1
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Zhang X, Chen R, Huo Z, Li W, Jiang M, Su G, Liu Y, Cai Y, Huang W, Xiong Y, Wang S. Blood-based molecular and cellular biomarkers of early response to neoadjuvant PD-1 blockade in patients with non-small cell lung cancer. Cancer Cell Int 2024; 24:225. [PMID: 38951894 PMCID: PMC11218110 DOI: 10.1186/s12935-024-03412-3] [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: 02/23/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Despite the improved survival observed in PD-1/PD-L1 blockade therapy, a substantial proportion of cancer patients, including those with non-small cell lung cancer (NSCLC), still lack a response. METHODS Transcriptomic profiling was conducted on a discovery cohort comprising 100 whole blood samples, as collected multiple times from 48 healthy controls (including 43 published data) and 31 NSCLC patients that under treatment with a combination of anti-PD-1 Tislelizumab and chemotherapy. Differentially expressed genes (DEGs), simulated immune cell subsets, and germline DNA mutational markers were identified from patients achieved a pathological complete response during the early treatment cycles. The predictive values of mutational markers were further validated in an independent immunotherapy cohort of 1661 subjects, and then confirmed in genetically matched lung cancer cell lines by a co-culturing model. RESULTS The gene expression of hundreds of DEGs (FDR p < 0.05, fold change < -2 or > 2) distinguished responders from healthy controls, indicating the potential to stratify patients utilizing early on-treatment features from blood. PD-1-mediated cell abundance changes in memory CD4 + and regulatory T cell subset were more significant or exclusively observed in responders. A panel of top-ranked genetic alterations showed significant associations with improved survival (p < 0.05) and heightened responsiveness to anti-PD-1 treatment in patient cohort and co-cultured cell lines. CONCLUSION This study discovered and validated peripheral blood-based biomarkers with evident predictive efficacy for early therapy response and patient stratification before treatment for neoadjuvant PD-1 blockade in NSCLC patients.
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Affiliation(s)
- Xi Zhang
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China.
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 710069, Shaanxi, Xi'an, China.
| | - Rui Chen
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Zirong Huo
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wenqing Li
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Mengju Jiang
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Guodong Su
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yuru Liu
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yu Cai
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wuhao Huang
- Department of Lung Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China
| | - Yuyan Xiong
- School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 710069, Shaanxi, Xi'an, China
| | - Shengguang Wang
- Department of Lung Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China.
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2
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Shen A, Arbesman M, Lodha R, Rayman P, Bungo B, Ni Y, Chan T, Gastman B, Ko J, Diaz-Montero CM, Arbesman J, Funchain P. Clinical and Immunologic Features of Germline Pathogenic Variant-Positive Patients with Melanoma. Clin Cancer Res 2024; 30:564-574. [PMID: 38032355 DOI: 10.1158/1078-0432.ccr-23-1964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/07/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
PURPOSE Malignant melanoma represents the most lethal skin cancer with germline predispositions thought to comprise 10% to 15% of all melanoma cases. No studies to date examine the immunologic features that may differentiate survival differences between germline pathogenic variant (gPV)-positive patients with melanoma from gPV-negative patients with melanoma. EXPERIMENTAL DESIGN Adult patients with melanoma and clinical characteristics suggesting hereditary predisposition to cancer were prospectively recruited to undergo germline testing and flow cytometric analysis of peripheral immune suppressor cells. RESULTS In this cohort, gPV-positive patients (n = 72) had a significantly improved melanoma-specific survival (MSS) compared with gPV-negative patients (n = 411; HRadj, 0.32; 95% CI, 0.13-0.82; P = 0.01). These survival improvements among gPV-positive patients were most apparent among cutaneous melanoma subtypes (HRadj, 0.12; 95% CI, 0.016-0.86; P = 0.03) and numerically improved in later-stage (IIB-IV) patients (HRadj, 0.34; 95% CI, 0.10-1.11; P = 0.06). Further, gPV-positive patients had a significantly lower level of total circulating PMN-MDSC compared with gPV-negative patients (P = 0.01), which was most apparent in those diagnosed with later stages (IIB-IV) of melanoma (P = 0.009). Finally, a significant upregulation of inflammatory transcriptome signatures in later-stage gPV-positive patients (n = 21) was observed in comparison with gPV-negative patients (n = 173) in the cutaneous melanoma cohort (SKCM) of The Cancer Genome Atlas (TCGA). CONCLUSIONS gPV-positive patients with melanoma exhibit improved MSS in addition to reduced peripheral PMN-MDSC and an enhanced inflammatory microenvironment.
