology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Xavier Matias-Guiu
- Departments of Pathology and Molecular Genetics, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida, IRBLLEIDA, IDIBELL, CIBERONC, Av. Alcalde Rovira Roure, 80 25198, Lleida, Spain
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24
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D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J, De Smedt J, Minnoye L, Amorim R, Khorasanizadeh S, Yu Q, Zhao L, De Borre M, Savvides SN, Simon MC, Carmeliet P, Reik W, Rastinejad F, Mazzone M, Thienpont B, Lambrechts D. DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance. Genome Biol 2020; 21:182. [PMID: 32718321 PMCID: PMC7384226 DOI: 10.1186/s13059-020-02087-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia. RESULTS We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth. CONCLUSIONS Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance.
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Affiliation(s)
- Flora D'Anna
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Laurien Van Dyck
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Hui Zhao
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Rebecca V Berrens
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- The Old Schools, University of Cambridge, Trinity Lane Cambridge, CB2 1TN, UK
| | - Junbin Qian
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Pawel Bieniasz-Krzywiec
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Vikas Chandra
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luc Schoonjans
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, 0372, Oslo, Norway
| | - Julie De Smedt
- Laboratory of Dermatology, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Liesbeth Minnoye
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Ricardo Amorim
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Sepideh Khorasanizadeh
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Liyun Zhao
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
- VIB Center for Inflammation Research, 9052, Ghent, Belgium
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Carmeliet
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, 3000, Leuven, Belgium
| | - Massimiliano Mazzone
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
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25
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Dai Y, Wang Z, Wang J. Survival of microsatellite-stable endometrioid endometrial cancer patients after minimally invasive surgery: An analysis of the Cancer Genome Atlas data. Gynecol Oncol 2020; 158:92-98. [PMID: 32376044 DOI: 10.1016/j.ygyno.2020.04.684] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/12/2020] [Indexed: 01/30/2023]
Abstract
OBJECTIVE This study aims to investigate the survival impact of minimally invasive surgery on endometrial cancer (EC) patients with different histology and microsatellite status. METHODS This is a retrospective study based on the Cancer Genome Atlas (TCGA) data. 519 eligible EC patients were divided into four subgroups according to histology and microsatellite status. Kaplan-Meier survival analyses were conducted in all patients and four subgroups to compare the survival outcome after two surgeries (open vs. minimally invasive). Propensity score matching and propensity score covariate adjustment models were used to control confounders. To establish survival prediction models for EC patients, multivariate stepwise Cox regressions were conducted. RESULTS Among the eligible patients, 318 (61.3%) received open surgery and 201 (38.7%) received minimally invasive surgery. Overall survival was similar between the two groups (p = 0.33), but the latter showed significantly shorter recurrence-free survival (RFS) (p = 0.005). Subgroup analyses revealed the survival influence of surgical approach was only significant in microsatellite-stable (MSS) endometrioid EC patients. These results were verified by Kaplan-Meier survival analyses after propensity score matching and propensity score covariate adjustment models. Finally, the survival influence of multiple clinicopathological factors was analyzed. After stepwise Cox regressions, minimally invasive surgery was found to be independent risk factor for shorter RFS of all patients (hazard ratio [HR] = 2.038, 95% confidence interval [CI] 1.111-3.741, p = 0.02) and MSS patients (HR = 2.449, 95% CI 1.064-5.639, p = 0.04). CONCLUSIONS Minimally invasive surgery is associated with more rapid recurrence in MSS endometrioid EC patients, thus indicating the necessity of microsatellite testing for guiding EC surgery.
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Affiliation(s)
- Yibo Dai
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Zhiqi Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.
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26
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Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Vöhringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. Mutational signatures are jointly shaped by DNA damage and repair. Nat Commun 2020; 11:2169. [PMID: 32358516 PMCID: PMC7195458 DOI: 10.1038/s41467-020-15912-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/26/2020] [Indexed: 02/08/2023] Open
Abstract
Cells possess an armamentarium of DNA repair pathways to counter DNA damage and prevent mutation. Here we use C. elegans whole genome sequencing to systematically quantify the contributions of these factors to mutational signatures. We analyse 2,717 genomes from wild-type and 53 DNA repair defective backgrounds, exposed to 11 genotoxins, including UV-B and ionizing radiation, alkylating compounds, aristolochic acid, aflatoxin B1, and cisplatin. Combined genotoxic exposure and DNA repair deficiency alters mutation rates or signatures in 41% of experiments, revealing how different DNA alterations induced by the same genotoxin are mended by separate repair pathways. Error-prone translesion synthesis causes the majority of genotoxin-induced base substitutions, but averts larger deletions. Nucleotide excision repair prevents up to 99% of point mutations, almost uniformly across the mutation spectrum. Our data show that mutational signatures are joint products of DNA damage and repair and suggest that multiple factors underlie signatures observed in cancer genomes.
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Affiliation(s)
- Nadezda V Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK
| | - Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland
| | - Víctor González-Huici
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, 08028, Barcelona, Spain
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland
| | - Santiago Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, 08028, Barcelona, Spain
| | - Harald Vöhringer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Haematology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 689-798, Republic of Korea.
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 689-798, Republic of Korea.
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK.
- European Molecular Biology Laboratory, Genome Biology Unit, 69177, Heidelberg, Germany.
