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Stal J, Miller KA, Mullett TW, Boughey JC, Francescatti AB, Funk E, Nelson H, Freyer DR. Cancer Survivorship Care in the United States at Facilities Accredited by the Commission on Cancer. JAMA Netw Open 2024; 7:e2418736. [PMID: 38958979 PMCID: PMC11222991 DOI: 10.1001/jamanetworkopen.2024.18736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/21/2024] [Indexed: 07/04/2024] Open
Abstract
Importance Since 2021, American College of Surgeons Commission on Cancer (CoC) accreditation standards require providing a survivorship program for patients with adult-onset cancer treated with curative intent. Since more than 70% of all patients with cancer in the US are treated at CoC-accredited facilities, this presents an opportunity for a landscape analysis of survivorship care availability. Objective To determine the prevalence, types, and outcomes of cancer survivorship services at CoC-accredited facilities. Design, Setting, and Participants This survey study used an anonymous, online, cross-sectional survey conducted from May 4 to 25, 2023. Participants were CoC-accredited facilities in the US representing diverse CoC program categories, institutional characteristics, geographic regions, and practice types. Department of Veterans Affairs cancer programs were excluded due to data usage restrictions. Data were analyzed from July to October 2023. Exposure CoC Survivorship Standard 4.8 was released in October 2019 and programs were expected to adhere to the Standard beginning January 1, 2021. Main Outcomes and Measures Questions included self-reported survivorship program characteristics, availability of services aligned to CoC Survivorship Standard 4.8, and perceived program impacts. Response frequencies and proportions were determined in aggregate and by CoC program category. Results There were 1400 eligible programs, and 384 programs participated (27.4% response rate). All regions and eligible program categories were represented, and most had analytic caseloads of 500 to 4999 patients in 2021. Most survivorship program personnel included nurses (334 programs [87.0%]) and social workers (278 programs [72.4%]), while physical (180 programs [46.9%]) and occupational (87 programs [22.7%]) therapists were less common. Services most endorsed as available for all survivors were screening for new cancers (330 programs [87.5%]), nutritional counseling (325 programs [85.3%]), and referrals to specialists (320 programs [84.7%]), while treatment summaries (242 programs [64.7%]), and survivorship care plans (173 programs [43.0%]), sexual health (217 programs [57.3%]), and fertility (214 programs [56.9%]) were less common. Survivorship services were usually delivered by cancer treatment teams (243 programs [63.3%]) rather than specialized survivorship clinics (120 programs [31.3%]). For resources needed, additional advanced practice clinicians with dedicated survivorship effort (205 programs [53.4%]) and electronic health record enhancements (185 programs [48.2%]) were most endorsed. Lack of referrals and low patient awareness were endorsed as the primary barriers. A total of 335 programs (87.2%) agreed that Survivorship Standard 4.8 helped advance their programs. Conclusions and Relevance These findings of this survey study of CoC-accredited programs establish a benchmark for survivorship care delivery in the US, identify gaps in specific services and opportunities for intervention, contribute to longitudinal reevaluation for tracking progress nationally, and suggest the value of survivorship care standards.
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Affiliation(s)
- Julia Stal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
- Cancer Research Program, American College of Surgeons, Chicago, Illinois
| | - Kimberly A. Miller
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Timothy W. Mullett
- Markey Cancer Center, Cancer Prevention and Control Program, University of Kentucky, Lexington
- Department of Surgery, College of Medicine, University of Kentucky, Lexington
- Commission on Cancer, American College of Surgeons, Chicago, Illinois
| | - Judy C. Boughey
- Cancer Research Program, American College of Surgeons, Chicago, Illinois
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | | | - Elizabeth Funk
- Cancer Research Program, American College of Surgeons, Chicago, Illinois
| | - Heidi Nelson
- Cancer Research Program, American College of Surgeons, Chicago, Illinois
- Commission on Cancer, American College of Surgeons, Chicago, Illinois
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - David R. Freyer
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
- USC Norris Comprehensive Cancer Center, Los Angeles, California
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, California
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Dangoni GD, Teixeira ACB, da Costa SS, Scliar MO, Carvalho LML, Silva LN, Novak EM, Vince CSC, Maschietto MC, Sugayama SMM, Odone-Filho V, Krepischi ACV. Germline mutations in cancer predisposition genes among pediatric patients with cancer and congenital anomalies. Pediatr Res 2024; 95:1346-1355. [PMID: 38182823 DOI: 10.1038/s41390-023-03000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Childhood cancer has a poorly known etiology, and investigating the underlying genetic background may provide novel insights. A recognized association exists between non-chromosomal birth defects and childhood cancer susceptibility. METHODS We performed whole-exome sequencing and chromosomal microarray analysis in a cohort of childhood cancer (22 individuals, 50% with congenital anomalies) to unravel deleterious germline variants. RESULTS A diagnostic yield of 14% was found, encompassing heterozygous variants in bona fide dominant Cancer Predisposition Genes (CPGs). Considering candidate and recessive CPGs harboring monoallelic variants, which were also deemed to play a role in the phenotype, the yield escalated to 45%. Most of the deleterious variants were mapped in genes not conventionally linked to the patient's tumor type. Relevant findings were detected in 55% of the syndromic individuals, mostly variants potentially underlying both phenotypes. CONCLUSION We uncovered a remarkable prevalence of germline deleterious CPG variants, highlighting the significance of a comprehensive genetic analysis in pediatric cancer, especially when coupled with additional clinical signs. Moreover, our findings emphasized the potential for oligogenic inheritance, wherein multiple genes synergistically increase cancer risk. Lastly, our investigation unveiled potentially novel genotype-phenotype associations, such as SETD5 in neuroblastoma, KAT6A in gliomas, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. IMPACT Novel gene-phenotype associations and candidate genes for pediatric cancer were unraveled, such as KAT6A in gliomas, SETD5 in neuroblastoma, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. Our analysis revealed a high frequency of deleterious germline variants, particularly in cases accompanied by additional clinical signs, highlighting the importance of a comprehensive genetic evaluation in childhood cancer. Our findings also underscored the potential for oligogenic inheritance in pediatric cancer risk. Understanding the cancer etiology is crucial for genetic counseling, often influencing therapeutic decisions and offering valuable insights into molecular targets for the development of oncological therapies.
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Affiliation(s)
- Gustavo D Dangoni
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Anne Caroline B Teixeira
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Silvia S da Costa
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Laura M L Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Luciana N Silva
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Estela M Novak
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | | | - Sofia M M Sugayama
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Vicente Odone-Filho
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina V Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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Bagger FO, Borgwardt L, Jespersen AS, Hansen AR, Bertelsen B, Kodama M, Nielsen FC. Whole genome sequencing in clinical practice. BMC Med Genomics 2024; 17:39. [PMID: 38287327 PMCID: PMC10823711 DOI: 10.1186/s12920-024-01795-w] [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: 08/14/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024] Open
Abstract
Whole genome sequencing (WGS) is becoming the preferred method for molecular genetic diagnosis of rare and unknown diseases and for identification of actionable cancer drivers. Compared to other molecular genetic methods, WGS captures most genomic variation and eliminates the need for sequential genetic testing. Whereas, the laboratory requirements are similar to conventional molecular genetics, the amount of data is large and WGS requires a comprehensive computational and storage infrastructure in order to facilitate data processing within a clinically relevant timeframe. The output of a single WGS analyses is roughly 5 MIO variants and data interpretation involves specialized staff collaborating with the clinical specialists in order to provide standard of care reports. Although the field is continuously refining the standards for variant classification, there are still unresolved issues associated with the clinical application. The review provides an overview of WGS in clinical practice - describing the technology and current applications as well as challenges connected with data processing, interpretation and clinical reporting.
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Affiliation(s)
- Frederik Otzen Bagger
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Sand Jespersen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anna Reimer Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Miyako Kodama
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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Horackova K, Janatova M, Kleiblova P, Kleibl Z, Soukupova J. Early-Onset Ovarian Cancer <30 Years: What Do We Know about Its Genetic Predisposition? Int J Mol Sci 2023; 24:17020. [PMID: 38069345 PMCID: PMC10707471 DOI: 10.3390/ijms242317020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Ovarian cancer (OC) is one of the leading causes of cancer-related deaths in women. Most patients are diagnosed with advanced epithelial OC in their late 60s, and early-onset adult OC diagnosed ≤30 years is rare, accounting for less than 5% of all OC cases. The most significant risk factor for OC development are germline pathogenic/likely pathogenic variants (GPVs) in OC predisposition genes (including BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, Lynch syndrome genes, or BRIP1), which contribute to the development of over 20% of all OC cases. GPVs in BRCA1/BRCA2 are the most prevalent. The presence of a GPV directs tailored cancer risk-reducing strategies for OC patients and their relatives. Identification of OC patients with GPVs can also have therapeutic consequences. Despite the general assumption that early cancer onset indicates higher involvement of hereditary cancer predisposition, the presence of GPVs in early-onset OC is rare (<10% of patients), and their heritability is uncertain. This review summarizes the current knowledge on the genetic predisposition to early-onset OC, with a special focus on epithelial OC, and suggests other alternative genetic factors (digenic, oligogenic, polygenic heritability, genetic mosaicism, imprinting, etc.) that may influence the development of early-onset OC in adult women lacking GPVs in known OC predisposition genes.
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Affiliation(s)
- Klara Horackova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic; (K.H.); (M.J.); (P.K.); (Z.K.)
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Ryu J, Lee SH, Kim S, Jeong JW, Kim KS, Nam S, Kim JE. Urban dust particles disrupt mitotic progression by dysregulating Aurora kinase B-related functions. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132238. [PMID: 37586242 DOI: 10.1016/j.jhazmat.2023.132238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023]
Abstract
Particulate matter (PM), a major component of outdoor air pollution, damages DNA and increases the risk of cancer. Although the harmful effects of PM at the genomic level are known, the detailed mechanism by which PM affects chromosomal stability remains unclear. In this study, we investigated the novel effects of PM on mitotic progression and identified the underlying mechanisms. Gene set enrichment analysis of lung cancer patients residing in countries with high PM concentrations revealed the downregulation of genes associated with mitosis and mitotic structures. We also showed that exposure of lung cancer cells in vitro to urban dust particles (UDPs) inhibits cell proliferation through a prolonged M phase. The mitotic spindles in UDP-treated cells were hyperstabilized, and the number of centrioles increased. The rate of ingression of the cleavage furrow and actin clearance from the polar cortex was reduced significantly. The defects in mitotic progression were attributed to inactivation of Aurora B at kinetochore during early mitosis, and spindle midzone and midbody during late mitosis. While previous studies demonstrated possible links between PM and mitosis, they did not specifically identify the dysregulation of spatiotemporal dynamics of mitotic proteins and structures (e.g., microtubules, centrosomes, cleavage furrow, and equatorial and polar cortex), which results in the accumulation of chromosomal instability, ultimately contributing to carcinogenicity. The data highlight the novel scientific problem of PM-induced mitotic disruption. Additionally, we introduce a practical visual method for assessing the genotoxic outcomes of airborne pollutants, which has implications for future environmental and public health research.
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Affiliation(s)
- Jaewook Ryu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, the Republic of Korea; Department of Pharmacology, College of Medicine, Kyung Hee University, Seoul 02447, the Republic of Korea
| | - Seung Hyeun Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul 02447, the Republic of Korea
| | - Sungyeon Kim
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, the Republic of Korea
| | - Joo-Won Jeong
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, the Republic of Korea; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul 02447, the Republic of Korea
| | - Kyung Sook Kim
- Department of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 02447, the Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, the Republic of Korea; Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, the Republic of Korea
| | - Ja-Eun Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, the Republic of Korea; Department of Pharmacology, College of Medicine, Kyung Hee University, Seoul 02447, the Republic of Korea; Department of Precision Medicine, Graduate School, Kyung Hee University, Seoul 02447, the Republic of Korea.