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Affiliation(s)
- Alan Shen
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | | | - Roshan Lodha
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Patricia Rayman
- Cleveland Clinic Immuno-monitoring Laboratory, Cleveland, Ohio
| | - Brandon Bungo
- Cleveland Clinic Taussig Cancer Institute, Cleveland, Ohio
| | - Ying Ni
- Cleveland Clinic Center for Precision Immunotherapy, Cleveland, Ohio
| | - Timothy Chan
- Cleveland Clinic Center for Precision Immunotherapy, Cleveland, Ohio
| | - Brian Gastman
- Cleveland Clinic Center for Precision Immunotherapy, Cleveland, Ohio
- Cleveland Clinic Department of Dermatology and Plastic Surgery, Cleveland, Ohio
| | - Jennifer Ko
- Cleveland Clinic Immuno-monitoring Laboratory, Cleveland, Ohio
- Cleveland Clinic Center for Precision Immunotherapy, Cleveland, Ohio
- Cleveland Clinic Department of Dermatology and Plastic Surgery, Cleveland, Ohio
| | - C Marcela Diaz-Montero
- Cleveland Clinic Immuno-monitoring Laboratory, Cleveland, Ohio
- Cleveland Clinic Center for Precision Immunotherapy, Cleveland, Ohio
| | - Joshua Arbesman
- Cleveland Clinic Department of Dermatology and Plastic Surgery, Cleveland, Ohio
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3
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Braunstein EM, Imada E, Pasca S, Wang S, Chen H, Alba C, Hupalo DN, Wilkerson M, Dalgard CL, Ghannam J, Liu Y, Marchionni L, Moliterno A, Hourigan CS, Gondek LP. Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms. Leukemia 2023; 37:627-635. [PMID: 36543879 DOI: 10.1038/s41375-022-01797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Genetic predisposition (familial risk) in the myeloproliferative neoplasms (MPNs) is more common than the risk observed in most other cancers, including breast, prostate, and colon. Up to 10% of MPNs are considered to be familial. Recent genome-wide association studies have identified genomic loci associated with an MPN diagnosis. However, the identification of variants with functional contributions to the development of MPN remains limited. In this study, we have included 630 MPN patients and whole genome sequencing was performed in 64 individuals with familial MPN to uncover recurrent germline predisposition variants. Both targeted and unbiased filtering of single nucleotide variants (SNVs) was performed, with a comparison to 218 individuals with MPN unselected for familial status. This approach identified an ATM L2307F SNV occurring in nearly 8% of individuals with familial MPN. Structural protein modeling of this variant suggested stabilization of inactive ATM dimer, and alteration of the endogenous ATM locus in a human myeloid cell line resulted in decreased phosphorylation of the downstream tumor suppressor CHEK2. These results implicate ATM, and the DNA-damage response pathway, in predisposition to MPN.
