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Barsouk A, Elghawy O, Stone S, Singh A. Patient with mediastinal carcinoma of unknown primary with RET fusion achieves durable response with RET inhibition. Anticancer Drugs 2024; 35:653-657. [PMID: 38696710 DOI: 10.1097/cad.0000000000001618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Selective RET inhibitors have shown promise in thyroid cancer (TC) and nonsmall cell lung cancer (NSCLC) harboring RET fusions on next-generation sequencing (NGS), although rarity of the rearrangement has led to limited data for certain tumor types, such as carcinoma of unknown primary. We present a 65-year-old female with no history of malignancy, smoking or radiation exposure, who was found to have an anterior mediastinum malignancy of unknown primary, with metastases to supraclavicular lymph nodes. Core biopsy of the mediastinum revealed poorly differentiated carcinoma, while a biopsy of the thyroid revealed atypia of indeterminate significance (Bethesda III). PD-L1 immunohistochemistry was positive (90%), and liquid NGS revealed mutations in TP53 and the TERT promoter (c.-124C>T), as well as a CCDC6-RET fusion. This genetic profile resembled an anaplastic TC vs. NSCLC primary, although thymic primary and poorly differentiated TC remained on the differential. The patient was initiated on selpercatinib, which was held after 3 weeks due to thrombocytopenia and hypertension. At a reduced dosage, patient developed transaminitis, and selpercatinib was switched to pralsetinib. Brain MRI showed a nonenhancing temporal lobe signal abnormality, which on biopsy proved to be glioblastoma (GBM) with TERT promoter c.-124C>T mutation and FGFR3-TACC3 fusion by NGS. Pralsetinib was held during adjuvant chemoradiation for the GBM, and again for 4 weeks due to pneumonitis that resolved with steroids, and pralsetinib was restarted at a reduced dose. The patient has since demonstrated a stable reduction of the mediastinal mass for >15 months with RET inhibition therapy, despite several treatment interruptions.
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Affiliation(s)
- Adam Barsouk
- Department of Medical Oncology, Abramson Cancer Center, Hospital of the University of Pennsylvania
| | - Omar Elghawy
- Department of Medical Oncology, Abramson Cancer Center, Hospital of the University of Pennsylvania
| | - Sara Stone
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aditi Singh
- Department of Medical Oncology, Abramson Cancer Center, Hospital of the University of Pennsylvania
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2
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Kypreou K, Stergiopoulou A, Plaka M, Befon A, Chardalia V, Stratigos IA, Stratigos AJ, Stefanaki I. Targeted sequencing analysis of loci implicated in familial melanoma in a Greek cohort. J Eur Acad Dermatol Venereol 2024; 38:e525-e527. [PMID: 38100224 DOI: 10.1111/jdv.19728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024]
Affiliation(s)
- K Kypreou
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - A Stergiopoulou
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - M Plaka
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - A Befon
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - V Chardalia
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - I A Stratigos
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - A J Stratigos
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - I Stefanaki
- 1st University Clinic of Dermatological and Venereal Diseases, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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3
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Narod SA, Metcalfe K, Finch A, Chan AW, Armel SR, Aeilts A, Eisen A, Karlan B, Bordeleau L, Tung N, Foulkes WD, Neuhausen SL, Eng C, Olopade O, Zakalik D, Couch F, Cullinane C, Pal T, Sun P, Kotsopoulos J. The risk of skin cancer in women who carry BRCA1 or BRCA2 mutations. Hered Cancer Clin Pract 2024; 22:7. [PMID: 38741145 DOI: 10.1186/s13053-024-00277-5] [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: 01/18/2024] [Accepted: 04/02/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND It has not been clearly established if skin cancer or melanoma are manifestations of BRCA1 or BRCA2 mutation carrier status. Estimating the risk of skin cancer is an important step towards developing screening recommendations. METHODS We report the findings of a prospective cohort study of 6,207 women from North America who carry BRCA1 or BRCA2 mutations. Women were followed from the date of baseline questionnaire to the diagnosis of skin cancer, to age 80 years, death from any cause, or the date of last follow-up. RESULTS During the mean follow-up period of eight years, 3.7% of women with a BRCA1 mutation (133 of 3,623) and 3.8% of women with a BRCA2 mutation (99 of 2,584) reported a diagnosis of skin cancer (including both keratinocyte carcinomas and melanoma). The cumulative risk of all types of skin cancer from age 20 to 80 years was 14.1% for BRCA1 carriers and 10.7% for BRCA2 carriers. The cumulative risk of melanoma was 2.5% for BRCA1 carriers and 2.3% for BRCA2 carriers, compared to 1.5% for women in the general population in the United States. The strongest risk factor for skin cancer was a prior diagnosis of skin cancer. CONCLUSION The risk of non-melanoma skin cancer in women who carry a mutation in BRCA1 or BRCA2 is similar to that of non-carrier women. The risk of melanoma appears to be slightly elevated. We suggest that a referral to a dermatologist or primary care provider for BRCA mutation carriers for annual skin examination and counselling regarding limiting UV exposure, the use of sunscreen and recognizing the early signs of melanoma might be warranted, but further studies are necessary.