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6
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Wang Y, Su M, Chen Y, Huang X, Ruan L, Lv Q, Li L. Research progress on the role and mechanism of DNA damage repair in germ cell development. Front Endocrinol (Lausanne) 2023; 14:1234280. [PMID: 37529603 PMCID: PMC10390305 DOI: 10.3389/fendo.2023.1234280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 06/28/2023] [Indexed: 08/03/2023] Open
Abstract
In the complex and dynamic processes of replication, transcription, and translation of DNA molecules, a large number of replication errors or damage can occur which lead to obstacles in the development process of germ cells and result in a decreased reproductive rate. DNA damage repair has attracted widespread attention due to its important role in the maintenance and regulation of germ cells. This study reports on a systematic review of the role and mechanism of DNA damage repair in germline development. First, the causes, detection methods, and repair methods of DNA damage, and the mechanism of DNA damage repair are summarized. Second, a summary of the causes of abnormal DNA damage repair in germ cells is introduced along with common examples, and the relevant effects of germ cell damage. Third, we introduce the application of drugs related to DNA damage repair in the treatment of reproductive diseases and related surgical treatment of abnormal DNA damage, and summarize various applications of DNA damage repair in germ cells. Finally, a summary and discussion is given of the current deficiencies in DNA damage repair during germ cell development and future research development. The purpose of this paper is to provide researchers engaged in relevant fields with a further systematic understanding of the relevant applications of DNA damage repair in germ cells and to gain inspiration from it to provide new research ideas for related fields.
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Affiliation(s)
- Yan Wang
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Mengrong Su
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Yujie Chen
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Xinyu Huang
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Lian Ruan
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Qizhuang Lv
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Li Li
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
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Andersen LVB, Larsen MJ, Davies H, Degasperi A, Nielsen HR, Jensen LA, Kroeldrup L, Gerdes AM, Lænkholm AV, Kruse TA, Nik-Zainal S, Thomassen M. Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness. Breast Cancer Res 2023; 25:69. [PMID: 37316882 DOI: 10.1186/s13058-023-01655-y] [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: 08/09/2022] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Familial breast cancer is in most cases unexplained due to the lack of identifiable pathogenic variants in the BRCA1 and BRCA2 genes. The somatic mutational landscape and in particular the extent of BRCA-like tumour features (BRCAness) in these familial breast cancers where germline BRCA1 or BRCA2 mutations have not been identified is to a large extent unknown. METHODS We performed whole-genome sequencing on matched tumour and normal samples from high-risk non-BRCA1/BRCA2 breast cancer families to understand the germline and somatic mutational landscape and mutational signatures. We measured BRCAness using HRDetect. As a comparator, we also analysed samples from BRCA1 and BRCA2 germline mutation carriers. RESULTS We noted for non-BRCA1/BRCA2 tumours, only a small proportion displayed high HRDetect scores and were characterized by concomitant promoter hypermethylation or in one case a RAD51D splice variant previously reported as having unknown significance to potentially explain their BRCAness. Another small proportion showed no features of BRCAness but had mutationally active tumours. The remaining tumours lacked features of BRCAness and were mutationally quiescent. CONCLUSIONS A limited fraction of high-risk familial non-BRCA1/BRCA2 breast cancer patients is expected to benefit from treatment strategies against homologue repair deficient cancer cells.
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Affiliation(s)
- Lars V B Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Helen Davies
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Andrea Degasperi
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Louise A Jensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lone Kroeldrup
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne-Vibeke Lænkholm
- Department of Surgical Pathology, Zealand University Hospital, 4000, Roskilde, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Serena Nik-Zainal
- Hutchison Research Centre, Early Cancer Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- European Sperm Bank, Copenhagen, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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Hathaway F, Martins R, Sorscher S, Bzura A, Dudbridge F, Fennell DA. Family Matters: Germline Testing in Thoracic Cancers. Am Soc Clin Oncol Educ Book 2023; 43:e389956. [PMID: 37167572 DOI: 10.1200/edbk_389956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Most thoracic cancers arise via a series of stepwise somatic alterations driven by a well-defined carcinogen (ie, tobacco or asbestos for lung cancer and mesothelioma, respectively). A small proportion can emerge on a background of pathogenic germline variants (PGVs), which have the property of heritability. In general, PGVs may be initially suspected on the basis of the presence of specific clinical features. Such gene × environment interactions significantly increase the risk of developing lung cancer (1.5- to 3.2-fold). PGVs have been discovered involving the actionable driver oncogene, epidermal growth factor receptor (EGFR), with an EGFR T790M PGV rate of 0.3%-0.9% in the nonsquamous non-small-cell lung cancer subtype. Its appearance during routine somatic DNA sequencing in those patients who have not had a previous tyrosine kinase inhibitor should raise suspicion. In patients with sporadic mesothelioma, BAP1 is the most frequently mutated tumor driver, with a PGV rate between 2.8% and 8%, associated with a favorable prognosis. BAP1 PGVs accelerate mesothelioma tumorigenesis after asbestos exposure in preclinical models and may be partly predicted by clinical criteria. At present, routine germline genetic testing for thoracic cancers is not a standard practice. Expert genetic counseling is, therefore, required for patients who carry a PGV. Ongoing studies aim to better understand the natural history of patients harboring PGVs to underpin future cancer prevention, precise counseling, and cancer management with the goal of improving the quality and length of life.
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Affiliation(s)
- Feighanne Hathaway
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago Comprehensive Cancer Center, Chicago, IL
| | - Renato Martins
- Department of Hematology, Oncology, Palliative Care, Virginia Commonwealth University, Richmond, VA
| | | | | | | | - Dean A Fennell
- The University of Leicester, Leicester, United Kingdom
- University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
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Ji SM, Choi JS, Lee JY, Kim S, Bae WY, Jang YW, Kim JE, Lee SH, Nam S, Jeong JW. Mild exposure to fine particulate matter promotes angiogenesis in non-small cell lung carcinoma. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121715. [PMID: 37120000 DOI: 10.1016/j.envpol.2023.121715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
Fine particulate matter (PM2.5) is associated with public health problems worldwide. Especially, PM2.5 induces epigenetic and microenvironmental changes in lung cancer. Angiogenesis is important for the development and growth of cancer and is mediated by angiogenic factors, including vascular endothelial growth factor. However, the effects of mild PM2.5 exposure on angiogenesis in lung cancer remain unclear. In this study, we examined angiogenic effects using relatively lower concentrations of PM2.5 than in other studies and found that PM2.5 increased angiogenic activities in both endothelial cells and non-small cell lung carcinoma cells. PM2.5 also promoted the growth and angiogenesis of lung cancer via the induction of hypoxia-inducible factor-1α (HIF-1α) in a xenograft mouse tumor model. Angiogenic factors, including vascular endothelial growth factor (VEGF), were highly expressed in lung cancer patients in countries with high PM2.5 levels in the atmosphere, and high expression of VEGF in lung cancer patients lowered the survival rate. Collectively, these results provide new insight into the mechanisms by which mild exposure to PM2.5 is involved in HIF-1α-mediated angiogenesis in lung cancer patients.
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Affiliation(s)
- Su Min Ji
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jae-Sun Choi
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea; Clinical Research Institute, Kyung Hee University Medical Center, Seoul, 02447, Republic of Korea
| | - Ji Young Lee
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Sungyeon Kim
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Woom-Yee Bae
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Ye Won Jang
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Ja-Eun Kim
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Pharmacology, College of Medicine, Kyung Hee Univeristy, Seoul, 02447, Republic of Korea
| | - Seung Hyeun Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Joo-Won Jeong
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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10
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Hoffman TL, Kershberg H, Goff J, Holmquist KJ, Haque R, Alvarado M. Next-generation universal hereditary cancer screening: implementation of an automated hereditary cancer screening program for patients with advanced cancer undergoing tumor sequencing in a large HMO. Fam Cancer 2023; 22:225-235. [PMID: 36261688 PMCID: PMC10020326 DOI: 10.1007/s10689-022-00317-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Abstract
Variants in hereditary cancer risk genes are frequently identified following tumor-based DNA sequencing and represent an opportunity to diagnose hereditary cancer. We implemented an automated hereditary cancer screening program in a large HMO for all patients who underwent tumor-based DNA sequencing to identify patients with hereditary cancer and determine if this approach augmented existing genetic counseling approaches driven by personal/family history criteria. Regular automated searches of a centralized tumor DNA variant database were performed for ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6, PALB2, and/or PMS2 variants, and germline hereditary cancer gene panel testing was offered to patients with tumor variants who had never undergone germline testing. Patients completing germline testing due to their tumor DNA test results were considered part of the tumor DNA safety net. Patients previously completing germline testing via traditional genetic counseling and tumor DNA safety net were compared for demographics, tumor type, presence of germline pathogenic/likely pathogenic (P/LP) variant, and whether NCCN criteria were met for hereditary cancer genetic testing. Germline P/LP variants were common in both groups. Patients who received germline testing through traditional genetic counseling were more likely to have cardinal hereditary tumors than the tumor DNA safety net group. Patients identified with hereditary cancer through traditional genetic counseling were more likely to meet NCCN personal/family history criteria for germline testing than the tumor DNA safety net group (99% versus 34%). A universal tumor DNA safety net screen is an important diagnostic strategy which augments traditional genetic counseling approaches based on personal/family history.
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Affiliation(s)
- Trevor L Hoffman
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA.
| | - Hilary Kershberg
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - John Goff
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - Kimberly J Holmquist
- Department of Research & Evaluation, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - Reina Haque
- Department of Research & Evaluation, Southern California Permanente Medical Group, Pasadena, CA, USA
- Dept. of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, 91101, Pasadena, CA, USA
| | - Monica Alvarado
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
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11
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Belcaid L, Bertelsen B, Wadt K, Tuxen I, Spanggaard I, Højgaard M, Benn Sørensen J, Ravn J, Lassen U, Cilius Nielsen F, Rohrberg K, Westmose Yde C. New pathogenic germline variants identified in mesothelioma. Lung Cancer 2023; 179:107172. [PMID: 36944283 DOI: 10.1016/j.lungcan.2023.03.008] [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: 11/15/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND Mesothelioma (MM) is associated with asbestos exposure, tumor heterogeneity and aggressive clinical behavior. Identification of germline pathogenic variants (PVs) in mesothelioma is relevant for identifying potential actionable targets and genetic counseling. METHODS 44 patients underwent whole exome sequencing (WES) or whole genome sequencing (WGS). Germline variants were selected according to association with inherited cancer using a 168-gene in silico panel, and variants classified according to ACMG/AMP classification as pathogenic (class 5) or likely pathogenic (class 4). RESULTS In total, 16 patients (36%) were found to carry pathogenic or likely pathogenic variants in 13 cancer associated genes (ATM, BAP1, BRCA2, CDKN2A, FANCA, FANCC, FANCD2, FANCM, MUTYH, NBN, RAD51B, SDHA and XPC). The germline PVs occurred in DNA repair pathways, including homologous recombination repair (HRR) (75%), nucleotide excision repair (6%), cell cycle regulatory (7%), base excision repair (6%), and hypoxic pathway (6%). Five (31%) patients with a germline PV had a first or second degree relative with mesothelioma compared to none for patients without a germline PV. Previously undiagnosed BRCA2 germline PVs were identified in two patients. Potential actionable targets based on the germline PVs were found in four patients (9%). CONCLUSION This study revealed a high frequency of germline PVs in patients with mesothelioma. Furthermore, we identified germline PVs in two genes (NBN & RAD51B) not previously associated with mesothelioma. The data support germline testing in mesothelioma and provide a rationale for additional investigation of the HRR pathway as a potential actionable target.
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Affiliation(s)
- Laila Belcaid
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark.