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27
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Qian J, Zhao S, Zou Y, Rahman SMJ, Senosain MF, Stricker T, Chen H, Powell CA, Borczuk AC, Massion PP. Genomic Underpinnings of Tumor Behavior in In Situ and Early Lung Adenocarcinoma. Am J Respir Crit Care Med 2020; 201:697-706. [PMID: 31747302 PMCID: PMC7068818 DOI: 10.1164/rccm.201902-0294oc] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 11/19/2019] [Indexed: 01/15/2023] Open
Abstract
Rationale: We have a limited understanding of the molecular underpinnings of early adenocarcinoma (ADC) progression. We hypothesized that the behavior of early ADC can be predicted based on genomic determinants.Objectives: To identify genomic alterations associated with resected indolent and aggressive early lung ADCs.Methods: DNA was extracted from 21 ADCs in situ (AISs), 27 minimally invasive ADCs (MIAs), and 54 fully invasive ADCs. This DNA was subjected to deep next-generation sequencing and tested against a custom panel of 347 cancer genes.Measurements and Main Results: Sequencing data was analyzed for associations among tumor mutation burden, frequency of mutations or copy number alterations, mutation signatures, intratumor heterogeneity, pathway alterations, histology, and overall survival. We found that deleterious mutation burden was significantly greater in invasive ADC, whereas more copy number loss was observed in AIS and MIA. Intratumor heterogeneity establishes early, as in AIS. Twenty-one significantly mutated genes were shared among the groups. Mutation signature profiling did not vary significantly, although the APOBEC signature was associated with ADC and poor survival. Subclonal KRAS mutations and a gene signature consisting of PIK3CG, ATM, EPPK1, EP300, or KMT2C mutations were also associated with poor survival. Mutations of KRAS, TP53, and NF1 were found to increase in frequency from AIS and MIA to ADC. A cancer progression model revealed selective early and late drivers.Conclusions: Our results reveal several genetic driver events, clonality, and mutational signatures associated with poor outcome in early lung ADC, with potential future implications for the detection and management of ADC.
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Affiliation(s)
- Jun Qian
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Early Cancer Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
- Center for Pecision Medicine, Department of Biomedical Informatics
| | | | - Yong Zou
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Early Cancer Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - S. M. Jamshedur Rahman
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Early Cancer Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - Maria-Fernanda Senosain
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Early Cancer Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - Thomas Stricker
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Heidi Chen
- Center for Pecision Medicine, Department of Biomedical Informatics
| | | | - Alain C. Borczuk
- Department of Pathology, Weill Cornell Medicine, New York, New York
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Early Cancer Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
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28
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Palmieri G, Casula M, Manca A, Palomba G, Sini MC, Doneddu V, Cossu A, Colombino M. Genetic Instability Markers in Cancer. Methods Mol Biol 2020; 2055:133-154. [PMID: 31502150 DOI: 10.1007/978-1-4939-9773-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High frequency of mutations seems to determine a higher occurrence of neoepitope formation and, thus, tumor immunogenicity. A somatic hypermutated status could thus act as a predictive biomarker of responsiveness to immunotherapy with recent immune checkpoint inhibitors. Among several factors involved in determining the hypermutated status, such as inactivating mutations in the DNA polymerases as well as exposure to external (cigarette smoke, UV radiation, chemicals) and endogenous (reactive oxygen species) mutagens, a defective DNA mismatch repair system may give rise to genetic instability and, particularly, to microsatellite instability (MSI). The occurrence of MSI has been associated with increased load of mutations and expression of abundant peptides that serve as neoantigens to elicit an immune response within a context of a favorable tumor microenvironment. Here we describe methodological strategies to investigate for the presence of the MSI phenotype in cancer samples, through a combination of molecular approaches performed on paraffin-embedded tissues.
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Affiliation(s)
- Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy.
| | - Milena Casula
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Antonella Manca
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Grazia Palomba
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Valentina Doneddu
- University Hospital Health Unit, Azienda Ospedaliero Universitaria (AOU), Sassari, Italy
| | - Antonio Cossu
- University Hospital Health Unit, Azienda Ospedaliero Universitaria (AOU), Sassari, Italy
| | - Maria Colombino
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
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29
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Zwaenepoel K, Holmgaard Duelund J, De Winne K, Maes V, Weyn C, Lambin S, Dendooven R, Broeckx G, Steiniche T, Pauwels P. Clinical Performance of the Idylla MSI Test for a Rapid Assessment of the DNA Microsatellite Status in Human Colorectal Cancer. J Mol Diagn 2019; 22:386-395. [PMID: 31881332 DOI: 10.1016/j.jmoldx.2019.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 12/24/2022] Open
Abstract
In this study, the clinical performance of the Idylla MSI test (investigational use only) was evaluated in 330 colorectal carcinoma samples (all stages). This test is fully automated, from formalin-fixed, paraffin-embedded slide to result, and gives a result in <2.5 hours. Compared with the Promega MSI Analysis System version 1.2, an overall agreement, sensitivity, and specificity of 99.7%, 98.7%, and 100%, respectively, was reached. Whereas seven samples were invalid with the Promega MSI Analysis System, only two were invalid with the Idylla MSI test. Compared with the historical immunohistochemistry (IHC) data, overall agreement, sensitivity, and specificity of 98.7%, 94.4%, and 100%, respectively, were observed. Tumor mutation burden analysis of the discordant IHC cases was in favor of the Idylla MSI test result in three of the four samples. Furthermore, for those cases where the IHC data were invalid or hard to interpret because sole loss of one DNA mismatch repair deficiency marker was observed, Idylla MSI test results were always valid and accurate. Herein, the Idylla MSI test has been shown to be an accurate, fast screening assay for the detection of microsatellite status in colorectal cancer patients, with a low number of invalid results.