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Affiliation(s)
- Steven A Narod
- Women's College Research Institute, Women's College Hospital, 76 Grenville St, M5S 1B1, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Kelly Metcalfe
- Women's College Research Institute, Women's College Hospital, 76 Grenville St, M5S 1B1, Toronto, ON, Canada
- Bloomberg School of Nursing, University of Toronto, Toronto, ON, Canada
| | - Amy Finch
- Women's College Research Institute, Women's College Hospital, 76 Grenville St, M5S 1B1, Toronto, ON, Canada
| | - An-Wen Chan
- Women's College Research Institute, Women's College Hospital, 76 Grenville St, M5S 1B1, Toronto, ON, Canada
- Division of Dermatology, Department of Medicine, University of Toronto, Toronto, Canada
| | - Susan Randall Armel
- Princess Margaret Hospital, Familial Cancer Clinic, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Amber Aeilts
- Division of Human Genetics, Comprehensive Cancer Center, the Ohio State University Medical Center, Columbus, OH, USA
| | | | - Beth Karlan
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Louise Bordeleau
- Department of Oncology, McMaster University, Hamilton, ON, Canada
| | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - William D Foulkes
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, QC, Canada
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Olufunmilayo Olopade
- Department of Medicine and Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dana Zakalik
- Cancer Genetics Program, Beaumont Hospital, Royal Oak, MI, USA
| | - Fergus Couch
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Tuya Pal
- Division of Genetics, Department of Medicine, Vanderbilt University Medical Centre and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ping Sun
- Women's College Research Institute, Women's College Hospital, 76 Grenville St, M5S 1B1, Toronto, ON, Canada
| | - Joanne Kotsopoulos
- Women's College Research Institute, Women's College Hospital, 76 Grenville St, M5S 1B1, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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4
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Naddeo M, Broseghini E, Venturi F, Vaccari S, Corti B, Lambertini M, Ricci C, Fontana B, Durante G, Pariali M, Scotti B, Milani G, Campione E, Ferracin M, Dika E. Association of miR-146a-5p and miR-21-5p with Prognostic Features in Melanomas. Cancers (Basel) 2024; 16:1688. [PMID: 38730639 PMCID: PMC11083009 DOI: 10.3390/cancers16091688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/12/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Cutaneous melanoma (CM) is one of the most lethal tumors among skin cancers and its incidence is rising worldwide. Recent data support the role of microRNAs (miRNAs) in melanoma carcinogenesis and their potential use as disease biomarkers. METHODS We quantified the expression of miR-146a-5p and miR-21-5p in 170 formalin-fixed paraffin embedded (FFPE) samples of CM, namely 116 superficial spreading melanoma (SSM), 26 nodular melanoma (NM), and 28 lentigo maligna melanoma (LMM). We correlated miRNA expression with specific histopathologic features including Breslow thickness (BT), histological subtype, ulceration and regression status, and mitotic index. RESULTS miR-146a-5p and miR-21-5p were significantly higher in NM compared to SSM and LMM. The positive correlation between miR-146a-5p and miR-21-5p expression and BT was confirmed for both miRNAs in SSM. Considering the ulceration status, we assessed that individual miR-21-5p expression was significantly higher in ulcerated CMs. The increased combined expression of the two miRNAs was strongly associated with ulceration (p = 0.0093) and higher mitotic rate (≥1/mm2) (p = 0.0005). We demonstrated that the combination of two-miRNA expression and prognostic features (BT and ulceration) can better differentiate cutaneous melanoma prognostic groups, considering overall survival and time-to-relapse clinical outcomes. Specifically, miRNA expression can further stratify prognostic groups among patients with BT ≥ 0.8 mm but without ulceration. Our findings provide further insights into the characterization of CM with specific prognostic features. The graphical abstract was created with BioRender.com.