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Karin Wadt
- Dept. of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Ida Tuxen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Iben Spanggaard
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Martin Højgaard
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jens Benn Sørensen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jesper Ravn
- Dept. of Thoracic Surgery, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Ulrik Lassen
- Dept. of Oncology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
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12
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Paiella S, Azzolina D, Gregori D, Malleo G, Golan T, Simeone DM, Davis MB, Vacca PG, Crovetto A, Bassi C, Salvia R, Biankin AV, Casolino R. A systematic review and meta-analysis of germline BRCA mutations in pancreatic cancer patients identifies global and racial disparities in access to genetic testing. ESMO Open 2023; 8:100881. [PMID: 36822114 PMCID: PMC10163165 DOI: 10.1016/j.esmoop.2023.100881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Germline BRCA1 and BRCA2 mutations (gBRCAm) can inform pancreatic cancer (PC) risk and treatment but most of the available information is derived from white patients. The ethnic and geographic variability of gBRCAm prevalence and of germline BRCA (gBRCA) testing uptake in PC globally is largely unknown. MATERIALS AND METHODS We carried out a systematic review and prevalence meta-analysis of gBRCA testing and gBRCAm prevalence in PC patients stratified by ethnicity. The main outcome was the distribution of gBRCA testing uptake across diverse populations worldwide. Secondary outcomes included: geographic distribution of gBRCA testing uptake, temporal analysis of gBRCA testing uptake in ethnic groups, and pooled proportion of gBRCAm stratified by ethnicity. The study is listed under PROSPERO registration number #CRD42022311769. RESULTS A total of 51 studies with 16 621 patients were included. Twelve of the studies (23.5%) enrolled white patients only, 10 Asians only (19.6%), and 29 (56.9%) included mixed populations. The pooled prevalence of white, Asian, African American, and Hispanic patients tested per study was 88.7%, 34.8%, 3.6%, and 5.2%, respectively. The majority of included studies were from high-income countries (HICs) (64; 91.2%). Temporal analysis showed a significant increase only in white and Asians patients tested from 2000 to present (P < 0.001). The pooled prevalence of gBRCAm was: 3.3% in white, 1.7% in Asian, and negligible (<0.3%) in African American and Hispanic patients. CONCLUSIONS Data on gBRCA testing and gBRCAm in PC derive mostly from white patients and from HICs. This limits the interpretation of gBRCAm for treating PC across diverse populations and implies substantial global and racial disparities in access to BRCA testing in PC.
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Affiliation(s)
- S Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/Totuccio83
| | - D Azzolina
- Department of Environmental and Preventive Science, University of Ferrara, Ferrara
| | - D Gregori
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy. https://twitter.com/gregoriDario
| | - G Malleo
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/gimalleo
| | - T Golan
- Oncology Institute, Sheba Medical Center at Tel-Hashomer, Tel Aviv University, Tel Aviv, Israel
| | - D M Simeone
- Department of Surgery, New York University, New York; Perlmutter Cancer Center, New York University, New York. https://twitter.com/MadameSurgeon
| | - M B Davis
- Department of Surgery and Surgical Oncology, Weill Cornell University, New York; Englander Institute of Precision Medicine, Weill Cornell University, New York, USA. https://twitter.com/MeliD32
| | - P G Vacca
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/pvhdfm
| | - A Crovetto
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/crovetto_a
| | - C Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona
| | - R Salvia
- General and Pancreatic Surgery Unit, Pancreas Institute, University of Verona, Verona. https://twitter.com/SalviaRobi
| | - A V Biankin
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK; Faculty of Medicine, South Western Sydney Clinical School, University of NSW, Liverpool, Australia.
| | - R Casolino
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow.
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13
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Borja NA, Silva-Smith R, Huang M, Parekh DJ, Sussman D, Tekin M. Atypical ATMs: Broadening the phenotypic spectrum of ATM-associated hereditary cancer. Front Oncol 2023; 13:1068110. [PMID: 36865800 PMCID: PMC9971806 DOI: 10.3389/fonc.2023.1068110] [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: 10/12/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Heterozygous, loss-of-function germline variants in ATM have been associated with an increased lifetime risk of breast, pancreas, prostate, stomach, ovarian, colorectal, and melanoma cancers. We conducted a retrospective review of thirty-one unrelated patients found to be heterozygous for a germline pathogenic variant in ATM and identified a significant proportion of patients in this cohort with cancers not currently associated with the ATM hereditary cancer syndrome, including carcinomas of the gallbladder, uterus, duodenum, kidney, and lung as well as a vascular sarcoma. A comprehensive review of the literature found 25 relevant studies where 171 individuals with a germline deleterious ATM variant have been diagnosed with the same or similar cancers. The combined data from these studies were then used to estimate the prevalence of germline ATM pathogenic variants in these cancers, which ranged between 0.45% and 2.2%. Analysis of tumor sequencing performed in large cohorts demonstrated that the frequency of deleterious somatic ATM alterations in these atypical cancers equaled or exceeded the alteration frequency in breast cancer and occurred at a significantly higher rate than in other DNA-damage response tumor suppressors, namely BRCA1 and CHEK2. Furthermore, multi-gene analysis of somatic alterations in these atypical cancers demonstrated significant co-occurrence of pathogenic alterations in ATM with BRCA1 and CHEK2, while there was significant mutual exclusivity between pathogenic alterations in ATM and TP53. This indicates that germline ATM pathogenic variants may play a role in cancer initiation and progression in these atypical ATM malignancies, potentially influencing these cancers to be driven toward DNA-damage repair deficiency and away from loss of TP53. As such, these findings provide evidence for broadening of the ATM-cancer susceptibility syndrome phenotype to improve the recognition of affected patients and provide more efficacious, germline-directed therapies.
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Affiliation(s)
- Nicholas A. Borja
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Rachel Silva-Smith
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Marilyn Huang
- Division of Gynecologic Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Dipen J. Parekh
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Daniel Sussman
- Division of Digestive Health and Liver Diseases, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States,John P. Hussmann Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States,*Correspondence: Mustafa Tekin,
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14
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Hoeger PH, Koehler LM, Reipschlaeger M, Mercier S. Hereditary fibrosing poikiloderma (POIKTMP syndrome) report of a new mutation and review of the literature. Pediatr Dermatol 2023; 40:182-187. [PMID: 36102338 DOI: 10.1111/pde.15133] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023]
Abstract
Hereditary fibrosing poikiloderma with tendon contractures, myopathy, and pulmonary fibrosis (POIKTMP) is a genodermatosis with autosomal dominant inheritance caused by mutations in FAM111B. We report another case with a new pathogenic variant and analyze all previously published 34 cases with a focus on sequence of clinical presentation and genotype-phenotype correlation. POIKTMP is characterized by marked age-dependent clinical expressivity. FAM111B encodes a catalytic nuclear protein, expressed in many tissues, which contributes to impaired DNA repair affecting multiple systems. Specific inhibition of catalytic activity might be a future strategy to halt progression of this otherwise untreatable disease. Given the relentless progression of the disease, it would make sense to start such treatment as early as possible. In order to achieve this objective, children with suspected POIKTMP should therefore undergo early imaging of all relevant organ systems.
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Affiliation(s)
- Peter H Hoeger
- Department of Pediatrics, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany.,Department of Pediatric Dermatology, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Lisa M Koehler
- Department of Pediatrics, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany.,Department of Pediatric Dermatology, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Maria Reipschlaeger
- Department of Pediatrics, Catholic Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Sandra Mercier
- CHU Nantes, Service de génétique médicale, Centre de Référence des Maladies Neuromusculaires AOC, Filnemus, Euro-NMD, Nantes, France.,Nantes Université, CNRS, INSERM, l'Institut du Thorax, Nantes, France
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15
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Rhoda C, Sunda F, Kidzeru E, Khumalo NP, Arowolo A. FAM111B dysregulation promotes malignancy in fibrosarcoma and POIKTMP and a low-cost method for its mutation screening. Cancer Treat Res Commun 2023; 34:100679. [PMID: 36610347 DOI: 10.1016/j.ctarc.2022.100679] [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: 10/20/2022] [Revised: 12/05/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Mutations in the uncharacterised human FAM111B gene are associated with POIKTMP, a rare multi-organ fibrosing disease. Recent studies also reported the overexpression of FAM111B in specific cancers. Moreover, FAM111B mutation screening may prove expensive in under-resourced facilities. Therefore, this study investigated its cellular function and dysfunction and described an inexpensive mutation screening method. MATERIALS AND METHODS FAM111B expression was assessed in silico and validated in vitro in cell lines and primary skin fibroblasts from a South African POIKTMP-patient with the heterozygous FAM111B gene mutation: NM_198947.4: c.1861T>G (p. Tyr621Asp or Y621D) by qPCR and western blot. The cellular function of FAM111B was studied in HT1080 using various cell-based functional assays, and the Y621D mutation was genotyped by PCR-RFLP. RESULTS Expression studies showed upregulated FAM111B mRNA and protein in the cancer cells. High FAM111B expression with robust nuclear localization occurred in HT1080. Additionally, expression data and cell-based assays indicated that FAM111B led to the upregulation of cell migration, decreased cell apoptosis, and modulatory effects on cell proliferation. Y621D mutation showed similar effects on cell migration but minimal impact on cell apoptosis. FAM111B mRNA and protein expression were markedly downregulated (p ≤ 0.05) in the POIKTMP-patient's fibroblasts. The PCR-RFLP method successfully genotyped Y621D gene mutation. DISCUSSION FAM111B is a cancer-associated nuclear protein: Its modulation by mutations or overexpression may contribute to the malignancy of cancers and POIKTMP/fibrosis and poor clinical outcomes and represents a viable prognostic marker or therapeutic target. Furthermore, the PCR-RFLP method could prove a valuable tool for FAM111B mutation validation or screening in resource-constrained laboratories.
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Affiliation(s)
- Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Falone Sunda
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Elvis Kidzeru
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nonhlanhla P Khumalo
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
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Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers. Ann Oncol 2022; 33:1186-1199. [PMID: 35988656 DOI: 10.1016/j.annonc.2022.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Germline variant evaluation in precision oncology opens new paths towards the identification of patients with genetic tumor risk syndromes and the exploration of therapeutic relevance. Here, we present the results of germline variant analysis and their clinical implications in a precision oncology study for patients with predominantly rare cancers. PATIENTS AND METHODS Matched tumor and control genome/exome and RNA sequencing was performed for 1,485 patients with rare cancers (79%) and/or young adults (77% younger than 51 years) in the NCT/DKTK MASTER trial, a German multicenter, prospective observational precision oncology study. Clinical and therapeutic relevance of prospective pathogenic germline variant (PGV) evaluation was analyzed and compared to other precision oncology studies. RESULTS Ten percent of patients (n=157) harbored PGVs in 35 genes associated with autosomal dominant cancer predisposition, whereof up to 75% were unknown before study participation. Another five percent of patients (n=75) were heterozygous carriers for recessive genetic tumor risk syndromes. Particularly high PGV yields were found in patients with gastrointestinal stromal tumors (GISTs) (28%, 11/40), and more specific in wild-type GISTS (50%, n=10/20), leiomyosarcomas (21%, n=19/89), and hepatopancreaticobiliary cancers (16%, n=16/97). Forty-five percent of PGVs (n=100/221) supported treatment recommendations, and its implementation led to a clinical benefit in 40% of patients (n=10/25). A comparison of different precision oncology studies revealed variable PGV yields and considerable differences in germline variant analysis workflows. We therefore propose a detailed workflow for germline variant evaluation. CONCLUSIONS Genetic germline testing in patients with rare cancers can identify the very first patient in a hereditary cancer family and can lead to clinical benefit in a broad range of entities. Its routine implementation in precision oncology accompanied by the harmonization of germline variant evaluation workflows will increase clinical benefit and boost research.
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17
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Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity. Nat Commun 2022; 13:4485. [PMID: 35918329 PMCID: PMC9346116 DOI: 10.1038/s41467-022-31866-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The benefit of molecularly-informed therapies in cancer of unknown primary (CUP) is unclear. Here, we use comprehensive molecular characterization by whole genome/exome, transcriptome and methylome analysis in 70 CUP patients to reveal substantial mutational heterogeneity with TP53, MUC16, KRAS, LRP1B and CSMD3 being the most frequently mutated known cancer-related genes. The most common fusion partner is FGFR2, the most common focal homozygous deletion affects CDKN2A. 56/70 (80%) patients receive genomics-based treatment recommendations which are applied in 20/56 (36%) cases. Transcriptome and methylome data provide evidence for the underlying entity in 62/70 (89%) cases. Germline analysis reveals five (likely) pathogenic mutations in five patients. Recommended off-label therapies translate into a mean PFS ratio of 3.6 with a median PFS1 of 2.9 months (17 patients) and a median PFS2 of 7.8 months (20 patients). Our data emphasize the clinical value of molecular analysis and underline the need for innovative, mechanism-based clinical trials. The identification of molecular biomarkers in cancer of unknown primary site (CUP) cases may enable the improvement of prognosis in these patients. Here, the authors integrate whole genome/exome, transcriptome and methylome data in 70 CUP patients, recommend therapies based on their analysis and report clinical outcome data.