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Affiliation(s)
- Karen Zwaenepoel
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium; Center for Oncological Research Antwerp (CORE), University of Antwerp, Wilrijk, Belgium.
| | | | - Koen De Winne
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Vincent Maes
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Christine Weyn
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium; Center for Oncological Research Antwerp (CORE), University of Antwerp, Wilrijk, Belgium
| | - Suzan Lambin
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Robina Dendooven
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Glenn Broeckx
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Patrick Pauwels
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium; Center for Oncological Research Antwerp (CORE), University of Antwerp, Wilrijk, Belgium
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30
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Germline and somatic mutations of homologous recombination-associated genes in Japanese ovarian cancer patients. Sci Rep 2019; 9:17808. [PMID: 31780705 PMCID: PMC6882827 DOI: 10.1038/s41598-019-54116-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/04/2019] [Indexed: 12/30/2022] Open
Abstract
We explored the frequency of germline and somatic mutations in homologous recombination (HR)-associated genes in major histological types of ovarian cancer. We performed targeted sequencing to assess germline and somatic mutations of 16 HR-associated genes and 4 mismatch repair (MMR) genes among 207 ovarian cancer patients (50 high-grade serous carcinomas (HGSC), 99 clear cell carcinomas (CCC), 39 endometrioid carcinomas (EC), 13 mucinous carcinomas (MC), and 6 low-grade serous carcinomas (LGSC)). Germline or somatic mutations of HR-associated genes were detected in 44% of HGSC, 28% of CCC, 23% of EC, 16% of MC, and 17% of LGSC patients. The profile of HR-associated gene mutations was remarkably different among each histological type. Germline BRCA1/2 mutations were frequently detected in HGSC and were rarely observed in CCC, EC, and MC patients. ATM somatic mutation was more frequently detected in CCC (9%) and EC patients (18%) than in HGSC patients (4%). There was a positive correlation between MMR gene mutations and HR-associated gene mutations (p = 0.0072). Our findings might be useful in selection of ovarian cancer patients that should be treated with PARP inhibitors.
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31
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Li H, Wang X, Zhao H, Wang F, Bao Y, Guo J, Chang S, Wu L, Cheng H, Chen S, Zou J, Cui X, Niswander L, Finnell RH, Wang H, Zhang T. Low folate concentration impacts mismatch repair deficiency in neural tube defects. Epigenomics 2019; 12:5-18. [PMID: 31769301 DOI: 10.2217/epi-2019-0279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: To know the cause of sequence variants in neural tube defect (NTD). Materials & methods: We sequenced genes implicated in neural tube closure (NTC) in a Chinese cohort and elucidated the molecular mechanism-driving mutations. Results: In NTD cases, an increase in specific variants was identified, potentially deleterious rare variants harbored in H3K36me3 occupancy regions that recruits mismatch repair (MMR) machinery. Lower folate concentrations in local brain tissues were also observed. In neuroectoderm cells, folic acid insufficiency attenuated association of Msh6 to H3K36me3, and reduced bindings to NTC genes. Rare variants in human NTDs were featured by MMR deficiency and more severe microsatellite instability. Conclusion: Our work suggests a mechanistic link between folate insufficiency and MMR deficiency that correlates with an increase of rare variants in NTC genes.
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Affiliation(s)
- Huili Li
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China.,Department of Molecular, Cellular & Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Xiaolei Wang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Huizhi Zhao
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Fang Wang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yihua Bao
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jin Guo
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Lihua Wu
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Haiqin Cheng
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Shuyuan Chen
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jizhen Zou
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Xiaodai Cui
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Lee Niswander
- Department of Molecular, Cellular & Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Richard H Finnell
- Obstetrics & Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction & Development, Fudan University, Shanghai 200011, China.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongyan Wang
- Obstetrics & Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction & Development, Fudan University, Shanghai 200011, China.,Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics & Development, Fudan University, Shanghai 200032, China.,Children's Hospital, Fudan University, Shanghai 201102, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
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32
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Póti Á, Gyergyák H, Németh E, Rusz O, Tóth S, Kovácsházi C, Chen D, Szikriszt B, Spisák S, Takeda S, Szakács G, Szallasi Z, Richardson AL, Szüts D. Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents. Genome Biol 2019; 20:240. [PMID: 31727117 PMCID: PMC6857305 DOI: 10.1186/s13059-019-1867-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/28/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint also give rise to somatic mutation patterns that can be used for treatment prediction. RESULTS Using whole genome sequencing of an isogenic knockout cell line panel, we find a universal HR deficiency-specific base substitution signature that is similar to COSMIC signature 3. In contrast, we detect different deletion phenotypes corresponding to specific HR mutants. The inactivation of BRCA2 or PALB2 leads to larger deletions, typically with microhomology, when compared to the disruption of BRCA1, RAD51 paralogs, or RAD54. Comparison with the deletion spectrum of Cas9 cut sites suggests that most spontaneously arising genomic deletions are not the consequence of double-strand breaks. Surprisingly, the inactivation of checkpoint kinases ATM and CHK2 has no mutagenic consequences. Analysis of tumor exomes with biallelic inactivating mutations in the investigated genes confirms the validity of the cell line models. We present a comprehensive analysis of sensitivity of the investigated mutants to 13 therapeutic agents for the purpose of correlating genomic mutagenic phenotypes with drug sensitivity. CONCLUSION Our results suggest that no single genomic mutational class shows perfect correlation with sensitivity to common treatments, but the contribution of COSMIC signature 3 to base substitutions, or a combined measure of different features, may be reasonably good at predicting platinum and PARP inhibitor sensitivity.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Hella Gyergyák
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Orsolya Rusz
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
- Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Szilárd Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Csenger Kovácsházi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University Medical School, Kyoto, 606-8501, Japan
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
- Institute of Cancer Research, Medical University Vienna, Vienna, Austria
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary.