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Affiliation(s)
- Maria Naddeo
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (M.N.); (E.B.)
| | - Elisabetta Broseghini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (M.N.); (E.B.)
| | - Federico Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (S.V.); (B.S.); (G.M.)
| | - Sabina Vaccari
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (S.V.); (B.S.); (G.M.)
| | - Barbara Corti
- Division of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy;
| | - Martina Lambertini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (S.V.); (B.S.); (G.M.)
| | - Costantino Ricci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
- Pathology Unit, Ospedale Maggiore, 40133 Bologna, Italy
| | - Beatrice Fontana
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
| | - Giorgio Durante
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
| | - Milena Pariali
- Center for Applied Biomedical Research, S. Orsola-Malpighi University Hospital, 40126 Bologna, Italy;
| | - Biagio Scotti
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (S.V.); (B.S.); (G.M.)
| | - Giulia Milani
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (S.V.); (B.S.); (G.M.)
| | - Elena Campione
- Dermatologic Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Manuela Ferracin
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (M.N.); (E.B.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
| | - Emi Dika
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; (F.V.); (M.L.); (C.R.); (B.F.); (G.D.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; (S.V.); (B.S.); (G.M.)
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Fares E, Thawabtah R, Sallam H, Khatib AAH, Qutob N, Salah Z. Genomic analysis of a Palestinian family with inherited cancer syndrome: a next-generation sequencing study. Front Genet 2023; 14:1230241. [PMID: 38028607 PMCID: PMC10643688 DOI: 10.3389/fgene.2023.1230241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023] Open
Abstract
Familial predisposition is a strong risk factor for different types of cancer and accounts for around 10% of the cases. In this study, we investigated cancer predisposition in a Palestinian family using whole-exome sequencing (WES) technologies. In this study, we focused more on cutaneous melanoma (CM). Our analysis identified three heterozygous rare missense variants, WRN (p.L383F and p.A995T) and TYRP1 (p.T262M) and a pathogenic homozygous missense mutation in ERCC2 (p.R683Q). Although WRN and TYRP1 genes and their variations were correlated with different types of cancer, including melanoma, the currently identified WRN and TYRP1 variants were not reported previously in melanoma cases. The pathogenic mutation was segregated with the clinical phenotypes and found in the two affected brothers, one with CM and the other with brain tumor, and was confirmed by Sanger sequencing analysis. Segregation analysis of this mutation revealed that family members are either heterozygous or wild type. Our findings confirm that the homozygous ERCC2 (p.R683Q) mutation was responsible for causing melanoma and other cancer types in the family. Our work highlights the value to decipher the mutational background of familial cancers, especially CM, in the Palestinian population to guide diagnosis, prevention, and treatment of affected patients and their families.