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18
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Arowolo A, Malebana M, Sunda F, Rhoda C. Proposed Cellular Function of the Human FAM111B Protein and Dysregulation in Fibrosis and Cancer. Front Oncol 2022; 12:932167. [PMID: 35860584 PMCID: PMC9293052 DOI: 10.3389/fonc.2022.932167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
FAM111B gene mutations are associated with a hereditary fibrosing poikiloderma known to cause poikiloderma, tendon contracture, myopathy, and pulmonary fibrosis (POIKTMP). In addition, the overexpression of FAM111B has been associated with cancer progression and poor prognosis. This review inferred the molecular function of this gene's protein product and mutational dysfunction in fibrosis and cancer based on recent findings from studies on this gene. In conclusion, FAM111B represents an uncharacterized protease involved in DNA repair, cell cycle regulation, and apoptosis. The dysregulation of this protein ultimately leads to fibrotic diseases like POIKTMP and cancers via the disruption of these cellular processes by the mutation of the FAM111B gene. Hence, it should be studied in the context of these diseases as a possible therapeutic target.
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Affiliation(s)
- Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Moses Malebana
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Falone Sunda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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19
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Carbone M, Pass HI, Ak G, Alexander HR, Baas P, Baumann F, Blakely AM, Bueno R, Bzura. A, Cardillo G, Churpek JE, Dianzani I, De Rienzo A, Emi M, Emri S, Felley-Bosco E, Fennell DA, Flores RM, Grosso F, Hayward NK, Hesdorffer M, Hoang CD, Johansson PA, Kindler HL, Kittaneh M, Krausz T, Mansfield A, Metintas M, Minaai M, Mutti L, Nielsen M, O’Byrne K, Opitz I, Pastorino S, Pentimalli F, de Perrot M, Pritchard A, Ripley RT, Robinson B, Rusch V, Taioli E, Takinishi Y, Tanji M, Tsao AS, Tuncer AM, Walpole S, Wolf A, Yang H, Yoshikawa Y, Zolodnick A, Schrump DS, Hassan R. Medical and surgical care of mesothelioma patients and their relatives carrying germline BAP1 mutations. J Thorac Oncol 2022; 17:873-889. [DOI: 10.1016/j.jtho.2022.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022]
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20
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Parsa FG, Nobili S, Karimpour M, Aghdaei HA, Nazemalhosseini-Mojarad E, Mini E. Fanconi Anemia Pathway in Colorectal Cancer: A Novel Opportunity for Diagnosis, Prognosis and Therapy. J Pers Med 2022; 12:396. [PMID: 35330396 PMCID: PMC8950345 DOI: 10.3390/jpm12030396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and has the second highest mortality rate globally. Thanks to the advent of next-generation sequencing technologies, several novel candidate genes have been proposed for CRC susceptibility. Germline biallelic mutations in one or more of the 22 currently recognized Fanconi anemia (FA) genes have been associated with Fanconi anemia disease, while germline monoallelic mutations, somatic mutations, or the promoter hypermethylation of some FANC genes increases the risk of cancer development, including CRC. The FA pathway is a substantial part of the DNA damage response system that participates in the repair of DNA inter-strand crosslinks through homologous recombination (HR) and protects genome stability via replication fork stabilization, respectively. Recent studies revealed associations between FA gene/protein tumor expression levels (i.e., FANC genes) and CRC progression and drug resistance. Moreover, the FA pathway represents a potential target in the CRC treatment. In fact, FANC gene characteristics may contribute to chemosensitize tumor cells to DNA crosslinking agents such as oxaliplatin and cisplatin besides exploiting the synthetic lethal approach for selective targeting of tumor cells. Hence, this review summarizes the current knowledge on the function of the FA pathway in DNA repair and genomic integrity with a focus on the FANC genes as potential predisposition factors to CRC. We then introduce recent literature that highlights the importance of FANC genes in CRC as promising prognostic and predictive biomarkers for disease management and treatment. Finally, we represent a brief overview of the current knowledge around the FANC genes as synthetic lethal therapeutic targets for precision cancer medicine.
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Affiliation(s)
- Fatemeh Ghorbani Parsa
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran; (F.G.P.); (H.A.A.)
| | - Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran; (F.G.P.); (H.A.A.)
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
- DENOTHE Excellence Center, University of Florence, 50139 Florence, Italy
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21
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McGuigan A, Whitworth J, Andreou A, Hearn T, Tischkowitz M, Maher ER. Multilocus Inherited Neoplasia Allele Syndrome (MINAS): an update. Eur J Hum Genet 2022; 30:265-270. [PMID: 34983940 PMCID: PMC8904543 DOI: 10.1038/s41431-021-01013-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Multi-locus Inherited Neoplasia Allele Syndrome (MINAS) refers to individuals with germline pathogenic variants in two or more cancer susceptibility genes(CSGs). With increased use of exome/genome sequencing it would be predicted that detection of MINAS would become more frequent. Here we review recent progress in knowledge of MINAS. A systematic literature search for reports of individuals with germline pathogenic variants in 2 or more of 94 CSGs was performed. In addition, participants with multiple primary tumours who underwent genome sequencing as part of the Rare Disease arm of the UK 100,000 Genomes Project were interrogated to detect additional cases. We identified 385 MINAS cases (211 reported in the last 5 years, 6 from 100,000 genomes participants). Most (287/385) cases contained at least one pathogenic variant in either BRCA1 or BRCA2. 108/385 MINAS cases had multiple primary tumours at presentation and a subset of cases presented unusual multiple tumour phenotypes. We conclude that, as predicted, increasing numbers of individuals with MINAS are being have been reported but, except for individuals with BRCA1/BRCA2 MINAS, individual CSG combinations are generally rare. In many cases it appears that the clinical phenotype is that which would be expected from the effects of the constituent CSG variants acting independently. However, in some instances the presence of unusual tumour phenotypes and/or multiple primary tumours suggests that there may be complex interactions between the relevant MINAS CSGs. Systematic reporting of MINAS cases in a MINAS database (e.g. https://databases.lovd.nl/shared/diseases/04296 ) will facilitate more accurate prognostic predictions for specific CSG combinations.
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Affiliation(s)
- Anthony McGuigan
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Avgi Andreou
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Timothy Hearn
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | | | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
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22
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Arowolo A, Rhoda C, Khumalo N. Mutations within the putative protease domain of the human FAM111B gene may predict disease severity and poor prognosis: A review of POIKTMP cases. Exp Dermatol 2022; 31:648-654. [PMID: 35122327 PMCID: PMC9344908 DOI: 10.1111/exd.14537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/22/2022] [Accepted: 02/01/2022] [Indexed: 11/27/2022]
Abstract
Mutations in the human FAM111B gene are associated with a rare, hereditary multi‐systemic fibrosing disease, POIKTMP. To date, there are ten POIKTMP‐associated FAM111B gene mutations reported in thirty‐six patients from five families globally. To investigate the clinical significance of these mutations, we summarized individual cases by clinical features and position of the reported FAM111B gene mutations as those within and outside the putative protease domain (MWPPD and MOPPD respectively). MWPPD cases had more clinical manifestations than MOPPD (25 versus 18). Although the most common clinical features of poikiloderma, alopecia and hypohidrosis overall occurred in 94%, 86% and 75% of all cases with no significant differences between the MOPPD and MWPPD group, less common features included life‐threatening (pulmonary fibrosis 47% vs. 13%; liver abnormalities specifically cirrhosis 26% vs. 7%) and physically disabling conditions (myopathy 53% vs. 20%; tendon contracture 55% vs. 7%) were more common in MWPPD cases. Similarly, the only 2 cases of POIKTMP with fatal pancreatic cancers were both only in the MWPPD group. This review thus suggests that mutations within the putative protease domain of the FAM111B protein are associated with a broader range of clinical features and may predict increased POIKTMP severity and a poorer prognosis.
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Affiliation(s)
- Afolake Arowolo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital and the Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital and the Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nonhlanhla Khumalo
- Hair and Skin Research Laboratory, Division of Dermatology, Groote Schuur Hospital and the Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
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23
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Xie Z, Ke Y, Chen J, Li Z, Wang C, Chen Y, Ding H, Cheng L. Prevalence and Spectrum of Predisposition Genes With Germline Mutations Among Chinese Patients With Bowel Cancer. Front Genet 2022; 12:755629. [PMID: 35154239 PMCID: PMC8829568 DOI: 10.3389/fgene.2021.755629] [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: 08/09/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Bowel cancer is the third-most common cancer and the second leading cause of cancer-related death worldwide. Bowel cancer has a substantial hereditary component; however, additional hereditary risk factors involved in bowel cancer pathogenesis have not been systematically defined. Materials and Methods: A total of 573 patients with bowel cancer were enrolled in the present study, of whom 93.72% had colorectal cancer (CRC). Germline mutations were integrated with somatic mutation information via utilizing target next-generation sequencing. Results: Pathogenic/Likely Pathogenic (P/LP) germline alterations were identified in 47 (8.2%) patients with bowel cancer and the ratio of the number of these patients with family history was significantly higher in the P/LP group than that noted in the non-pathogenic (Non-P) group. Certain rare germline alterations were noted, such as those noted in the following genes: FANCD2, CDH1, and FLCN. A total of 32 patients (68.1%) had germline alterations in the DNA-damage repair (DDR) genes and homologous recombination (HR) accounted for the highest proportion of this subgroup. By comparing 573 patients with bowel cancer with reference controls (China_MAPs database), significant associations (p < 0.01) were observed between the incidence of bowel cancer and the presence of mutations in APC, ATM, MLH1, FANCD2, MSH3, MSH6, PMS1, and RAD51D. Somatic gene differential analysis revealed a marked difference in 18 genes and a significant difference was also noted in tumor mutation burden (TMB) between germline mutation carriers and non-germline mutation subjects (p < 0.001). In addition, TMB in DDR mutation groups indicated a dramatic difference compared with the non-DDR mutation group (p < 0.01). However, no statistically significant differences in TMB were noted among detailed DDR pathways for patients with bowel cancer, irrespective of the presence of germline mutations. Moreover, a significantly higher level (p < 0.0001) of mutation count was observed in the DDR group from The Cancer Genome Atlas (TCGA) database and the DDR and non-DDR alteration groups displayed various immune profiles. Conclusion: Chinese patients with bowel cancer exhibited a distinct spectrum of germline variants, with distinct molecular characteristics such as TMB and DDR. Furthermore, the information on somatic mutations obtained from TCGA database indicated that a deeper understanding of the interactions among DDR and immune cells would be useful to further investigate the role of DDR in bowel cancer.
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24
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Lebedeva A, Shaykhutdinova Y, Seriak D, Ignatova E, Rozhavskaya E, Vardhan D, Manicka S, Sharova M, Grigoreva T, Baranova A, Mileyko V, Ivanov M. Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles. J Transl Med 2022; 20:29. [PMID: 35033101 PMCID: PMC8760669 DOI: 10.1186/s12967-022-03230-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Background A fraction of patients referred for complex molecular profiling of biopsied tumors may harbor germline variants in genes associated with the development of hereditary cancer syndromes (HCS). Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized. Methods Data from Next-Generation Sequencing (NGS) of biopsied tumor samples referred for complex molecular profiling were analyzed for germline variants in HCS-associated genes. Analysis of variant origin was performed employing bioinformatic algorithms followed by manual curation. When possible, the origin of the variant was validated by Sanger sequencing of the sample of normal tissue. The variants’ pathogenicity was assessed according to ACMG/AMP. Results Tumors were sampled from 183 patients (Males: 75 [41.0%]; Females: 108 [59.0%]; mean [SD] age, 57.7 [13.3] years) and analysed by targeted NGS. The most common tumor types were colorectal (19%), pancreatic (13%), and lung cancer (10%). A total of 56 sequence variants in genes associated with HCS were detected in 40 patients. Of them, 17 variants found in 14 patients were predicted to be of germline origin, with 6 variants interpreted as pathogenic (PV) or likely pathogenic (LPV), and 9 as variants of uncertain significance (VUS). For the 41 out of 42 (97%) missense variants in HCS-associated genes, the results of computational prediction of variant origin were concordant with that of experimental examination. We estimate that Sanger sequencing of a sample of normal tissue would be required for ~ 1–7% of the total assessed cases with PV or LPV, when necessity to follow with genetic counselling referral in ~ 2–15% of total assessed cases (PV, LPV or VUS found in HCS genes). Conclusion Incidental findings of pathogenic germline variants are common in data from cancer patients referred for complex molecular profiling. We propose an algorithm for the management of patients with newly detected variants in genes associated with HCS.