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Affiliation(s)
- Evan M Braunstein
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Eddie Imada
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Shiyu Wang
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hang Chen
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA.,Committee on Genetics, Genomics and Systems Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Camille Alba
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Dan N Hupalo
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew Wilkerson
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yujia Liu
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Luigi Marchionni
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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4
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Vanni I, Pastorino L, Tanda ET, Andreotti V, Dalmasso B, Solari N, Mascherini M, Cabiddu F, Guadagno A, Coco S, Allavena E, Bruno W, Pietra G, Croce M, Gangemi R, Piana M, Zoppoli G, Ferrando L, Spagnolo F, Queirolo P, Ghiorzo P. Whole-Exome Sequencing and cfDNA Analysis Uncover Genetic Determinants of Melanoma Therapy Response in a Real-World Setting. Int J Mol Sci 2023; 24:ijms24054302. [PMID: 36901733 PMCID: PMC10002464 DOI: 10.3390/ijms24054302] [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: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023] Open
Abstract
Although several studies have explored the molecular landscape of metastatic melanoma, the genetic determinants of therapy resistance are still largely unknown. Here, we aimed to determine the contribution of whole-exome sequencing and circulating free DNA (cfDNA) analysis in predicting response to therapy in a consecutive real-world cohort of 36 patients, undergoing fresh tissue biopsy and followed during treatment. Although the underpowered sample size limited statistical analysis, samples from non-responders had higher copy number variations and mutations in melanoma driver genes compared to responders in the BRAF V600+ subset. In the BRAF V600- subset, Tumor Mutational Burden (TMB) was twice that in responders vs. non-responders. Genomic layout revealed commonly known and novel potential intrinsic/acquired resistance driver gene variants. Among these, RAC1, FBXW7, GNAQ mutations, and BRAF/PTEN amplification/deletion were present in 42% and 67% of patients, respectively. Both Loss of Heterozygosity (LOH) load and tumor ploidy were inversely associated with TMB. In immunotherapy-treated patients, samples from responders showed higher TMB and lower LOH and were more frequently diploid compared to non-responders. Secondary germline testing and cfDNA analysis proved their efficacy in finding germline predisposing variants carriers (8.3%) and following dynamic changes during treatment as a surrogate of tissue biopsy, respectively.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
| | - Enrica Teresa Tanda
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Nicola Solari
- Surgical Oncology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Matteo Mascherini
- Surgical Clinic Unit 1, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Cabiddu
- Anatomic Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Antonio Guadagno
- Anatomic Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Eleonora Allavena
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
| | - Gabriella Pietra
- IRCCS Ospedale Policlinico San Martino, U.O. Immunologia, 16132 Genoa, Italy
- Department of Experimental Medicine (DiMES), University of Genoa, 16132 Genoa, Italy
| | - Michela Croce
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Rosaria Gangemi
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Michele Piana
- Dipartimento di Matematica (MIDA), University of Genoa, 16132 Genoa, Italy
- Life Science Computational Laboratory (LISCOMP), IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Lorenzo Ferrando
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Spagnolo
- Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate (DISC), University of Genoa, 16132 Genoa, Italy
| | - Paola Queirolo
- Melanoma, Sarcoma & Rare Tumors Division, European Institute of Oncology (IEO), 20141 Milan, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132 Genoa, Italy
- Correspondence: ; Tel.: +39-010-5557255
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5
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Chat V, Dagayev S, Moran U, Snuderl M, Weber J, Ferguson R, Osman I, Kirchhoff T. A genome-wide association study of germline variation and melanoma prognosis. Front Oncol 2023; 12:1050741. [PMID: 36741706 PMCID: PMC9894711 DOI: 10.3389/fonc.2022.1050741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 01/20/2023] Open
Abstract
Background The high mortality of cutaneous melanoma (CM) is partly due to unpredictable patterns of disease progression in patients with early-stage lesions. The reliable prediction of advanced disease risk from early-stage CM, is an urgent clinical need, especially given the recent expansion of immune checkpoint inhibitor therapy to the adjuvant setting. In our study, we comprehensively investigated the role of germline variants as CM prognostic markers. Methods We performed a genome-wide association analysis in two independent cohorts of N=551 (discovery), and N=550 (validation) early-stage immunotherapy-naïve melanoma patients. A multivariable Cox proportional hazard regression model was used to identify associations with overall survival in the discovery group, followed by a validation analysis. Transcriptomic profiling and survival analysis were used to elucidate the biological relevance of candidate genes associated with CM progression. Results We found two independent associations of germline variants with melanoma prognosis. The alternate alleles of these two SNPs were both associated with an increased risk of death [rs60970102 in MELK: HR=3.14 (2.05-4.81), p=1.48×10-7; and rs77480547 in SH3BP4: HR=3.02 (2.02-4.52), p=7.58×10-8, both in the pooled cohort]. The addition of the combined risk alleles (CRA) of the identified variants into the prognostic model improved the predictive power, as opposed to a model of clinical covariates alone. Conclusions Our study provides suggestive evidence of novel melanoma germline prognostic markers, implicating two candidate genes: an oncogene MELK and a tumor suppressor SH3BP4, both previously suggested to affect CM progression. Pending further validation, these findings suggest that the genetic factors may improve the prognostic stratification of high-risk early-stage CM patients, and propose putative biological insights for potential therapeutic investigation of these targets to prevent aggressive outcome from early-stage melanoma.