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Affiliation(s)
- Eman Fares
- Health Sciences Department, Faculty of Graduate Studies, Arab American University, Ramallah, Palestine
| | - Rua Thawabtah
- Health Sciences Department, Faculty of Graduate Studies, Arab American University, Ramallah, Palestine
| | - Husam Sallam
- Health Sciences Department, Faculty of Graduate Studies, Arab American University, Ramallah, Palestine
| | - Areej A. H. Khatib
- Women Health Research Unit, McGill University Health Center, Montreal, QC, Canada
| | - Nouar Qutob
- *Correspondence: Nouar Qutob, ; Zaidoun Salah,
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Jensen MR, Jelsig AM, Gerdes AM, Hölmich LR, Kainu KH, Lorentzen HF, Hansen MH, Bak M, Johansson PA, Hayward NK, Van Overeem Hansen T, Wadt KA. TINF2 is a major susceptibility gene in Danish patients with multiple primary melanoma. HGG ADVANCES 2023; 4:100225. [PMID: 37646013 PMCID: PMC10461021 DOI: 10.1016/j.xhgg.2023.100225] [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: 05/04/2023] [Accepted: 07/19/2023] [Indexed: 09/01/2023] Open
Abstract
TINF2 encodes the TINF2 protein, which is a subunit in the shelterin complex critical for telomere regulation. Three recent studies have associated six truncating germline variants in TINF2 that have previously been associated with a cancer predisposition syndrome (CPS) caused by elongation of the telomeres. This has added TINF2 to the long telomere syndrome genes, together with other telomere maintenance genes such as ACD, POT1, TERF2IP, and TERT. We report a clinical study of 102 Danish patients with multiple primary melanoma (MPM) in which a germline truncating variant in TINF2 (p.(Arg265Ter)) was identified in four unrelated participants. The telomere lengths of three variant carriers were >90% percentile. In a routine diagnostic setting, the variant was identified in two more families, including an additional MPM patient and monozygotic twins with thyroid cancer and other cancer types. A total of 10 individuals from six independent families were confirmed carriers, all with cancer history, predominantly melanoma. Our findings suggest a major role of TINF2 in Danish patients with MPM. In addition to melanoma, other cancers in the six families include thyroid, renal, breast, and sarcoma, supporting a CPS in which melanoma, thyroid cancer, and sarcoma predominate. Further studies are needed to establish the full spectrum of associated cancer types and characterize lifetime cancer risk in carriers.
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Affiliation(s)
- Marlene Richter Jensen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne Marie Jelsig
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisbet Rosenkrantz Hölmich
- Department of Plastic and Reconstructive Surgery, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kati Hannele Kainu
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Dermatology and Allergology, Herlev and Gentofte Hospital, 2900 Gentofte, Denmark
| | | | | | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | | | | | - Thomas Van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin A.W. Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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7
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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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8
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Oh KS, Mahalingam M. Melanoma and Glioblastoma-Not a Serendipitous Association. Adv Anat Pathol 2023; 30:00125480-990000000-00051. [PMID: 36624550 DOI: 10.1097/pap.0000000000000393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recently, we came across a patient with malignant melanoma and primary glioblastoma. Given this, we parsed the literature to ascertain the relationship, if any, between these 2 malignancies. We begin with a brief overview of melanoma and glioma in isolation followed by a chronologic overview of case reports and epidemiologic studies documenting both neoplasms. This is followed by studies detailing genetic abnormalities common to both malignancies with a view to identifying unifying genetic targets for therapeutic strategies as well as to explore the possibility of a putative association and an inherited cancer susceptibility trait. From a scientific perspective, we believe we have provided evidence favoring an association between melanoma and glioma. Future studies that include documentation of additional cases, as well as a detailed molecular analyses, will lend credence to our hypothesis that the co-occurrence of these 2 conditions is likely not serendipitous.