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Affiliation(s)
- Alexandra Lebedeva
- Atlas Oncodiagnostics, LLC, Moscow, Russia. .,Sechenov University, Moscow, Russia.
| | | | | | - Ekaterina Ignatova
- Atlas Oncodiagnostics, LLC, Moscow, Russia.,Department of chemotherapy №2, Federal State Budgetary Institution «N.N. Blokhin National Medical Research Center of Oncology» of the Ministry of Health of the Russian Federation, Moscow, Russia.,Department of Oncogenetics, Institute of Higher and Additional Professional Education, Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Sofia Manicka
- School of Systems Biology, George Mason University, Mannas, VA, USA
| | | | | | - Ancha Baranova
- School of Systems Biology, George Mason University, Mannas, VA, USA
| | | | - Maxim Ivanov
- Atlas Oncodiagnostics, LLC, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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25
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Beltrami CM, do Canto LM, Villacis RAR, Petersen AH, Aagaard MM, Cury SS, Formiga MNDC, Junior SA, Rogatto SR. The repertoire of germline variants in patients with early-onset rectal cancer. Cancer Commun (Lond) 2022; 42:481-485. [PMID: 35029067 PMCID: PMC9118063 DOI: 10.1002/cac2.12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/06/2021] [Accepted: 01/05/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Caroline Moraes Beltrami
- International Research Center - CIPE, A.C.Camargo Cancer Center, São Paulo, SP, 04002-010, Brazil.,Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Luisa Matos do Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Rolando André Rios Villacis
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília - UnB, Brasília, DF, 70910-900, Brazil
| | - Annabeth Høgh Petersen
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Mads Malik Aagaard
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | | | - Samuel Aguiar Junior
- Department of Pelvic Surgery, A.C.Camargo Cancer Center, São Paulo, SP, 04002-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark.,Faculty of Health Sciences, Institute of Regional Health Research, University of Southern Denmark, Odense, 5000, Denmark.,The Danish Colorectal Cancer Center South, University Hospital of Southern Denmark, Vejle, 7100, Denmark
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26
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Sculco M, La Vecchia M, Aspesi A, Pinton G, Clavenna MG, Casalone E, Allione A, Grosso F, Libener R, Muzio A, Rena O, Baietto G, Parini S, Boldorini R, Giachino D, Papotti M, Scagliotti GV, Migliore E, Mirabelli D, Moro L, Magnani C, Ferrante D, Matullo G, Dianzani I. Malignant pleural mesothelioma: Germline variants in DNA repair genes may steer tailored treatment. Eur J Cancer 2022; 163:44-54. [PMID: 35032816 DOI: 10.1016/j.ejca.2021.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/25/2021] [Accepted: 12/19/2021] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Malignant pleural mesothelioma (MPM) is a tumour associated with asbestos exposure. Approximately, 10% of patients with MPM carry a germline pathogenic variant (PV), mostly in DNA repair genes, suggesting the occurrence of inherited predispositions. AIM This article aimed to 1) search for new predisposing genes and assess the prevalence of PVs in DNA repair genes, by next-generation sequencing (NGS) analysis of germline DNA from 113 unselected patients with MPM and 2) evaluate whether these patients could be sensitive to tailored treatments. METHODS NGS was performed using a custom panel of 107 cancer-predisposing genes. To investigate the response to selected drugs in conditions of DNA repair insufficiency, we created a three-dimensional-MPM cell model that had a defect in ataxia telangiectasia mutated (ATM), the master regulator of DNA repair. RESULTS We identified PVs in approximately 7% of patients with MPM (8/113) and a new PV in BAP1 in a further patient with familial MPM. Most of these PVs were in genes involved or supposedly involved in DNA repair (BRCA1, BRIP1, CHEK2, SLX4, FLCN and BAP1). In vitro studies showed apoptosis induction in ATM-silenced/inhibited MPM spheroids treated with an enhancer of zeste homologue 2 inhibitor (tazemetostat). CONCLUSIONS Overall these data suggest that patients with MPM and DNA repair insufficiency may benefit from this treatment, which induces synthetic lethality.
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Affiliation(s)
- Marika Sculco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Marta La Vecchia
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Anna Aspesi
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Giulia Pinton
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Michela G Clavenna
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | | | - Federica Grosso
- Mesothelioma Unit, AO SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberta Libener
- Department of Integrated Activities Research and Innovation, AO SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Alberto Muzio
- Division of Medical Oncology, Ospedale Santo Spirito, Casale Monferrato (Alessandria), Italy
| | - Ottavio Rena
- Thoracic Surgery Unit, AOU Maggiore della Carità, Novara, Italy
| | - Guido Baietto
- Thoracic Surgery Unit, AOU Maggiore della Carità, Novara, Italy
| | - Sara Parini
- Thoracic Surgery Unit, AOU Maggiore della Carità, Novara, Italy
| | - Renzo Boldorini
- Department of Health Sciences, Section of Pathological Anatomy, Università del Piemonte Orientale, Novara, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, Università di Torino, AOU S. Luigi Gonzaga, Orbassano, (Torino), Italy
| | | | - Giorgio V Scagliotti
- Department of Oncology, Università di Torino, AOU S. Luigi Gonzaga, Orbassano, Torino, Italy
| | - Enrica Migliore
- Unit of Cancer Epidemiology, CPO-Piemonte and Università di Torino, Italy
| | - Dario Mirabelli
- Unit of Cancer Epidemiology, CPO-Piemonte and Università di Torino, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", Università di Torino, Italy
| | - Laura Moro
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Corrado Magnani
- Department of Translational Medicine, Unit of Medical Statistics, Università del Piemonte Orientale and Cancer Epidemiology, CPO Piemonte, Novara, Italy
| | - Daniela Ferrante
- Department of Translational Medicine, Unit of Medical Statistics, Università del Piemonte Orientale and Cancer Epidemiology, CPO Piemonte, Novara, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, Università di Torino, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", Università di Torino, Italy; Medical Genetics Unit, AOU Città Della Salute e della Scienza di Torino, Italy.
| | - Irma Dianzani
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Interdepartmental Center for Studies on Asbestos and Other Toxic Particulates "G. Scansetti", Università di Torino, Italy.
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27
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Klebe S, Hocking AJ, Soeberg M, Leigh J. The Significance of Short Latency in Mesothelioma for Attribution of Causation: Report of a Case with Predisposing Germline Mutations and Review of the Literature. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182413310. [PMID: 34948918 PMCID: PMC8702130 DOI: 10.3390/ijerph182413310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
Malignant mesothelioma is a tumour of the serosal membranes, related to asbestos exposure. Median latency is in the order of 40 years in various registries, but small numbers of cases with shorter latencies have long been reported and often dismissed as unrelated to asbestos exposure. However, emerging data regarding the significance of inherited mutations leading to a predisposition to mesothelioma suggest that the causative effect of asbestos may be associated with shorter latencies in a subset of patients. Here, we describe a male patient with germline mutations in RAD51 and p53 who developed peritoneal mesothelioma 8.5 years after well-documented asbestos exposure and discuss the current literature on the subject. Mesothelioma in situ is now a WHO-accepted diagnosis, but preliminary data reveal a potential lead time of 5 or more years to invasive disease, and this is also a factor which may affect the recording of latency (and potentially survival) in the future.
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Affiliation(s)
- Sonja Klebe
- Department of Anatomical Pathology, SA Pathology at Flinders Medical Centre, Adelaide, SA 5042, Australia
- Department of Anatomical Pathology, Flinders University, Adelaide, SA 5042, Australia;
- Correspondence:
| | - Ashleigh J. Hocking
- Department of Anatomical Pathology, Flinders University, Adelaide, SA 5042, Australia;
| | - Matthew Soeberg
- Asbestos Diseases Research Institute, Concord, NSW 2139, Australia; (M.S.); (J.L.)
| | - James Leigh
- Asbestos Diseases Research Institute, Concord, NSW 2139, Australia; (M.S.); (J.L.)
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28
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Germline variants in DNA repair genes are associated with young-onset head and neck cancer. Oral Oncol 2021; 122:105545. [PMID: 34598035 DOI: 10.1016/j.oraloncology.2021.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023]
Abstract
The genetic predisposition to head and neck carcinomas (HNSCC) and how the known risk factors (papillomavirus infection, alcohol, and tobacco consumption) contribute to the early-onset disease are barely explored. Although HNSCC at early onset is rare, its frequency is increasing in recent years. Germline and somatic variants were assessed to build a comprehensive genetic influence pattern in HNSCC predisposition and patient outcome. Whole-exome sequencing was performed in 45 oral and oropharynx carcinomas paired with normal samples of young adults (≤49 years). We found FANCG, CDKN2A, and TPP germline variants previously associated with HNSCC risk. At least one germline variant in DNA repair pathway genes was detected in 67% of cases. Germline and somatic variants (including copy number variations) in FAT1 gene were identified in 9 patients (20%) and 12 tumors (30%), respectively. Somatic variants were found in HNSCC associated genes, such as TP53, CDKN2A, and PIK3CA. To date, 55 of 521 cases from the large cohort of TCGA presented < 49 years old. A comparison between the somatic alterations of TCGA-HNSCC at early onset and our dataset revealed strong similarities. Protein-protein interaction analysis between somatic and germline altered genes revealed a central role of TP53. Altogether, germline alterations in DNA repair genes potentially contribute to an increased risk of developing HNSCC at early-onset, while FAT1 could impact the prognosis.
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29
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Roversi G, Colombo EA, Magnani I, Gervasini C, Maggiore G, Paradisi M, Larizza L. Spontaneous chromosomal instability in peripheral blood lymphocytes from two molecularly confirmed Italian patients with Hereditary Fibrosis Poikiloderma: insights into cancer predisposition. Genet Mol Biol 2021; 44:e20200332. [PMID: 34358284 PMCID: PMC8345126 DOI: 10.1590/1678-4685-gmb-2020-0332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Two Italian patients with the initial clinical diagnosis of Rothmund-Thomson
syndrome were negative for RECQL4 mutations but showed in
peripheral blood cells a spontaneous chromosomal instability significantly
higher than controls. Revisiting after time their clinical phenotype, the
suggestive matching with the autosomal dominant syndrome Poikiloderma,
Hereditary Fibrosing with Tendon Contracture, Myopathy and Pulmonary fibrosis
(POIKTMP) was confirmed by identification of the c.1879A>G (p.Arg627Gly)
alteration in FAM111B. We compare the overall clinical signs of
our patients with those of reported carriers of the same mutation and present
the up-to-date mutational repertoire of FAM111B and the related
phenotypic spectrum. Our snapshot highlights the age-dependent clinical
expressivity of POIKTMP and the need to follow-up patients to monitor the
multi-tissue impairment caused by FAM111B alterations. We link
our chromosomal instability data to the role of FAM111B in
cancer predisposition, pointed out by its implication in DNA-repair pathways and
the outcome of pancreatic cancer in 2 out of 17 adult POIKTMP patients. The
chromosomal instability herein highlighted well connects POIKTMP to
cancer-predisposing syndromes, such as Rothmund-Thomson which represents the
first hereditary poikiloderma entering in differential diagnosis with
POIKTMP.