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Affiliation(s)
- Vylyny Chat
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Sasha Dagayev
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Una Moran
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Matija Snuderl
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Jeffrey Weber
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States
| | - Robert Ferguson
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States,*Correspondence: Tomas Kirchhoff, ; Robert Ferguson,
| | - Iman Osman
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States,Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, United States
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States,Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY, United States,The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, NY, United States,*Correspondence: Tomas Kirchhoff, ; Robert Ferguson,
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6
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Mordoh A, Triviño Pardo JC, Carri I, Barrio MM, Mordoh J, Aris M. Early contribution of germline and nevi genetic alterations to a rapidly-progressing cutaneous melanoma patient: a case report. BMC Med Genomics 2023; 16:1. [PMID: 36604730 PMCID: PMC9814418 DOI: 10.1186/s12920-022-01426-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Cutaneous melanoma is the skin cancer with the highest mutational burden and metastatic rate. Early genetic alterations and biomarkers of distant progression are a point of interest. In addition to germline-susceptibility loci, almost 30% of melanomas arise from precursor benign nevi lesions, providing a source for malignant transformation. CASE PRESENTATION Patient#009 developed a cutaneous melanoma over a nevus, followed by progression to regional and distant metastases in months, unresponsive to targeted therapy. To search for the genetic contribution to this rapid progression, a longitudinal analysis was performed through WES of germline, nevi, primary tumor, and a metastatic lymph node. Differential SNP/INDEL and CNV gene alterations, with functional impact on key pathways and cancer hallmarks in each step of evolution, were discerned. Tumor-associated nevus was, for the first time, split into two sections, distant and adjacent to the primary tumor, to study its heterogeneity. Shared SNP alterations, with stable allele fraction from germline to metastasis were detected, mainly affecting DNA repair genes and promoting genome instability. Early somatic alterations, shared by nevi and primary and metastatic tumors, included BRAFV600E and focal copy-loss of several genes, acquiring additional cancer hallmarks. Phylogenetic analyses revealed that these common somatic alterations would provide a "bridge", allowing progression from a benign to a malignant state. Distant and adjacent nevi were rich in alterations, presenting differential SNP and CNV alterations. Upon tumor transformation, a marked increase in CNV over SNP alterations was determined. Both the number of SNP and CNV-affected genes, including known driver genes, increased throughout progression, although TMB levels remained lower than expected for melanoma. Typical alterations in BRAFV600E tumors related to intrinsic resistance to targeted therapy were found, including BRAF amplification and loss of PTEN, CDKN2A/B, and TP53 surveillance genes. Finally, numerous metastatic alterations were detected, further promoting tumor progression. CONCLUSIONS In this patient, longitudinal WES analysis revealed a sequential and cumulative pattern of genetic alterations, where germline and nevi somatic events contributed early to its rapid clinical progression. In this case report, we found tumor-associated nevi as genetically heterogeneous precursor entities, in which potential prognostic biomarkers should be studied prospectively.