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33
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Truncated PPM1D impairs stem cell response to genotoxic stress and promotes growth of APC-deficient tumors in the mouse colon. Cell Death Dis 2019; 10:818. [PMID: 31659152 PMCID: PMC6817818 DOI: 10.1038/s41419-019-2057-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023]
Abstract
Protein phosphatase magnesium-dependent 1 delta (PPM1D) terminates cell response to genotoxic stress by negatively regulating the tumor suppressor p53 and other targets at chromatin. Mutations in the exon 6 of the PPM1D result in production of a highly stable, C-terminally truncated PPM1D. These gain-of-function PPM1D mutations are present in various human cancers but their role in tumorigenesis remains unresolved. Here we show that truncated PPM1D impairs activation of the cell cycle checkpoints in human non-transformed RPE cells and allows proliferation in the presence of DNA damage. Next, we developed a mouse model by introducing a truncating mutation in the PPM1D locus and tested contribution of the oncogenic PPM1DT allele to colon tumorigenesis. We found that p53 pathway was suppressed in colon stem cells harboring PPM1DT resulting in proliferation advantage under genotoxic stress condition. In addition, truncated PPM1D promoted tumor growth in the colon in Apcmin mice and diminished survival. Moreover, tumor organoids derived from colon of the ApcminPpm1dT/+ mice were less sensitive to 5-fluorouracil when compared to ApcminPpm1d+/+and the sensitivity to 5-fluorouracil was restored by inhibition of PPM1D. Finally, we screened colorectal cancer patients and identified recurrent somatic PPM1D mutations in a fraction of colon adenocarcinomas that are p53 proficient and show defects in mismatch DNA repair. In summary, we provide the first in vivo evidence that truncated PPM1D can promote tumor growth and modulate sensitivity to chemotherapy.
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34
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Matsuno Y, Atsumi Y, Shimizu A, Katayama K, Fujimori H, Hyodo M, Minakawa Y, Nakatsu Y, Kaneko S, Hamamoto R, Shimamura T, Miyano S, Tsuzuki T, Hanaoka F, Yoshioka KI. Replication stress triggers microsatellite destabilization and hypermutation leading to clonal expansion in vitro. Nat Commun 2019; 10:3925. [PMID: 31477700 PMCID: PMC6718401 DOI: 10.1038/s41467-019-11760-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
Mismatch repair (MMR)-deficient cancers are characterized by microsatellite instability (MSI) and hypermutation. However, it remains unclear how MSI and hypermutation arise and contribute to cancer development. Here, we show that MSI and hypermutation are triggered by replication stress in an MMR-deficient background, enabling clonal expansion of cells harboring ARF/p53-module mutations and cells that are resistant to the anti-cancer drug camptothecin. While replication stress-associated DNA double-strand breaks (DSBs) caused chromosomal instability (CIN) in an MMR-proficient background, they induced MSI with concomitant suppression of CIN via a PARP-mediated repair pathway in an MMR-deficient background. This was associated with the induction of mutations, including cancer-driver mutations in the ARF/p53 module, via chromosomal deletions and base substitutions. Immortalization of MMR-deficient mouse embryonic fibroblasts (MEFs) in association with ARF/p53-module mutations was ~60-fold more efficient than that of wild-type MEFs. Thus, replication stress-triggered MSI and hypermutation efficiently lead to clonal expansion of cells with abrogated defense systems. Mismatch repair (MMR)-deficient cancers are characterized by microsatellite instability (MSI) and hypermutation. Here authors reveal a mechanism by which replication stress induces MSI and associated induction of mutations in vitro.
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Affiliation(s)
- Yusuke Matsuno
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Yuko Atsumi
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Atsuhiro Shimizu
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kotoe Katayama
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Haruka Fujimori
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mai Hyodo
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yusuke Minakawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yoshimichi Nakatsu
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, 103-0027, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Graduate School of Medicine, Nagoya University, Tsurumai-cho, Syouwa-ku, Nagoya, 466-8550, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Teruhisa Tsuzuki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Fumio Hanaoka
- Faculty of Science, Gakushuin University, Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.,National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ken-Ichi Yoshioka
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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35
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Boretto M, Maenhoudt N, Luo X, Hennes A, Boeckx B, Bui B, Heremans R, Perneel L, Kobayashi H, Van Zundert I, Brems H, Cox B, Ferrante M, Uji-I H, Koh KP, D'Hooghe T, Vanhie A, Vergote I, Meuleman C, Tomassetti C, Lambrechts D, Vriens J, Timmerman D, Vankelecom H. Patient-derived organoids from endometrial disease capture clinical heterogeneity and are amenable to drug screening. Nat Cell Biol 2019; 21:1041-1051. [PMID: 31371824 DOI: 10.1038/s41556-019-0360-z] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 06/12/2019] [Indexed: 12/15/2022]
Abstract
Endometrial disorders represent a major gynaecological burden. Current research models fail to recapitulate the nature and heterogeneity of these diseases, thereby hampering scientific and clinical progress. Here we developed long-term expandable organoids from a broad spectrum of endometrial pathologies. Organoids from endometriosis show disease-associated traits and cancer-linked mutations. Endometrial cancer-derived organoids accurately capture cancer subtypes, replicate the mutational landscape of the tumours and display patient-specific drug responses. Organoids were also established from precancerous pathologies encompassing endometrial hyperplasia and Lynch syndrome, and inherited gene mutations were maintained. Endometrial disease organoids reproduced the original lesion when transplanted in vivo. In summary, we developed multiple organoid models that capture endometrial disease diversity and will provide powerful research models and drug screening and discovery tools.
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Affiliation(s)
- Matteo Boretto
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.