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Affiliation(s)
- Gaia Roversi
- University of Milano-Bicocca, School of Medicine and Surgery, Department of Medicine and Surgery, Monza, Italy.,Università degli Studi di Milano, Genetica Medica, Dipartimento di Scienze della Salute, Milan, Italy
| | - Elisa Adele Colombo
- Università degli Studi di Milano, Genetica Medica, Dipartimento di Scienze della Salute, Milan, Italy
| | - Ivana Magnani
- Università degli Studi di Milano, Genetica Medica, Dipartimento di Scienze della Salute, Milan, Italy
| | - Cristina Gervasini
- Università degli Studi di Milano, Genetica Medica, Dipartimento di Scienze della Salute, Milan, Italy
| | - Giuseppe Maggiore
- Bambino Gesù Children's Hospital IRCCS, Division of Hepatology and Gastroenterology, Rome, Italy
| | - Mauro Paradisi
- Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Laboratory of Molecular and Cell Biology, Rome, Italy
| | - Lidia Larizza
- IRCCS Istituto Auxologico Italiano, Laboratorio di Citogenetica e Genetica Molecolare Umana, Milan, Italy
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30
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Kotoula V, Papadopoulou K, Tikas I, Fostira F, Vrettou E, Chrisafi S, Fountzilas E, Koliou GA, Apostolou P, Papazisis K, Zaramboukas T, Asimaki-Vlachopoulou A, Miliaras S, Ananiadis A, Poulios C, Natsiopoulos I, Tsiftsoglou A, Demiri E, Fountzilas G. Follow-up of tissue genomics in BRCA1/2 carriers who underwent prophylactic surgeries. Breast Cancer 2021; 28:1367-1382. [PMID: 34304347 DOI: 10.1007/s12282-021-01276-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE The genomic status of non-malignant tissues from carriers of pathogenic germline BRCA1/2 (gBRCA1/2) variants may reveal information towards individualized prophylaxis. We performed spatiotemporal tissue genotype comparisons in a real-life cohort of gBRCA1/2 carriers of Greek origin, who underwent multiple risk-reducing/prophylactic surgeries at various time points. METHODS Fifty-three women (median age 36 years) within cancer families were observed for up to 37.5 years; 43 were cancer carriers and 10 were healthy carriers. Histology review and genotyping were performed for 187 paraffin tissues (average: 3.5 per carrier) including 46 carcinomas (40 breast) and 141 non-malignant breast and gynecological samples. RESULTS High allelic imbalance (AI) and somatic pathogenic TP53 variants were present in cancer carriers only (p values < 0.0001). High AI was associated with gBRCA1/2 indels (p < 0.0001) and gBRCA2 alterations (p = 0.0109). Somatic (pathogenic) variants were infrequently shared between non-malignant tissues and matched carcinomas. Aberrations of gBRCA1 variant heterozygosity were noticed in tissues from cancer carriers only (13/43, 30.2%). These pertained to classic LOH (neoplastic lesions in 9/43 carriers, 20.9%) and under-representation of the germline variants (5 samples, 4 non-malignant, all in the breast). Both aberrations coexisted in matched samples in one case. Over time, germline variant heterozygosity prevailed in non-malignant tissues; intra-carrier genomic alterations were aggravated (21.1%), ameliorated (26.3%) or remained stable. CONCLUSION This real-life case study supports the need to address tissue genotypes from prophylactic surgeries in combination with polygenic scores towards personalized prophylaxis. To this end, knowing the traditionally classified pathogenic potential of a gBRCA1/2 variant may not be enough.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece. .,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece.
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Ioannis Tikas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Eleni Vrettou
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic of Thessaloniki, Thessaloníki, Greece.,European University of Cyprus, Nicosia, Cyprus
| | | | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Konstantinos Papazisis
- Department of Medical Oncology, Interbalkan European Medical Center, Thessaloníki, Greece
| | - Thomas Zaramboukas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | | | - Spyros Miliaras
- First Department of Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloníki, Greece
| | | | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Ioannis Natsiopoulos
- Department of Breast Surgery, Interbalkan European Medical Center, Thessaloníki, Greece
| | - Aris Tsiftsoglou
- Department of Surgery, St. Luke's Hospital, Thessaloníki, Greece
| | - Efterpi Demiri
- Department of Plastic Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloníki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece.,Aristotle University of Thessaloniki, Thessaloníki, Greece.,German Oncology Center, Limassol, Cyprus
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Fountzilas E, Kotoula V, Koliou GA, Liontos M, Papadopoulou K, Giannoulatou E, Papanikolaou A, Tikas I, Chrisafi S, Mauri D, Chatzopoulos K, Fostira F, Pectasides D, Oikonomopoulos G, Aivazi D, Andrikopoulou A, Visvikis A, Aravantinos G, Zagouri F, Fountzilas G. Tumor Genotyping and Homologous Recombination Repair Gene Variants in Patients With Epithelial Ovarian Cancer: Is Pathogenic Enough? Front Oncol 2021; 11:683057. [PMID: 34141624 PMCID: PMC8204021 DOI: 10.3389/fonc.2021.683057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
Our hypothesis was that the predictive accuracy of pathogenic variants in genes participating in the homologous recombination repair (HRR) system in patients with epithelial ovarian cancer (EOC) could be improved by considering additional next-generation sequencing (NGS) metrics. NGS genotyping was performed in tumor tissue, retrospectively and prospectively collected from patients with EOC, diagnosed from 8/1998 to 10/2016. Variants were considered clonal when variant allele frequencies corresponded to >25%. The primary endpoint was overall survival (OS). This study included 501 patients with EOC, predominantly with high-grade serous (75.2%) and advanced stage tumors (81.7%); median age was 58 years (22-84). Pathogenic and clonal pathogenic variants in HRR and/or TP53 genes were identified in 72.8% and 66.5% tumors, respectively. With a median follow-up of 123.9 months, the presence of either pathogenic or clonal pathogenic HRR-only variants was associated with longer OS compared to HRR/TP53 co-mutation (HR=0.54; 95% CI, 0.34-0.87, Wald's p=0.012 and HR=0.45; 95% CI, 0.27-0.78, Wald's p=0.004, respectively). However, only the presence of clonal HRR-only variants was independently associated with improved OS (HR=0.55; 95% CI, 0.32-0.94, p=0.030). Variant clonality and co-occuring TP53 variants affect the predictive value of HRR pathogenic variants for platinum agents in patients with EOC. Clinical Trial Registration [ClinicalTrials.gov], identifier [NCT04716374].
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Affiliation(s)
- Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic of Thessaloniki, Thessaloniki, Greece
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Michalis Liontos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Alexios Papanikolaou
- First Department of Obstetrics and Gynecology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Ioannis Tikas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Davide Mauri
- Department of Medical Oncology, Medical School, University of Ioannina, Ioannina, Greece.,Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Kyriakos Chatzopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | | | - Dimitra Aivazi
- First Department of Obstetrics and Gynecology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Angeliki Andrikopoulou
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Anastasios Visvikis
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Medical Oncology, German Oncology Center, Limassol, Cyprus
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Petrosino M, Novak L, Pasquo A, Chiaraluce R, Turina P, Capriotti E, Consalvi V. Analysis and Interpretation of the Impact of Missense Variants in Cancer. Int J Mol Sci 2021; 22:ijms22115416. [PMID: 34063805 PMCID: PMC8196604 DOI: 10.3390/ijms22115416] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Large scale genome sequencing allowed the identification of a massive number of genetic variations, whose impact on human health is still unknown. In this review we analyze, by an in silico-based strategy, the impact of missense variants on cancer-related genes, whose effect on protein stability and function was experimentally determined. We collected a set of 164 variants from 11 proteins to analyze the impact of missense mutations at structural and functional levels, and to assess the performance of state-of-the-art methods (FoldX and Meta-SNP) for predicting protein stability change and pathogenicity. The result of our analysis shows that a combination of experimental data on protein stability and in silico pathogenicity predictions allowed the identification of a subset of variants with a high probability of having a deleterious phenotypic effect, as confirmed by the significant enrichment of the subset in variants annotated in the COSMIC database as putative cancer-driving variants. Our analysis suggests that the integration of experimental and computational approaches may contribute to evaluate the risk for complex disorders and develop more effective treatment strategies.
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Affiliation(s)
- Maria Petrosino
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Leonore Novak
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory FSN-TECFIS-DIM, 00044 Frascati, Italy;
| | - Roberta Chiaraluce
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Paola Turina
- Dipartimento di Farmacia e Biotecnologie (FaBiT), University of Bologna, 40126 Bologna, Italy;
| | - Emidio Capriotti
- Dipartimento di Farmacia e Biotecnologie (FaBiT), University of Bologna, 40126 Bologna, Italy;
- Correspondence: (E.C.); (V.C.)
| | - Valerio Consalvi
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
- Correspondence: (E.C.); (V.C.)
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33
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Cheung M, Kadariya Y, Sementino E, Hall MJ, Cozzi I, Ascoli V, Ohar JA, Testa JR. Novel LRRK2 mutations and other rare, non-BAP1-related candidate tumor predisposition gene variants in high-risk cancer families with mesothelioma and other tumors. Hum Mol Genet 2021; 30:1750-1761. [PMID: 34008015 DOI: 10.1093/hmg/ddab138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
There is irrefutable evidence that germline BAP1 mutations contribute to malignant mesothelioma (MM) susceptibility. However, BAP1 mutations are not found in all cases with evidence of familial MM or in other high-risk cancer families affected by various cancers, including MM. The goal of this study was to use whole genome sequencing (WGS) to determine the frequency and types of germline gene variants occurring in 12 MM patients selected from a series of 141 asbestos-exposed MM patients with a family history of cancer but without a germline BAP1 mutation. WGS was also performed on 2 MM cases, a proband and sibling, from a previously reported family with multiple cases of MM without inheritance of a predisposing BAP1 mutation. Altogether, germline DNA sequencing variants were identified in 20 cancer-related genes in 10 of the 13 probands. Germline indel, splice site, and missense mutations and two large deletions were identified. Among the 13 MM index cases, 6 (46%) exhibited one or more predicted pathogenic mutations. Affected genes encode proteins involved in DNA repair (ATM, ATR, BRCA2, BRIP1, CHEK2, MLH3, MUTYH, POLE, POLE4, POLQ, XRCC1), chromatin modification (ARID1B, DNMT3A, JARID2, SETD1B) or other cellular pathways: LRRK2 (2 cases) and MSH4. Notably, somatic truncating mutation or deletions of LRRK2 were occasionally found in MMs in The Cancer Genome Atlas, and expression of LRRK2 was undetectable or downregulated in a majority of primary MMs and MM cell lines we examined, implying that loss of LRRK2 expression is a newly recognized tumor suppressor alteration in MM.
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Affiliation(s)
| | | | | | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111 USA
| | - Ilaria Cozzi
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University of Rome, Italy
| | - Valeria Ascoli
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University of Rome, Italy
| | - Jill A Ohar
- Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1054 USA
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Zimmermann MT, Mathison AJ, Stodola T, Evans DB, Abrudan JL, Demos W, Tschannen M, Aldakkak M, Geurts J, Lomberk G, Tsai S, Urrutia R. Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level. Front Oncol 2021; 11:606820. [PMID: 33747920 PMCID: PMC7973372 DOI: 10.3389/fonc.2021.606820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
We investigated germline variation in pancreatic ductal adenocarcinoma (PDAC) predisposition genes in 535 patients, using a custom-built panel and a new complementary bioinformatic approach. Our panel assessed genes belonging to DNA repair, cell cycle checkpoints, migration, and preneoplastic pancreatic conditions. Our bioinformatics approach integrated annotations of variants by using data derived from both germline and somatic references. This integrated approach with expanded evidence enabled us to consider patterns even among private mutations, supporting a functional role for certain alleles, which we believe enhances individualized medicine beyond classic gene-centric approaches. Concurrent evaluation of three levels of evidence, at the gene, sample, and cohort level, has not been previously done. Overall, we identified in PDAC patient germline samples, 12% with mutations previously observed in pancreatic cancers, 23% with mutations previously discovered by sequencing other human tumors, and 46% with mutations with germline associations to cancer. Non-polymorphic protein-coding pathogenic variants were found in 18.4% of patient samples. Moreover, among patients with metastatic PDAC, 16% carried at least one pathogenic variant, and this subgroup was found to have an improved overall survival (22.0 months versus 9.8; p=0.008) despite a higher pre-treatment CA19-9 level (p=0.02). Genetic alterations in DNA damage repair genes were associated with longer overall survival among patients who underwent resection surgery (92 months vs. 46; p=0.06). ATM alterations were associated with more frequent metastatic stage (p = 0.04) while patients with BRCA1 or BRCA2 alterations had improved overall survival (79 months vs. 39; p=0.05). We found that mutations in genes associated with chronic pancreatitis were more common in non-white patients (p<0.001) and associated with longer overall survival (52 months vs. 26; p=0.004), indicating the need for greater study of the relationship among these factors. More than 90% of patients were found to have variants of uncertain significance, which is higher than previously reported. Furthermore, we generated 3D models for selected mutant proteins, which suggested distinct mechanisms underlying their dysfunction, likely caused by genetic alterations. Notably, this type of information is not predictable from sequence alone, underscoring the value of structural bioinformatics to improve genomic interpretation. In conclusion, the variation in PDAC predisposition genes appears to be more extensive than anticipated. This information adds to the growing body of literature on the genomic landscape of PDAC and brings us closer to a more widespread use of precision medicine for this challenging disease.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Angela J Mathison
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tim Stodola
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Douglas B Evans
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jenica L Abrudan
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Wendy Demos
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael Tschannen
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Mohammed Aldakkak
- Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jennifer Geurts
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,Genetic Counseling Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Gwen Lomberk
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Susan Tsai
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Division of Surgical Oncology, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Raul Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States.,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States
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35
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Arend RC, Jackson-Fisher A, Jacobs IA, Chou J, Monk BJ. Ovarian cancer: new strategies and emerging targets for the treatment of patients with advanced disease. Cancer Biol Ther 2021; 22:89-105. [PMID: 33427569 PMCID: PMC7928025 DOI: 10.1080/15384047.2020.1868937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/01/2020] [Accepted: 12/22/2020] [Indexed: 10/25/2022] Open
Abstract
Recently approved therapies have contributed to a significant progress in the management of ovarian cancer; yet, more options are needed to further improve outcomes in patients with advanced disease. Here we review the rationale and ongoing clinical trials of novel combination strategies involving chemotherapy, poly ADP ribose polymerase, programmed death 1 (PD-1)/PD-ligand 1 immune checkpoint and/or vascular endothelial growth factor receptor inhibitors. Further, we discuss novel agents aimed at targets associated with ovarian cancer growth or progression that are emerging as potential new treatment approaches. Among them, agents targeted to folate receptor α, tissue factor, and protein kinase-mediated pathways (WEE1 kinase, phosphatidylinositol-3 kinase α, cell cycle checkpoint kinase 1/2, ATR kinase) are currently in clinical development as mono- or combination therapies. If successful, findings from these extensive development efforts may further transform treatment of patients with advanced ovarian cancer.