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Affiliation(s)
- Ana Mordoh
- grid.412714.50000 0004 0426 1806Hospital de Clínicas, Buenos Aires, Argentina
| | | | - Ibel Carri
- grid.108365.90000 0001 2105 0048Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - María Marcela Barrio
- grid.428809.fCentro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
| | - José Mordoh
- grid.428809.fCentro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina ,grid.488972.80000 0004 0637 445XInstituto Alexander Fleming, Buenos Aires, Argentina
| | - Mariana Aris
- grid.428809.fCentro de Investigaciones Oncológicas-Fundación Cáncer, Buenos Aires, Argentina
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7
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Association of TYR SNP rs1042602 with Melanoma Risk and Prognosis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122004. [PMID: 36556369 PMCID: PMC9785037 DOI: 10.3390/life12122004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Cutaneous melanoma is the most aggressive of skin tumors. In order to discover new biomarkers that could help us improve prognostic prediction in melanoma patients, we have searched for germline DNA variants associated with melanoma progression. Thus, after exome sequencing of a set of melanoma patients and healthy control individuals, we identified rs1042602, an SNP within TYR, as a good candidate. After genotyping rs1042602 in 1025 patients and 773 healthy donors, we found that the rs1042602-A allele was significantly associated with susceptibility to melanoma (CATT test: p = 0.0035). Interestingly, we also observed significant differences between patients with good and bad prognosis (5 years of follow-up) (n = 664) (CATT test for all samples p = 0.0384 and for men alone p = 0.0054). Disease-free-survival (DFS) analyses also showed that patients with the A allele had shorter DFS periods. In men, the association remained significant even in a multivariate Cox Proportional-hazards model, which was adjusted for age at diagnosis, Breslow thickness, ulceration and melanoma subtype (HR 0.4; 95% confidence interval (CI) 0.20-0.83; p = 0.0139). Based on our results, we propose that rs1042602-A is a risk allele for melanoma, which also seems to be responsible for a poorer prognosis of the disease, particularly in men.
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8
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Feltes BC, Menck CFM. Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108436. [PMID: 35952573 DOI: 10.1016/j.mrrev.2022.108436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 01/01/2023]
Abstract
POLη, encoded by the POLH gene, is a crucial protein for replicating damaged DNA and the most studied specialized translesion synthesis polymerases. Mutations in POLη are associated with cancer and the human syndrome xeroderma pigmentosum variant, which is characterized by extreme photosensitivity and an increased likelihood of developing skin cancers. The myriad of structural information about POLη is vast, covering dozens of different mutants, numerous crucial residues, domains, and posttranslational modifications that are essential for protein function within cells. Since POLη is key vital enzyme for cell survival, and mutations in this protein are related to aggressive diseases, understanding its structure is crucial for biomedical sciences, primarily due to its similarities with other Y-family polymerases and its potential as a targeted therapy-drug for tumors. This work provides an up-to-date review on structural aspects of the human POLη: from basic knowledge about critical residues and protein domains to its mutant variants, posttranslational modifications, and our current understanding of therapeutic molecules that target POLη. Thus, this review provides lessons about POLη's structure and gathers critical discussions and hypotheses that may contribute to understanding this protein's vital roles within the cells.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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9
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Zheng B, Cheng F, Yao Z, Zhang Y, Cong Z, Wang J, Niu Z, He W. Identification of New m6A Methylation Modification Patterns and Tumor Microenvironment Infiltration Landscape that Predict Clinical Outcomes for Papillary Renal Cell Carcinoma Patients. Front Cell Dev Biol 2022; 10:818194. [PMID: 35372339 PMCID: PMC8968637 DOI: 10.3389/fcell.2022.818194] [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: 11/19/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
N6-methyladenosine (m6A) is the product of the most prevalent mRNA modification in eukaryotic cells. Accumulating evidence shows that tumor microenvironment (TME) plays a pivotal role in tumor development. However, the underlying relationship between m6A modification and the TME of a papillary renal cell carcinoma (PRCC) is still unclear. To investigate the relationship between m6A modification and prognosis and immunotherapeutic efficacy for PRCC, we looked for distinct m6A modification patterns based on 23 m6A-related genes. Next, the correlation between m6A modification patterns and TME-related characteristics was investigated. Then, the intersected differentially expressed genes were selected and the scoring system, denoted as m6A score, was established to evaluate m6A modification, prognosis, and immunotherapeutic efficacy. In this study, three distinct m6A expression clusters were identified. Based on the results of immune cell infiltration analysis and functional analysis, carcinogenic pathways, TME-related immune cells, and pathways were identified as well. More importantly, the established m6A score showed good value in predicting clinical outcomes according to results using external cohorts. Specifically, PRCC patients with low m6A score value showed better survival, immunotherapeutic response, and higher tumor mutation burden. Furthermore, immunohistochemistry using PRCC clinical samples from our medical center was carried out and verified our results. In conclusion, this study highlights the underlying correlation between m6A modification and the immune landscape and, hence, enhances our understanding of the TME and improved the therapeutic outlook for PRCC patients.