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Affiliation(s)
- Kei Shing Oh
- Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL
| | - Meera Mahalingam
- Dermatopathology Section, Department of Pathology and Laboratory Medicine, VA-Integrated-Service-Network-1 (VISN1), West Roxbury, MA
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9
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Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles‐Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton‐Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 2023; 259:56-68. [PMID: 36219477 PMCID: PMC10098817 DOI: 10.1002/path.6019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Melanoma is a heterogenous malignancy with an unpredictable clinical course. Most patients who present in the clinic are diagnosed with primary melanoma, yet large-scale sequencing efforts have focused primarily on metastatic disease. In this study we sequence-profiled 524 American Joint Committee on Cancer Stage I-III primary tumours. Our analysis of these data reveals recurrent driver mutations, mutually exclusive genetic interactions, where two genes were never or rarely co-mutated, and an absence of co-occurring genetic events. Further, we intersected copy number calls from our primary melanoma data with whole-genome CRISPR screening data to identify the transcription factor interferon regulatory factor 4 (IRF4) as a melanoma-associated dependency. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sofia Birkeälv
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Mark Harland
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Larissa Satiko Alcantara Sekimoto Matsuyama
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Mamun Rashid
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Ishan Mehta
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Jonathan P Laye
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | | | - Tracey Mell
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Vivek Iyer
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Carla Daniela Robles‐Espinoza
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de México, Campus JuriquillaSantiago de QuerétaroMexico
| | - Ultan McDermott
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | | | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Pathology and Leiden Center for Computational OncologyLeiden University Medical CenterLeidenthe Netherlands
| | - Patricia A Possik
- Division of Experimental and Translational ResearchBrazilian National Cancer InstituteRio de JaneiroBrazil
| | - Silvya Stuchi Maria Engler
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - D Timothy Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Julia Newton‐Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - David J Adams
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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10
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Rashid S, Gupta S, McCormick SR, Tsao H. New Insights into Melanoma Tumor Syndromes. JID INNOVATIONS 2022; 2:100152. [DOI: 10.1016/j.xjidi.2022.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 10/14/2022] Open
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11
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Zaremba A, Meier F, Schlein C, Jansen P, Lodde G, Song M, Kretz J, Möller I, Stadtler N, Livingstone E, Zimmer L, Hadaschik E, Sucker A, Schadendorf D, Griewank K. Clinical and pathological characteristics of familial melanoma with germline TERT promoter variants. Pigment Cell Melanoma Res 2022; 35:573-586. [PMID: 35912549 DOI: 10.1111/pcmr.13060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022]
Abstract
Around 10% of melanoma occur in patients with a suspected familial predisposition. TERT promoter mutations are the most common somatic hotspot mutations in human cancers. However, only two families with germline mutations have been identified to date. We present detailed histological, clinical and molecular pathologic analyses of affected patients and details of newly identified individuals in one of these previously reported families. TERT (NM_198253.3) Chr.5:1,295,161T>C (c.-57 T>C) promoter variants were detected in all melanoma-affected (n=18) and one non-diseased family member. Median age at diagnosis was 30 years (n=18, range 16-46 years, 2 unknown). While most primary melanoma arose on the upper extremities (n=7, 21%) and were superficial spreading melanoma (SSM, n=8, 24%), many primary melanoma also originated from non UV-exposed mucosal (n=2, 6%) and acral (n=4, 12%) locations. One SSM sample harboured a Chr.5:1,295,228C>T TERT promoter region in addition to the germline Chr.5:1,295,161T>C variant, arguing additional pathway activation can support tumor pathogenesis. Patients treated with BRAF inhibitor and/or immune checkpoint inhibition (ICI) showed responses, although of limited duration. One mucosal melanoma harboured both a KIT copy number gain and an activating c.1727 p.Leu576Pro mutation. Following modest response to ICI, subsequent KIT inhibitor (imatinib) therapy demonstrated an ongoing complete pathological response (currently 7 months).
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Affiliation(s)
- Anne Zaremba
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Friedegund Meier
- Skin Cancer Center at the University Cancer Centre and National Center for Tumor Diseases, Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Jansen
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinic and Polyclinic for Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Georg Lodde
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Mingxia Song
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Julia Kretz
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Inga Möller
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Nadine Stadtler
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Elisabeth Livingstone
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lisa Zimmer
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Eva Hadaschik
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Klaus Griewank
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
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12
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Familial Melanoma and Susceptibility Genes: A Review of the Most Common Clinical and Dermoscopic Phenotypic Aspect, Associated Malignancies and Practical Tips for Management. J Clin Med 2021; 10:jcm10163760. [PMID: 34442055 PMCID: PMC8397216 DOI: 10.3390/jcm10163760] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022] Open
Abstract
A family history of melanoma greatly increases the risk of developing cutaneous melanoma, a highly aggressive skin cancer whose incidence has been steadily increasing worldwide. Familial melanomas account for about 10% of all malignant melanomas and display an inheritance pattern consistent with the presence of pathogenic germline mutations, among which those involving CDKN2A are the best characterized. In recent years, a growing number of genes, such as MC1R, MITF, CDK4, POT1, TERT, ACD, TERF2IP, and BAP1, have been implicated in familial melanoma. The fact that individuals harboring these germline mutations along with their close blood relatives have a higher risk of developing multiple primary melanomas as well as other internal organ malignancies, especially pancreatic cancer, makes cascade genetic testing and surveillance of these families of the utmost importance. Unfortunately, due to a polygenic inheritance mechanism involving multiple low-risk alleles, genetic modifiers, and environmental factors, it is still very difficult to predict the presence of these mutations. It is, however, known that germline mutation carriers can sometimes develop specific clinical traits, such as high atypical nevus counts and specific dermoscopic features, which could theoretically help clinicians predict the presence of these mutations in prone families. In this review, we provide a comprehensive overview of the high- and intermediate-penetrance genes primarily linked to familial melanoma, highlighting their most frequently associated non-cutaneous malignancies and clinical/dermoscopic phenotypes.