| | - Nina Maenhoudt
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Xinlong Luo
- Stem Cell Institute Leuven, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Aurélie Hennes
- Laboratory of Endometrium, Endometriosis and Reproductive Medicine, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Bich Bui
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Woman and Baby Division, Reproductive Medicine, University Medical Centre Utrecht (UMCU), Utrecht, The Netherlands
| | - Ruben Heremans
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Woman and Child Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Gynecology and Obstetrics, University Hospitals Leuven (UZ Leuven), Leuven, Belgium
| | - Lisa Perneel
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Hiroto Kobayashi
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Anatomy and Structural Science, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Indra Van Zundert
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Hilde Brems
- Laboratory for Neurofibromatosis Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Benoit Cox
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Marc Ferrante
- Unit of Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Hiroshi Uji-I
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Kian Peng Koh
- Stem Cell Institute Leuven, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Thomas D'Hooghe
- Woman and Child Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Arne Vanhie
- Laboratory of Endometrium, Endometriosis and Reproductive Medicine, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Leuven University Fertility Center (LUFC), UZ Leuven, Leuven, Belgium
| | - Ignace Vergote
- Woman and Child Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Gynecology and Obstetrics, University Hospitals Leuven (UZ Leuven), Leuven, Belgium
| | - Christel Meuleman
- Laboratory of Endometrium, Endometriosis and Reproductive Medicine, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Leuven University Fertility Center (LUFC), UZ Leuven, Leuven, Belgium
| | - Carla Tomassetti
- Laboratory of Endometrium, Endometriosis and Reproductive Medicine, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Leuven University Fertility Center (LUFC), UZ Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joris Vriens
- Laboratory of Endometrium, Endometriosis and Reproductive Medicine, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Dirk Timmerman
- Woman and Child Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Gynecology and Obstetrics, University Hospitals Leuven (UZ Leuven), Leuven, Belgium
| | - Hugo Vankelecom
- Laboratory of Tissue Plasticity in Health and Disease, Stem Cell and Developmental Biology Cluster, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.
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Supek F, Lehner B. Scales and mechanisms of somatic mutation rate variation across the human genome. DNA Repair (Amst) 2019; 81:102647. [PMID: 31307927 DOI: 10.1016/j.dnarep.2019.102647] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer genome sequencing has revealed that somatic mutation rates vary substantially across the human genome and at scales from megabase-sized domains to individual nucleotides. Here we review recent work that has both revealed the major mutation biases that operate across the genome and the molecular mechanisms that cause them. The default mutation rate landscape in mammalian genomes results in active genes having low mutation rates because of a combination of factors that increase DNA repair: early DNA replication, transcription, active chromatin modifications and accessible chromatin. Therefore, either an increase in the global mutation rate or a redistribution of mutations from inactive to active DNA can increase the rate at which consequential mutations are acquired in active genes. Several environmental carcinogens and intrinsic mechanisms operating in tumor cells likely cause cancer by this second mechanism: by specifically increasing the mutation rate in active regions of the genome.
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Affiliation(s)
- Fran Supek
- Genome Data Science, Institut de Recerca Biomedica (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain; Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
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37
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Evaluation of a Fully Automated Idylla Test System for Microsatellite Instability in Colorectal Cancer. Clin Colorectal Cancer 2019; 18:e316-e323. [PMID: 31375292 DOI: 10.1016/j.clcc.2019.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/05/2019] [Accepted: 05/28/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) is a phenotype commonly observed in colorectal cancer, and is caused by a deficient mismatch repair system. Determining MSI status greatly aids tumor prognosis and treatment plans in colorectal cancer, and plays a critical role in recent United States Food and Drug Administration-approved immunotherapies. As recognition of its importance grows, MSI has been identified in more types of cancers, underscoring the importance of accurate assays for determining MSI status in tumor cells. Currently, tumor MSI status is detected via polymerase chain reaction-based methods or immunohistochemistry. MATERIALS AND METHODS In this study, we tested a new, fully automated MSI detection system (Idylla MSI detection kit) released by Biocartis. We evaluated 42 formalin-fixed paraffin-embedded tumor tissues, which were clinically tested for MSI status using the polymerase chain reaction or immunohistochemistry method, with the Idylla MSI detection system. RESULTS The Idylla MSI detection system showed an overall 97.62% concordance rate with previously used methods. Moreover, this fully automated system requires less than 5 minutes "hands on" preparation time and 150 minutes total run time per sample. CONCLUSION The Biocartis Idylla MSI kit proves a powerful tool to accurately detect MSI status in tumor cells in a rapid and almost labor-free manner.
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38
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Yamamoto H, Imai K. An updated review of microsatellite instability in the era of next-generation sequencing and precision medicine. Semin Oncol 2019; 46:261-270. [DOI: 10.1053/j.seminoncol.2019.08.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/27/2019] [Accepted: 08/14/2019] [Indexed: 12/23/2022]
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39
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Hayashida G, Shioi S, Hidaka K, Fujikane R, Hidaka M, Tsurimoto T, Tsuzuki T, Oda S, Nakatsu Y. Differential genomic destabilisation in human cells with pathogenic MSH2 mutations introduced by genome editing. Exp Cell Res 2019; 377:24-35. [PMID: 30802454 DOI: 10.1016/j.yexcr.2019.02.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
Abstract
Repeat destabilisation is variously associated with human disease. In neoplastic diseases, microsatellite instability (MSI) has been regarded as simply reflecting DNA mismatch repair (MMR) deficiency. However, several discrepancies have been pointed out. Firstly, the MSI+ phenotype is not uniform in human neoplasms. Established classification utilises the frequency of microsatellite changes, i.e. MSI-H (high) and -L (low), the former regarded as an authentic MMR-defective phenotype. In addition, we have observed the qualitatively distinct modes of MSI, i.e. Type A and Type B. One discrepancy we previously pointed out is that tumours occurring in MMR gene knockout mice exhibited not drastic microsatellite changes typical in MSI-H tumours (i.e. Type B mode) but minor and more subtle alterations (i.e. Type A mode). In the present study, MSH2 mutations reported in Lynch syndrome (LS) kindred have been introduced into HeLa cells using the CRISPR/Cas9 system. The established mutant clones clearly exhibited MMR-defective phenotypes with alkylating agent-tolerance and elevated mutation frequencies. Nevertheless, microsatellites were not markedly destabilised as in MSI-H tumours occurring in LS patients, and all the observed alterations were uniformly Type A, which confirms the results in mice. Our findings suggest added complexities to the molecular mechanisms underlying repeat destabilisation in human genome.