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Affiliation(s)
- Rebecca C. Arend
- Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Jeffrey Chou
- Research and Development, Pfizer, San Francisco, CA, USA
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36
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Majd N, Yap TA, Yung WKA, de Groot J. The Promise of Poly(ADP-Ribose) Polymerase (PARP) Inhibitors in Gliomas. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2020; 3:157-164. [PMID: 35665372 PMCID: PMC9165443 DOI: 10.36401/jipo-20-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/29/2020] [Indexed: 05/09/2023]
Abstract
Diffuse infiltrating gliomas are a clinically and molecularly heterogeneous group of tumors that are uniformly incurable. Despite our growing knowledge of genomic and epigenomic alterations in gliomas, standard treatments have not changed in the past 2 decades and remain limited to surgical resection, ionizing radiation, and alkylating chemotherapeutic agents. Development of novel therapeutics for diffuse gliomas has been challenging due to inter- and intra-tumoral heterogeneity, diffuse infiltrative nature of gliomas, inadequate tumor/drug concentration due to blood-brain barrier, and an immunosuppressive tumor microenvironment. Given the high frequency of DNA damage pathway alterations in gliomas, researchers have focused their efforts in targeting the DNA damage pathways for the treatment of gliomas. A growing body of data has shed light on the role of poly(ADP-ribose) polymerase (PARP) in combination with radiation and temozolomide in high-grade gliomas. Furthermore, a novel therapeutic strategy in low-grade glioma is the recent elucidation for a potential role of PARP inhibitors in gliomas with IDH1/2 mutations. This review highlights the concepts behind targeting PARP in gliomas with a focus on putative predictive biomarkers of response. We further discuss the challenges involved in the successful development of PARP inhibitors in gliomas, including the intracranial location of the tumor and overlapping toxicities with current standards of care, and promising strategies to overcome these hurdles.
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Affiliation(s)
- Nazanin Majd
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy A. Yap
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W. K. Alfred Yung
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John de Groot
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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37
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Meggendorfer M, Walter W, Haferlach T. WGS and WTS in leukaemia: A tool for diagnostics? Best Pract Res Clin Haematol 2020; 33:101190. [DOI: 10.1016/j.beha.2020.101190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
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38
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Fuso Nerini I, Roca E, Mannarino L, Grosso F, Frapolli R, D'Incalci M. Is DNA repair a potential target for effective therapies against malignant mesothelioma? Cancer Treat Rev 2020; 90:102101. [PMID: 32892058 DOI: 10.1016/j.ctrv.2020.102101] [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: 05/26/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a rare malignancy mainly caused by asbestos exposure. Germinal and acquired mutations in genes of DNA repair pathways, in particular of homologous recombination repair, are frequent in MPM. Here we overview the available experimental data suggesting that an impaired DNA repair system affects MPM pathogenesis by leaving lesions through the genome unresolved. DNA repair defects represent a vulnerability of MPM, and it seems plausible to propose that leveraging these deficiencies could have therapeutic potential for patients with MPM, for whom there is an urgent need of more effective therapies.
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Affiliation(s)
- Ilaria Fuso Nerini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Elisa Roca
- Lung Unit, Thoracic Oncology, Pederzoli Hospital-Peschiera del Garda, Verona, Italy
| | - Laura Mannarino
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Federica Grosso
- Mesothelioma Unit, SS Antonio and Biagio General Hospital, Alessandria, Italy
| | - Roberta Frapolli
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Maurizio D'Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy.
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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Expanding cancer predisposition genes with ultra-rare cancer-exclusive human variations. Sci Rep 2020; 10:13462. [PMID: 32778766 PMCID: PMC7418036 DOI: 10.1038/s41598-020-70494-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
It is estimated that up to 10% of cancer incidents are attributed to inherited genetic alterations. Despite extensive research, there are still gaps in our understanding of genetic predisposition to cancer. It was theorized that ultra-rare variants partially account for the missing heritable component. We harness the UK BioBank dataset of ~ 500,000 individuals, 14% of which were diagnosed with cancer, to detect ultra-rare, possibly high-penetrance cancer predisposition variants. We report on 115 cancer-exclusive ultra-rare variations and nominate 26 variants with additional independent evidence as cancer predisposition variants. We conclude that population cohorts are valuable source for expanding the collection of novel cancer predisposition genes.
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Suszynska M, Kozlowski P. Summary of BARD1 Mutations and Precise Estimation of Breast and Ovarian Cancer Risks Associated with the Mutations. Genes (Basel) 2020; 11:genes11070798. [PMID: 32679805 PMCID: PMC7397132 DOI: 10.3390/genes11070798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
Over the last two decades, numerous BARD1 mutations/pathogenic variants (PVs) have been found in patients with breast cancer (BC) and ovarian cancer (OC). However, their role in BC and OC susceptibility remains controversial, and strong evidence-based guidelines for carriers are not yet available. Herein, we present a comprehensive catalog of BARD1 PVs identified in large cumulative cohorts of ~48,700 BC and ~20,800 OC cases (retrieved from 123 studies examining the whole coding sequence of BARD1). Using these resources, we compared the frequency of BARD1 PVs in the cases and ~134,100 controls from the gnomAD database and estimated the effect of the BARD1 PVs on BC and OC risks. The analysis revealed that BARD1 is a BC moderate-risk gene (odds ratio (OR) = 2.90, 95% CIs:2.25–3.75, p < 0.0001) but not an OC risk gene (OR = 1.36, 95% CIs:0.87–2.11, p = 0.1733). In addition, the BARD1 mutational spectrum outlined in this study allowed us to determine recurrent PVs and evaluate the variant-specific risk for the most frequent PVs. In conclusion, these precise estimates improve the understanding of the role of BARD1 PVs in BC and OC predisposition and support the need for BARD1 diagnostic testing in BC patients.
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Affiliation(s)
| | - Piotr Kozlowski
- Correspondence: ; Tel.: +48-618-528-503 (ext. 261); Fax: +48-618-520-532
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Caggiari L, Fornasarig M, De Zorzi M, Cannizzaro R, Steffan A, De Re V. Family's History Based on the CDH1 Germline Variant (c.360delG) and a Suspected Hereditary Gastric Cancer Form. Int J Mol Sci 2020; 21:ijms21144904. [PMID: 32664545 PMCID: PMC7402300 DOI: 10.3390/ijms21144904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 11/16/2022] Open
Abstract
Hereditary diffuse gastric cancer (HDGC) is a cancer susceptibility syndrome caused by germline pathogenic variant in CDH1, the gene encoding E-cadherin. The germline loss-of-function variants are the only proven cause of the cancer syndrome HDGC, occurring in approximately 10-18% of cases and representing a helpful tool in genetic counseling. The current case reports the family history based on a CDH1 gene variant, c.360delG, p.His121Thr in a suspected family for hereditary gastric cancer form. This frameshift deletion generates a premature stop codon at the amino acid 214, which leads to a truncated E-cadherin protein detecting it as a deleterious variant. The present study expands the mutational spectra of the family with the CDH1 variant. Our results highlight the clinical impact of the reported CDH1 variant running in gastric cancer families.
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Affiliation(s)
- Laura Caggiari
- Immunopathology and Cancer Biomarkers, Bioproteomic facility, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano (PN), Italy; (L.C.); (M.D.Z.); (A.S.)
| | - Mara Fornasarig
- Gastroenterology, Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano (PN), Italy; (M.F.); (R.C.)
| | - Mariangela De Zorzi
- Immunopathology and Cancer Biomarkers, Bioproteomic facility, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano (PN), Italy; (L.C.); (M.D.Z.); (A.S.)
| | - Renato Cannizzaro
- Gastroenterology, Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano (PN), Italy; (M.F.); (R.C.)
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Bioproteomic facility, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano (PN), Italy; (L.C.); (M.D.Z.); (A.S.)
| | - Valli De Re
- Immunopathology and Cancer Biomarkers, Bioproteomic facility, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano (PN), Italy; (L.C.); (M.D.Z.); (A.S.)
- Correspondence: ; Tel.: +39-0434-659672
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Melas M, Subbiah S, Saadat S, Rajurkar S, McDonnell KJ. The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations. J Clin Med 2020; 9:E2125. [PMID: 32640668 PMCID: PMC7408957 DOI: 10.3390/jcm9072125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. The active engagement of community oncology practices with academic partners helps with meeting these challenges; community/academic alliances result in improved cancer patient care and provider efficacy. Here, we review the community oncology and academic medical center alliance. We examine how practitioners may leverage academic center precision medicine-based cancer genetics and genomics programs to advance their patients' needs. We highlight a number of project initiatives at the City of Hope Comprehensive Cancer Center that seek to optimize community oncology and academic cancer center precision medicine interactions.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Glendora, CA 91741, USA;
| | - Siamak Saadat
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Colton, CA 92324, USA;
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Upland, CA 91786, USA;
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
- Center for Precision Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
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Shahid S, Shakeel M, Siddiqui S, Ahmed S, Sohail M, Khan IA, Abid A, Shamsi T. Novel Genetic Variations in Acute Myeloid Leukemia in Pakistani Population. Front Genet 2020; 11:560. [PMID: 32655615 PMCID: PMC7324646 DOI: 10.3389/fgene.2020.00560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by clonal expansion of blast cells that exhibit great genetic heterogeneity. In this study, we describe the mutational landscape and its clinico-pathological significance in 26 myeloid neoplasm patients from a South Asian population (Pakistan) by using ultra-deep targeted next-generation DNA sequencing of 54 genes (∼5000×) and its subsequent bioinformatics analysis. The data analysis indicated novel non-silent somatic mutational events previously not reported in AML, including nine non-synonymous and one stop-gain mutations. Notably, two recurrent somatic non-synonymous mutations, i.e., STAG2 (causing p.L526F) and BCORL1 (p.A400V), were observed in three unrelated cases each. The BCOR was found to have three independent non-synonymous somatic mutations in three cases. Further, the SRSF2 with a protein truncating somatic mutation (p.Q88X) was observed for the first time in AML in this study. The prioritization of germline mutations with ClinVar, SIFT, Polyphen2, and Combined Annotation Dependent Depletion (CADD) highlighted 18 predicted deleterious/pathogenic mutations, including two recurrent deleterious mutations, i.e., a novel heterozygous non-synonymous SNV in GATA2 (p.T358P) and a frameshift insertion in NPM1 (p.L258fs), found in two unrelated cases each. The WT1 was observed with three independent potential detrimental germline mutations in three different cases. Collectively, non-silent somatic and/or germline mutations were observed in 23 (88.46%) of the cases (0.92 mutation per case). Furthermore, the pharmGKB database exploration showed a missense SNV rs1042522 in TP53, exhibiting decreased response to anti-cancer drugs, in 19 (73%) of the cases. This genomic profiling of AML provides deep insight into the disease pathophysiology. Identification of pharmacogenomics markers will help to adopt personalized approach for the management of AML patients in Pakistan.