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Affiliation(s)
- Bin Zheng
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fajuan Cheng
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhongshun Yao
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yiming Zhang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zixiang Cong
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianwei Wang
- Department of Urology, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, China
| | - Zhihong Niu
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Zhihong Niu, ; Wei He,
| | - Wei He
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Zhihong Niu, ; Wei He,
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10
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Song P, Zhou S, Qi X, Jiao Y, Gong Y, Zhao J, Yang H, Qian Z, Qian J, Tang L. RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy. J Bioinform Comput Biol 2022; 20:2250004. [PMID: 35287562 DOI: 10.1142/s0219720022500044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: RNA adenosine modifications are crucial for regulating RNA levels. N6-methyladenosine (m6A), N1-methyladenosine (m1A), adenosine-to-inosine RNA editing, and alternative polyadenylation (APA) are four major RNA modification types. Methods: We evaluated the altered mRNA expression profiles of 27 RNA modification enzymes and compared the differences in tumor microenvironment (TME) and clinical prognosis between two RNA modification patterns using unsupervised clustering. Then, we constructed a scoring system, WM_score, and quantified the RNA modifications in patients of gastric cancer (GC), associating WM_score with TME, clinical outcomes, and effectiveness of targeted therapies. Results: RNA adenosine modifications strongly correlated with TME and could predict the degree of TME cell infiltration, genetic variation, and clinical prognosis. Two modification patterns were identified according to high and low WM_scores. Tumors in the WM_score-high subgroup were closely linked with survival advantage, CD4[Formula: see text] T-cell infiltration, high tumor mutation burden, and cell cycle signaling pathways, whereas those in the WM_score-low subgroup showed strong infiltration of inflammatory cells and poor survival. Regarding the immunotherapy response, a high WM_score showed a significant correlation with PD-L1 expression, predicting the effect of PD-L1 blockade therapy. Conclusion: The WM_scoring system could facilitate scoring and prediction of GC prognosis.
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Affiliation(s)
- Peng Song
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Sheng Zhou
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Xiaoyang Qi
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Yuwen Jiao
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Yu Gong
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Jie Zhao
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Haojun Yang
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Zhifen Qian
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Jun Qian
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Liming Tang
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
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11
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Zebian A, El-Dor M, Shaito A, Mazurier F, Rezvani HR, Zibara K. XPC multifaceted roles beyond DNA damage repair: p53-dependent and p53-independent functions of XPC in cell fate decisions. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108400. [PMID: 35690409 DOI: 10.1016/j.mrrev.2021.108400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/15/2023]
Abstract
Xeroderma pigmentosum group C protein (XPC) acts as a DNA damage recognition factor for bulky adducts and as an initiator of global genome nucleotide excision repair (GG-NER). Novel insights have shown that the role of XPC is not limited to NER, but is also implicated in DNA damage response (DDR), as well as in cell fate decisions upon stress. Moreover, XPC has a proteolytic role through its interaction with p53 and casp-2S. XPC is also able to determine cellular outcomes through its interaction with downstream proteins, such as p21, ARF, and p16. XPC interactions with effector proteins may drive cells to various fates such as apoptosis, senescence, or tumorigenesis. In this review, we explore XPC's involvement in different molecular pathways in the cell and suggest that XPC can be considered not only as a genomic caretaker and gatekeeper but also as a tumor suppressor and cellular-fate decision maker. These findings envisage that resistance to cell death, induced by DNA-damaging therapeutics, in highly prevalent P53-deficent tumors might be overcome through new therapeutic approaches that aim to activate XPC in these tumors. Moreover, this review encourages care providers to consider XPC status in cancer patients before chemotherapy in order to improve the chances of successful treatment and enhance patients' survival.
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Affiliation(s)
- Abir Zebian
- University of Bordeaux, INSERM U1035, BMGIC, Bordeaux, France; PRASE, Lebanese University, Beirut, Lebanon
| | | | - Abdullah Shaito
- Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | | | | | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon; Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon.