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Affiliation(s)
- Genki Hayashida
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Japan; Department of Biology, School of Sciences, Kyushu University, Fukuoka, Japan
| | - Seijiro Shioi
- Clinical Research Institute, Cancer Genetics Laboratory, National Kyushu Cancer Center, Fukuoka, Japan
| | - Kyoko Hidaka
- Centre for Fundamental Education, University of Kitakyushu, Kitakyushu, Japan
| | - Ryosuke Fujikane
- Department of Odontology and Fukuoka Dental College, Fukuoka, Japan
| | - Masumi Hidaka
- Department of Odontology and Fukuoka Dental College, Fukuoka, Japan
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, Fukuoka, Japan
| | - Teruhisa Tsuzuki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Japan; Advanced Science Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Shinya Oda
- Clinical Research Institute, Cancer Genetics Laboratory, National Kyushu Cancer Center, Fukuoka, Japan.
| | - Yoshimichi Nakatsu
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Japan.
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40
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Wiesweg M, Kasper S, Worm K, Herold T, Reis H, Sara L, Metzenmacher M, Abendroth A, Darwiche K, Aigner C, Wedemeyer HH, Helfritz FA, Stuschke M, Schumacher B, Markus P, Paul A, Rahmann S, Schmid KW, Schuler M. Impact of RAS mutation subtype on clinical outcome—a cross-entity comparison of patients with advanced non-small cell lung cancer and colorectal cancer. Oncogene 2018; 38:2953-2966. [DOI: 10.1038/s41388-018-0634-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/21/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
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41
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Smeets D, Miller IS, O'Connor DP, Das S, Moran B, Boeckx B, Gaiser T, Betge J, Barat A, Klinger R, van Grieken NCT, Cremolini C, Prenen H, Mazzone M, Depreeuw J, Bacon O, Fender B, Brady J, Hennessy BT, McNamara DA, Kay E, Verheul HM, Maarten N, Gallagher WM, Murphy V, Prehn JHM, Koopman M, Punt CJA, Loupakis F, Ebert MPA, Ylstra B, Lambrechts D, Byrne AT. Copy number load predicts outcome of metastatic colorectal cancer patients receiving bevacizumab combination therapy. Nat Commun 2018; 9:4112. [PMID: 30291241 PMCID: PMC6173768 DOI: 10.1038/s41467-018-06567-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 09/04/2018] [Indexed: 02/07/2023] Open
Abstract
Increased copy number alterations (CNAs) indicative of chromosomal instability (CIN) have been associated with poor cancer outcome. Here, we study CNAs as potential biomarkers of bevacizumab (BVZ) response in metastatic colorectal cancer (mCRC). We cluster 409 mCRCs in three subclusters characterized by different degrees of CIN. Tumors belonging to intermediate-to-high instability clusters have improved outcome following chemotherapy plus BVZ versus chemotherapy alone. In contrast, low instability tumors, which amongst others consist of POLE-mutated and microsatellite-instable tumors, derive no further benefit from BVZ. This is confirmed in 81 mCRC tumors from the phase 2 MoMa study involving BVZ. CNA clusters overlap with CRC consensus molecular subtypes (CMS); CMS2/4 xenografts correspond to intermediate-to-high instability clusters and respond to FOLFOX chemotherapy plus mouse avastin (B20), while CMS1/3 xenografts match with low instability clusters and fail to respond. Overall, we identify copy number load as a novel potential predictive biomarker of BVZ combination therapy. Increased copy number alterations, indicative of chromosomal instability, is associated with poor cancer outcome. Here, metastatic colorectal cancer patients displaying intermediate-high CIN associate with improved outcome following chemotherapy and bevacizumab treatment, suggesting CIN as a predictive biomarker.
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Affiliation(s)
- Dominiek Smeets
- VIB Center for Cancer Biology, VIB, Herestraat 49, 3000, Leuven, Belgium.,Department of Human Genetics, University of Leuven (KULeuven), Herestraat 49, 3000, Leuven, Belgium
| | - Ian S Miller
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D2, Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St.Stephen's Green, Dublin, D2, Ireland.,UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St.Stephen's Green, Dublin, D2, Ireland.,UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Ireland
| | - Bruce Moran
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Ireland
| | - Bram Boeckx
- VIB Center for Cancer Biology, VIB, Herestraat 49, 3000, Leuven, Belgium.,Department of Human Genetics, University of Leuven (KULeuven), Herestraat 49, 3000, Leuven, Belgium
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Johannes Betge
- Department of Medicine II, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Ana Barat
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D2, Ireland
| | - Rut Klinger
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Ireland
| | - Nicole C T van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Istituto Toscano Tumori, Lungarno Antonio Pacinotti, 43, 56126, Pisa, Italy
| | - Hans Prenen
- Department of Oncology, University Hospital Antwerp, Edegem, 2650, Belgium.,Center for Oncological Research, Antwerp University, 2650, Edegem, Belgium
| | - Massimiliano Mazzone
- VIB Center for Cancer Biology, VIB, Herestraat 49, 3000, Leuven, Belgium.,Department of Oncology, University of Leuven (KULeuven), Herestraat 49, 3000, Leuven, Belgium
| | - Jeroen Depreeuw
- VIB Center for Cancer Biology, VIB, Herestraat 49, 3000, Leuven, Belgium.,Department of Human Genetics, University of Leuven (KULeuven), Herestraat 49, 3000, Leuven, Belgium.,Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University Hospitals Leuven, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Orna Bacon
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D2, Ireland
| | - Bozena Fender
- OncoMark Limited, NovaUCD, Belfield Innovation Park, Dublin, D4, Ireland
| | - Joseph Brady
- Veterinary Pathobiology, School of Veterinary Medicine, University College Dublin, Stillorgan Rd, Belfield, Dublin, D4, Ireland
| | - Bryan T Hennessy
- Department of Surgery, Beaumont Hospital, Beaumont Rd, Beaumont, Dublin, D9, Ireland
| | - Deborah A McNamara
- Department of Surgery, Beaumont Hospital, Beaumont Rd, Beaumont, Dublin, D9, Ireland
| | - Elaine Kay
- Department of Pathology, Beaumont Hospital, Beaumont Rd, Beaumont, Dublin, D9, Ireland
| | - Henk M Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Neerincx Maarten
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Ireland.,OncoMark Limited, NovaUCD, Belfield Innovation Park, Dublin, D4, Ireland
| | - Verena Murphy
- Cancer Trials Ireland, Innovation House, Old Finglas Road, Dublin, D9, Ireland
| | - Jochen H M Prehn
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D2, Ireland
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Cornelis J A Punt
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Fotios Loupakis
- Oncologia Medica 1, Istituto Oncologico Veneto, Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Via Gattamelata, 64, 35128, Padova, Italy
| | - Matthias P A Ebert
- Department of Medicine II, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Herestraat 49, 3000, Leuven, Belgium. .,Department of Human Genetics, University of Leuven (KULeuven), Herestraat 49, 3000, Leuven, Belgium.