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Affiliation(s)
- Saba Shahid
- Department of Genomics, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Saima Siddiqui
- Department of Hematology, National Institute of Blood Diseases and Bone Marrow Transplantation Karachi, Karachi, Pakistan
| | - Shariq Ahmed
- Department of Genomics, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
| | - Misha Sohail
- Department of Genomics, National Institute of Blood Diseases and Bone Marrow Transplantation, Karachi, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Aiysha Abid
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Karachi, Pakistan
| | - Tahir Shamsi
- Department of Hematology, National Institute of Blood Diseases and Bone Marrow Transplantation Karachi, Karachi, Pakistan
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Sprissler R, Perkins B, Johnstone L, Babiker HM, Chalasani P, Lau B, Hammer M, Mahadevan D. Rare Tumor-Normal Matched Whole Exome Sequencing Identifies Novel Genomic Pathogenic Germline and Somatic Aberrations. Cancers (Basel) 2020; 12:E1618. [PMID: 32570879 PMCID: PMC7352311 DOI: 10.3390/cancers12061618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022] Open
Abstract
Whole exome sequencing (WES) of matched tumor-normal pairs in rare tumors has the potential to identify genome-wide mutations and copy number alterations (CNAs). We evaluated 27 rare cancer patients with tumor-normal matching by WES and tumor-only next generation sequencing (NGS) as a comparator. Our goal was to: 1) identify known and novel variants and CNAs in rare cancers with comparison to common cancers; 2) examine differences between germline and somatic variants and how that functionally impacts rare tumors; 3) detect and characterize alleles in biologically relevant genes-pathways that may be of clinical importance but not represented in classical cancer genes. We identified 3343 germline single nucleotide variants (SNVs) and small indel variants-1670 in oncogenes and 1673 in tumor suppressor genes-generating an average of 124 germline variants/case. The number of somatic SNVs and small indels detected in all cases was 523:306 in oncogenes and 217 in tumor suppressor genes. Of the germline variants, six were identified to be pathogenic or likely pathogenic. In the 27 analyzed rare cancer cases, CNAs are variable depending on tumor type, germline pathogenic variants are more common. Cell fate pathway mutations (e.g., Hippo, Notch, Wnt) dominate pathogenesis and double hit (mutation + CNV) represent ~18% cases.
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Affiliation(s)
- Ryan Sprissler
- Department of Health Sciences, Center for Applied Genetics and Genomic Medicine, University of Arizona, Tucson, AZ 85721, USA;
- Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ 85721, USA; (L.J.); (B.L.)
| | - Bryce Perkins
- Department of Medicine, Division of Hematology and Oncology, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (B.P.); (H.M.B.); (P.C.)
| | - Laurel Johnstone
- Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ 85721, USA; (L.J.); (B.L.)
| | - Hani M. Babiker
- Department of Medicine, Division of Hematology and Oncology, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (B.P.); (H.M.B.); (P.C.)
- Department of Medicine—Hematology/Oncology, University of Texas Health San Antonio, Mays Cancer Center, San Antonio, TX 78229, USA
| | - Pavani Chalasani
- Department of Medicine, Division of Hematology and Oncology, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (B.P.); (H.M.B.); (P.C.)
- Department of Medicine—Hematology/Oncology, University of Texas Health San Antonio, Mays Cancer Center, San Antonio, TX 78229, USA
| | - Branden Lau
- Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ 85721, USA; (L.J.); (B.L.)
| | - Michael Hammer
- Department of Health Sciences, Center for Applied Genetics and Genomic Medicine, University of Arizona, Tucson, AZ 85721, USA;
- Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ 85721, USA; (L.J.); (B.L.)
- Department of Medicine, Division of Hematology and Oncology, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (B.P.); (H.M.B.); (P.C.)
| | - Daruka Mahadevan
- Department of Medicine—Hematology/Oncology, University of Texas Health San Antonio, Mays Cancer Center, San Antonio, TX 78229, USA
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Panou V, Røe OD. Inherited Genetic Mutations and Polymorphisms in Malignant Mesothelioma: A Comprehensive Review. Int J Mol Sci 2020; 21:ijms21124327. [PMID: 32560575 PMCID: PMC7352726 DOI: 10.3390/ijms21124327] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Malignant mesothelioma (MM) is mainly caused by air-born asbestos but genetic susceptibility is also suspected to be a risk factor. Recent studies suggest an increasing number of candidate genes that may predispose to MM besides the well-characterized BRCA1-associated protein-1 gene. The aim of this review is to summarize the most important studies on germline mutations for MM. A total of 860 publications were retrieved from Scopus, PubMed and Web of Science, of which 81 met the inclusion criteria and were consider for this review. More than 50% of the genes that are reported to predispose to MM are involved in DNA repair mechanisms, and the majority of them have a role in the homologous recombination pathway. Genetic alterations in tumor suppressor genes involved in chromatin, transcription and hypoxia regulation have also been described. Furthermore, we identified several single nucleotide polymorphisms (SNPs) that may promote MM tumorigenesis as a result of an asbestos-gene interaction, including SNPs in DNA repair, carcinogen detoxification and other genes previously associated with other malignancies. The identification of inherited mutations for MM and an understanding of the underlying pathways may allow early detection and prevention of malignancies in high-risk individuals and pave the way for targeted therapies.
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Affiliation(s)
- Vasiliki Panou
- Department of Respiratory Medicine, Odense University Hospital, 5000 Odense, Denmark
- Department of Respiratory Medicine, Aalborg University Hospital, 9000 Aalborg, Denmark
- Clinical Institute, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Correspondence:
| | - Oluf Dimitri Røe
- Clinical Institute, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Suszynska M, Ratajska M, Kozlowski P. BRIP1, RAD51C, and RAD51D mutations are associated with high susceptibility to ovarian cancer: mutation prevalence and precise risk estimates based on a pooled analysis of ~30,000 cases. J Ovarian Res 2020; 13:50. [PMID: 32359370 PMCID: PMC7196220 DOI: 10.1186/s13048-020-00654-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background It is estimated that more than 20% of ovarian cancer cases are associated with a genetic predisposition that is only partially explained by germline mutations in the BRCA1 and BRCA2 genes. Recently, several pieces of evidence showed that mutations in three genes involved in the homologous recombination DNA repair pathway, i.e., BRIP1, RAD51C, and RAD51D, are associated with a high risk of ovarian cancer. To more precisely estimate the ovarian cancer risk attributed to BRIP1, RAD51C, and RAD51D mutations, we performed a meta-analysis based on a comparison of a total of ~ 29,400 ovarian cancer patients from 63 studies and a total of ~ 116,000 controls from the gnomAD database. Results The analysis allowed precise estimation of ovarian cancer risks attributed to mutations in BRIP1, RAD51C, and RAD51D, confirming that all three genes are ovarian cancer high-risk genes (odds ratio (OR) = 4.94, 95%CIs:4.07–6.00, p < 0.0001; OR = 5.59, 95%CIs:4.42–7.07, p < 0.0001; and OR = 6.94, 95%CIs:5.10–9.44, p < 0.0001, respectively). In the present report, we show, for the first time, a mutation-specific risk analysis associated with distinct, recurrent, mutations in the genes. Conclusions The meta-analysis provides evidence supporting the pathogenicity of BRIP1, RAD51C, and RAD51D mutations in relation to ovarian cancer. The level of ovarian cancer risk conferred by these mutations is relatively high, indicating that after BRCA1 and BRCA2, the BRIP1, RAD51C, and RAD51D genes are the most important ovarian cancer risk genes, cumulatively contributing to ~ 2% of ovarian cancer cases. The inclusion of the genes into routine diagnostic tests may influence both the prevention and the potential treatment of ovarian cancer.
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Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Street, 61-704, Poznan, Poland
| | - Magdalena Ratajska
- Department of Pathology, Dunedin School of Medicine, University of Otago, 60 Hanover Street, Dunedin, 9016, New Zealand.,Department of Biology and Medical Genetics, Medical University of Gdansk, Debinki 1 St., 80-210, Gdansk, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Street, 61-704, Poznan, Poland.
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Yoshikawa Y, Emi M, Nakano T, Gaudino G. Mesothelioma developing in carriers of inherited genetic mutations. Transl Lung Cancer Res 2020; 9:S67-S76. [PMID: 32206572 PMCID: PMC7082255 DOI: 10.21037/tlcr.2019.11.15] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Malignant mesothelioma is associated with the exposure to asbestos fibers. Recent discovery of the BAP1 cancer syndrome, a Mendelian disorder with high-penetrance autosomal dominant inheritance fostered the genotyping for nucleotide-level or larger structural alteration of germline DNA. Inherited heterozygous mutations of the BAP1 gene increase the susceptibility to carcinogenic fibers, leading to a concept of gene x environment interaction (GxE) as a pathogenetic mechanism of mesothelioma. Several studies on cohorts of unselected patients with mesothelioma or on familial/early-onset cohorts of mesothelioma cases converged on BAP1 as the more frequent germline mutated gene, followed by other genes involved in DNA repair and homologous recombination. Evidence has been emerging that patients with mesothelioma carrying germline mutations of BAP1 and of other genes, such as those involved in DNA repair and tumor suppressor genes, have better prognosis and higher chemosensitivity when compared with patients with germline wildtype Bap1. We report here a germline genomic analysis targeted 22 genes in a cohort of 101 Japanese patients irrespective of asbestos exposure, age at diagnosis, or personal or family history of cancer. By comparing the results with the Human Genetic Variation Database (HGVD) and the Genome Aggregation Database (gnomAD) we selected rare germline variants with a Combined Annotation Dependent Depletion (CADD) >20. We show here that 31 of 101 subjects were carrying 25 rare variants in 14 genes, neither reported in the HGVD nor in the gnomAD database for 14/25 variants. Besides pathogenic variants of BAP1, rare missense variants were found in genes encoding lysine-specific histone methyltransferase SETD2 and SETDB1 and genes encoding subunits of the mSWI/SNF chromatin remodeling complex. The complete scenario of the genetic background consisting of pathogenic germline variants required for the predisposition and GxE for pathogenesis of mesothelioma appears complex, and further large-scale studies are warranted.
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Affiliation(s)
- Yoshie Yoshikawa
- Department of Genetic, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Mitsuru Emi
- Department of Genetic, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan.,University of Hawai'i Cancer Center, Honolulu, HI, USA
| | - Takashi Nakano
- Center for Respiratory Medicine, Otemae Hospital, Chuo-ku, Osaka, Japan
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Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med 2020; 12:8. [PMID: 31937368 PMCID: PMC6961404 DOI: 10.1186/s13073-019-0703-1] [Citation(s) in RCA: 437] [Impact Index Per Article: 109.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
The number of druggable tumor-specific molecular aberrations has grown substantially in the past decade, with a significant survival benefit obtained from biomarker matching therapies in several cancer types. Molecular pathology has therefore become fundamental not only to inform on tumor diagnosis and prognosis but also to drive therapeutic decisions in daily practice. The introduction of next-generation sequencing technologies and the rising number of large-scale tumor molecular profiling programs across institutions worldwide have revolutionized the field of precision oncology. As comprehensive genomic analyses become increasingly available in both clinical and research settings, healthcare professionals are faced with the complex tasks of result interpretation and translation. This review summarizes the current and upcoming approaches to implement precision cancer medicine, highlighting the challenges and potential solutions to facilitate the interpretation and to maximize the clinical utility of molecular profiling results. We describe novel molecular characterization strategies beyond tumor DNA sequencing, such as transcriptomics, immunophenotyping, epigenetic profiling, and single-cell analyses. We also review current and potential applications of liquid biopsies to evaluate blood-based biomarkers, such as circulating tumor cells and circulating nucleic acids. Last, lessons learned from the existing limitations of genotype-derived therapies provide insights into ways to expand precision medicine beyond genomics.
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Affiliation(s)
- Eoghan R Malone
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Marc Oliva
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Peter J B Sabatini
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Tracy L Stockley
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada.
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50
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Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019; 10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Helena Reyes-Gopar
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
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