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12
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Vergani E, Frigerio S, Dugo M, Devecchi A, Feltrin E, De Cecco L, Vallacchi V, Cossa M, Di Guardo L, Manoukian S, Peissel B, Ferrari A, Gallino G, Maurichi A, Rivoltini L, Sensi M, Rodolfo M. Genetic Variants and Somatic Alterations Associated with MITF-E318K Germline Mutation in Melanoma Patients. Genes (Basel) 2021; 12:1440. [PMID: 34573422 PMCID: PMC8469310 DOI: 10.3390/genes12091440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
The MITF-E318K variant has been implicated in genetic predisposition to cutaneous melanoma. We addressed the occurrence of MITF-E318K and its association with germline status of CDKN2A and MC1R genes in a hospital-based series of 248 melanoma patients including cohorts of multiple, familial, pediatric, sporadic and melanoma associated with other tumors. Seven MITF-E318K carriers were identified, spanning every group except the pediatric patients. Three carriers showed mutated CDKN2A, five displayed MC1R variants, while the sporadic carrier revealed no variants. Germline/tumor whole exome sequencing for this carrier revealed germline variants of unknown significance in ATM and FANCI genes and, in four BRAF-V600E metastases, somatic loss of the MITF wild-type allele, amplification of MITF-E318K and deletion of a 9p21.3 chromosomal region including CDKN2A and MTAP. In silico analysis of tumors from MITF-E318K melanoma carriers in the TCGA Pan-Cancer-Atlas dataset confirmed the association with BRAF mutation and 9p21.3 deletion revealing a common genetic pattern. MTAP was the gene deleted at homozygous level in the highest number of patients. These results support the utility of both germline and tumor genome analysis to define tumor groups providing enhanced information for clinical strategies and highlight the importance of melanoma prevention programs for MITF-E318K patients.
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Affiliation(s)
- Elisabetta Vergani
- Unit of Immunotherapy, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (E.V.); (S.F.); (V.V.); (L.R.)
| | - Simona Frigerio
- Unit of Immunotherapy, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (E.V.); (S.F.); (V.V.); (L.R.)
| | - Matteo Dugo
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy; (M.D.); (A.D.); (L.D.C.); (M.S.)
| | - Andrea Devecchi
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy; (M.D.); (A.D.); (L.D.C.); (M.S.)
| | - Erika Feltrin
- CRIBI Biotechnology Center, Via Bassi 58/B, 35131 Padua, Italy;
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy; (M.D.); (A.D.); (L.D.C.); (M.S.)
| | - Viviana Vallacchi
- Unit of Immunotherapy, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (E.V.); (S.F.); (V.V.); (L.R.)
| | - Mara Cossa
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
| | - Lorenza Di Guardo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
| | - Siranoush Manoukian
- Unit of Medical Genetics, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (S.M.); (B.P.)
| | - Bernard Peissel
- Unit of Medical Genetics, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (S.M.); (B.P.)
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
| | - Gianfrancesco Gallino
- Melanoma and Sarcoma Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (G.G.); (A.M.)
| | - Andrea Maurichi
- Melanoma and Sarcoma Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (G.G.); (A.M.)
| | - Licia Rivoltini
- Unit of Immunotherapy, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (E.V.); (S.F.); (V.V.); (L.R.)
| | - Marialuisa Sensi
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, Italy; (M.D.); (A.D.); (L.D.C.); (M.S.)
| | - Monica Rodolfo
- Unit of Immunotherapy, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy; (E.V.); (S.F.); (V.V.); (L.R.)