| | - Annette T Byrne
- Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, 31A York Street, Dublin, D2, Ireland.,UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Ireland
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42
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Zhang L, Peng Y, Peng G. Mismatch repair-based stratification for immune checkpoint blockade therapy. Am J Cancer Res 2018; 8:1977-1988. [PMID: 30416850 PMCID: PMC6220134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 09/17/2018] [Indexed: 06/09/2023] Open
Abstract
Mismatch repair (MMR) plays a key role in maintaining genomic stability. Mismatch repair deficiency (MMR-D) causes a molecular feature of microsatellite instability (MSI) and contributes to the development of human cancers and genetic diseases with cancer predisposition such as Lynch syndrome. Recent studies have shown that immune checkpoint blockade therapy has a promising response in MMR-D cancers regardless of the tissue of origin. Being able to identify patients with MMR-D cancers is an important challenge in clinical practice. Although immunohistochemistry (IHC) and polymerase chain reaction (PCR)-based MSI analysis combined with a subsequent MMR gene test are used as the standard of care in the clinical setting to identify patients with MMR-D cancers, these methods have limitations as a pan-cancer testing strategy. Next-generation sequencing (NGS) has developed and matured as a clinical option and NGS has advantages for use as a novel testing strategy for MMR-D detection. In this review, we describe the genetic basis of MMR-D, current diagnostic algorithms in the clinical management of MMR-D, the novel NGS approach, and potential detection strategy of anti-cancer immunity biomarkers of MMR-D.
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Affiliation(s)
- Lihong Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, China
| | - Yang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer CenterHouston, Texas, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer CenterHouston, Texas, USA
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43
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Tomkova M, Tomek J, Kriaucionis S, Schuster-Böckler B. Mutational signature distribution varies with DNA replication timing and strand asymmetry. Genome Biol 2018; 19:129. [PMID: 30201020 PMCID: PMC6130095 DOI: 10.1186/s13059-018-1509-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. RESULTS We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. CONCLUSIONS Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jakub Tomek
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Benjamin Schuster-Böckler
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
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44
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Meijer TG, Verkaik NS, Sieuwerts AM, van Riet J, Naipal KA, van Deurzen CH, den Bakker MA, Sleddens HF, Dubbink HJ, den Toom TD, Dinjens WN, Lips E, Nederlof PM, Smid M, van de Werken HJ, Kanaar R, Martens JW, Jager A, van Gent DC. Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects. Clin Cancer Res 2018; 24:6277-6287. [DOI: 10.1158/1078-0432.ccr-18-0063] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/17/2018] [Accepted: 08/17/2018] [Indexed: 11/16/2022]
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45
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Kaina B, Izzotti A, Xu J, Christmann M, Pulliero A, Zhao X, Dobreanu M, Au WW. Inherent and toxicant-provoked reduction in DNA repair capacity: A key mechanism for personalized risk assessment, cancer prevention and intervention, and response to therapy. Int J Hyg Environ Health 2018; 221:993-1006. [PMID: 30041861 DOI: 10.1016/j.ijheh.2018.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 02/05/2023]
Abstract
Genomic investigations reveal novel evidence which indicates that genetic predisposition and inherent drug response are key factors for development of cancer and for poor response to therapy. However, mechanisms for these outcomes and interactions with environmental factors have not been well-characterized. Therefore, cancer risk, prevention, intervention and prognosis determinations have still mainly been based on population, rather than on individualized, evaluations. The objective of this review was to demonstrate that a key mechanism which contributes to the determination is inherent and/or toxicant-provoked reduction in DNA repair capacity. In addition, functional and quantitative determination of DNA repair capacity on an individual basis would dramatically change the evaluation and management of health problems from a population to a personalized basis. In this review, justifications for the scenario were delineated. Topics to be presented include assays for detection of functional DNA repair deficiency, mechanisms for DNA repair defects, toxicant-perturbed DNA repair capacity, epigenetic mechanisms (methylation and miRNA expression) for alteration of DNA repair function, and bioinformatics approach to analyze large amount of genomic data. Information from these topics has recently been and will be used for better understanding of cancer causation and of response to therapeutic interventions. Consequently, innovative genomic- and mechanism-based evidence can be increasingly used to develop more precise cancer risk assessment, and target-specific and personalized medicine.
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Affiliation(s)
| | - Alberto Izzotti
- University of Genoa, Genoa, Italy; IRCCS Policlinico San Martino Genoa, Italy
| | - Jianzhen Xu
- Shantou University Medical College, Shantou, China
| | | | | | - Xing Zhao
- Shantou University Medical College, Shantou, China
| | | | - William W Au
- Shantou University Medical College, Shantou, China; University of Medicine and Pharmacy, Tirgu Mures, Romania; University of Texas Medical Branch, Galveston, TX, USA.
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46
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Identification and preclinical characterization of a novel and potent poly (ADP-ribose) polymerase (PARP) inhibitor ZYTP1. Cancer Chemother Pharmacol 2018; 82:635-647. [DOI: 10.1007/s00280-018-3653-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022]
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47
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Tomkova M, Schuster-Böckler B. DNA Modifications: Naturally More Error Prone? Trends Genet 2018; 34:627-638. [PMID: 29853204 DOI: 10.1016/j.tig.2018.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/31/2022]
Abstract
Epigenetic DNA modifications are essential for normal cell function in vertebrates, but they can also be hotspots of mutagenesis. Methylcytosine in particular has long been known to be less stable than other nucleotides and spontaneously deaminates to thymine. Beyond this well-established phenomenon, however, the influence of epigenetic marks on mutagenesis has recently become an active field of investigation. In this review, we summarize current knowledge of the interactions between different DNA modifications and other mutagenic processes. External mutagens, such as UV light or smoking carcinogens, affect modified cytosines differently from unmodified ones, and modified cytosine can in some cases be protective rather than mutagenic. Notably, cell-intrinsic processes, such as DNA replication, also appear to influence the mutagenesis of modified cytosines. Altogether, evidence is accumulating to show that epigenetic changes have a profound influence on tissue-specific mutation accumulation.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Benjamin Schuster-Böckler
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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48
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Fleury H, Carmona E, Morin VG, Meunier L, Masson JY, Tonin PN, Provencher D, Mes-Masson AM. Cumulative defects in DNA repair pathways drive the PARP inhibitor response in high-grade serous epithelial ovarian cancer cell lines. Oncotarget 2018; 8:40152-40168. [PMID: 27374179 PMCID: PMC5522225 DOI: 10.18632/oncotarget.10308] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/09/2016] [Indexed: 01/17/2023] Open
Abstract
PARP inhibitors (PARPi), such as Olaparib, have shown promising results in high-grade serous (HGS) epithelial ovarian cancer (EOC) treatment. PARPi sensitivity has been mainly associated with homologous recombination (HR) deficiency, but clinical trials have shown that predicting actual patient response is complex. Here, we investigated gene expression microarray, HR functionality and Olaparib sensitivity of 18 different HGS EOC cell lines and demonstrate that PARPi sensitivity is not only associated with HR defects. Gene target validation show that down regulation of genes in the nucleotide excision repair (NER) and mismatch repair (MMR) pathways (ERCC8 and MLH1, respectively) increases PARPi response. The highest sensitivity was observed when genes in both the HR and either NER or MMR pathways were concomitantly down regulated. Using clinical samples, patients with these concurrent down regulations could be identified. Based on these results, a novel model to predict PARPi sensitivity is herein proposed. This model implies that the extreme responders identified in clinical trials have deficiencies in HR and either NER or MMR.
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Affiliation(s)
- Hubert Fleury
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada.,Institut du cancer de Montréal, Montreal, Canada
| | - Euridice Carmona
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada.,Institut du cancer de Montréal, Montreal, Canada
| | - Vincent G Morin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada.,Institut du cancer de Montréal, Montreal, Canada
| | - Liliane Meunier
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada.,Institut du cancer de Montréal, Montreal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Patricia N Tonin
- Cancer Research Program (CRP), The Research Institute of the McGill University Health Centre, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada.,Department of Medicine, McGill University, Montreal, Canada
| | - Diane Provencher
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada.,Institut du cancer de Montréal, Montreal, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Canada
| | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada.,Institut du cancer de Montréal, Montreal, Canada.,Department of Medicine, Université de Montréal, Montreal, Canada
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49
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ARID1A deficiency promotes mutability and potentiates therapeutic antitumor immunity unleashed by immune checkpoint blockade. Nat Med 2018; 24:556-562. [PMID: 29736026 DOI: 10.1038/s41591-018-0012-z] [Citation(s) in RCA: 365] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
ARID1A (the AT-rich interaction domain 1A, also known as BAF250a) is one of the most commonly mutated genes in cancer1,2. The majority of ARID1A mutations are inactivating mutations and lead to loss of ARID1A expression 3 , which makes ARID1A a poor therapeutic target. Therefore, it is of clinical importance to identify molecular consequences of ARID1A deficiency that create therapeutic vulnerabilities in ARID1A-mutant tumors. In a proteomic screen, we found that ARID1A interacts with mismatch repair (MMR) protein MSH2. ARID1A recruited MSH2 to chromatin during DNA replication and promoted MMR. Conversely, ARID1A inactivation compromised MMR and increased mutagenesis. ARID1A deficiency correlated with microsatellite instability genomic signature and a predominant C>T mutation pattern and increased mutation load across multiple human cancer types. Tumors formed by an ARID1A-deficient ovarian cancer cell line in syngeneic mice displayed increased mutation load, elevated numbers of tumor-infiltrating lymphocytes, and PD-L1 expression. Notably, treatment with anti-PD-L1 antibody reduced tumor burden and prolonged survival of mice bearing ARID1A-deficient but not ARID1A-wild-type ovarian tumors. Together, these results suggest ARID1A deficiency contributes to impaired MMR and mutator phenotype in cancer, and may cooperate with immune checkpoint blockade therapy.
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50
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Abbosh PH, Plimack ER. Molecular and Clinical Insights into the Role and Significance of Mutated DNA Repair Genes in Bladder Cancer. Bladder Cancer 2018; 4:9-18. [PMID: 29430503 PMCID: PMC5798524 DOI: 10.3233/blc-170129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA damage response and repair genes (DDR genes) are commonly mutated in bladder cancer. The biological impact of these mutations is an area of intense basic, translational, and clinical interest. As next generation sequencing increases its foothold in the treatment of localized and advanced bladder cancer, the role of DDR genes will continue to evolve. We review the inventory and biology of DDR genes in bladder cancer and describe known and candidate roles for loss of DDR genes to engender therapeutic susceptibilities to various anti-cancer agents.
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Affiliation(s)
- Philip H Abbosh
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.,Department of Urology, Einstein Medical Center, Philadelphia, PA, USA
| | - Elizabeth R Plimack
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
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