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13
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Aoude LG, Wong BZY, Bonazzi VF, Brosda S, Walters SB, Koufariotis LT, Naeini MM, Pearson JV, Oey H, Patel K, Bradford JJ, Bloxham CJ, Atkinson V, Law P, Strutton G, Bayley G, Yang S, Smithers BM, Waddell N, Miles K, Barbour AP. Radiomics Biomarkers Correlate with CD8 Expression and Predict Immune Signatures in Melanoma Patients. Mol Cancer Res 2021; 19:950-956. [PMID: 33811161 DOI: 10.1158/1541-7786.mcr-20-1038] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/18/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022]
Abstract
Treatment for metastatic melanoma includes targeted and/or immunotherapy. Although many patients respond, only a subset has complete response. As late-stage patients often have multiple tumors in difficult access sites, non-invasive techniques are necessary for the development of predictive/prognostic biomarkers. PET/CT scans from 52 patients with stage III/IV melanoma were assessed and CT image parameters were evaluated as prognostic biomarkers. Analysis indicated patients with high standard deviation or high mean of positive pixels (MPP) had worse progression-free survival (P = 0.00047 and P = 0.0014, respectively) and worse overall survival (P = 0.0223 and P = 0.0465, respectively). Whole-exome sequencing showed high MPP was associated with BRAF mutation status (P = 0.0389). RNA-sequencing indicated patients with immune "cold" signatures had worse survival, which was associated with CT biomarker, MPP4 (P = 0.0284). Multiplex immunofluorescence confirmed a correlation between CD8 expression and image biomarkers (P = 0.0028). IMPLICATIONS: CT parameters have the potential to be cost-effective biomarkers of survival in melanoma, and reflect the tumor immune-microenvironment. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/6/950/F1.large.jpg.
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Affiliation(s)
- Lauren G Aoude
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia.
| | - Bernadette Z Y Wong
- Princess Alexandra Hospital, Department of Medical Imaging, Woolloongabba, Queensland, Australia
- Department of Medical Imaging, Gold Coast University Hospital, Southport, Australia
| | - Vanessa F Bonazzi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Sandra Brosda
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Shaun B Walters
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Marjan M Naeini
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Harald Oey
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Kalpana Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Julia J Bradford
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Conor J Bloxham
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Victoria Atkinson
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
- Faculty of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Phillip Law
- Princess Alexandra Hospital, Department of Medical Imaging, Woolloongabba, Queensland, Australia
| | - Geoffrey Strutton
- Department of Anatomical Pathology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Gerard Bayley
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Samuel Yang
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - B Mark Smithers
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
- Faculty of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kenneth Miles
- Princess Alexandra Hospital, Department of Medical Imaging, Woolloongabba, Queensland, Australia
| | - Andrew P Barbour
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
- Queensland Melanoma Project, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
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14
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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15
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Lu H, Davis AJ. Human RecQ Helicases in DNA Double-Strand Break Repair. Front Cell Dev Biol 2021. [DOI: 10.3389/fcell.2021.640755 order by 1-- znbp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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16
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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17
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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18
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Lu H, Davis AJ. Human RecQ Helicases in DNA Double-Strand Break Repair. Front Cell Dev Biol 2021. [DOI: 10.3389/fcell.2021.640755 order by 1-- azli] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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19
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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20
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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21
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund–Thomson syndrome (RTS), Baller–Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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Lu H, Davis AJ. Human RecQ Helicases in DNA Double-Strand Break Repair. Front Cell Dev Biol 2021; 9:640755. [PMID: 33718381 PMCID: PMC7947261 DOI: 10.3389/fcell.2021.640755] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
RecQ DNA helicases are a conserved protein family found in bacteria, fungus, plants, and animals. These helicases play important roles in multiple cellular functions, including DNA replication, transcription, DNA repair, and telomere maintenance. Humans have five RecQ helicases: RECQL1, Bloom syndrome protein (BLM), Werner syndrome helicase (WRN), RECQL4, and RECQL5. Defects in BLM and WRN cause autosomal disorders: Bloom syndrome (BS) and Werner syndrome (WS), respectively. Mutations in RECQL4 are associated with three genetic disorders, Rothmund-Thomson syndrome (RTS), Baller-Gerold syndrome (BGS), and RAPADILINO syndrome. Although no genetic disorders have been reported due to loss of RECQL1 or RECQL5, dysfunction of either gene is associated with tumorigenesis. Multiple genetically independent pathways have evolved that mediate the repair of DNA double-strand break (DSB), and RecQ helicases play pivotal roles in each of them. The importance of DSB repair is supported by the observations that defective DSB repair can cause chromosomal aberrations, genomic instability, senescence, or cell death, which ultimately can lead to premature aging, neurodegeneration, or tumorigenesis. In this review, we will introduce the human RecQ helicase family, describe in detail their roles in DSB repair, and provide relevance between the dysfunction of RecQ helicases and human diseases.
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Affiliation(s)
- Huiming Lu
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Anthony J. Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, United States
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