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13
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Rachakonda S, Hoheisel JD, Kumar R. Occurrence, functionality and abundance of the TERT promoter mutations. Int J Cancer 2021; 149:1852-1862. [PMID: 34313327 DOI: 10.1002/ijc.33750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/14/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022]
Abstract
Telomere shortening at chromosomal ends due to the constraints of the DNA replication process acts as a tumor suppressor by restricting the replicative potential in primary cells. Cancers evade that limitation primarily through the reactivation of telomerase via different mechanisms. Mutations within the promoter of the telomerase reverse transcriptase (TERT) gene represent a definite mechanism for the ribonucleic enzyme regeneration predominantly in cancers that arise from tissues with low rates of self-renewal. The promoter mutations cause a moderate increase in TERT transcription and consequent telomerase upregulation to the levels sufficient to delay replicative senescence but not prevent bulk telomere shortening and genomic instability. Since the discovery, a staggering number of studies have resolved the discrete aspects, effects and clinical relevance of the TERT promoter mutations. The promoter mutations link transcription of TERT with oncogenic pathways, associate with markers of poor outcome and define patients with reduced survivals in several cancers. In this review, we discuss the occurrence and impact of the promoter mutations and highlight the mechanism of TERT activation. We further deliberate on the foundational question of the abundance of the TERT promoter mutations and a general dearth of functional mutations within noncoding sequences, as evident from pan-cancer analysis of the whole-genomes. We posit that the favorable genomic constellation within the TERT promoter may be less than a common occurrence in other noncoding functional elements. Besides, the evolutionary constraints limit the functional fraction within the human genome, hence the lack of abundant mutations outside the coding sequences.
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Affiliation(s)
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
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14
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Pellegrini S, Elefanti L, Dall’Olmo L, Menin C. The Interplay between Nevi and Melanoma Predisposition Unravels Nevi-Related and Nevi-Resistant Familial Melanoma. Genes (Basel) 2021; 12:1077. [PMID: 34356093 PMCID: PMC8303673 DOI: 10.3390/genes12071077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Genetic susceptibility to nevi may affect the risk of developing melanoma, since common and atypical nevi are the main host risk factors implicated in the development of cutaneous melanoma. Recent genome-wide studies defined a melanoma polygenic risk score based on variants in genes involved in different pathways, including nevogenesis. Moreover, a predisposition to nevi is a hereditary trait that may account for melanoma clustering in some families characterized by cases with a high nevi density. On the other hand, familial melanoma aggregation may be due to a Mendelian inheritance of high/moderate-penetrance pathogenic variants affecting melanoma risk, regardless of the nevus count. Based on current knowledge, this review analyzes the complex interplay between nevi and melanoma predisposition in a familial context. We review familial melanoma, starting from Whiteman's divergent pathway model to overall melanoma development, distinguishing between nevi-related (cases with a high nevus count and a high polygenic risk score) and nevi-resistant (high/moderate-penetrance variant-carrier cases) familial melanoma. This distinction could better direct future research on genetic factors useful to identify high-risk subjects.
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Affiliation(s)
- Stefania Pellegrini
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, 35128 Padua, Italy; (S.P.); (L.D.)
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy;
| | - Lisa Elefanti
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy;
| | - Luigi Dall’Olmo
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padua, 35128 Padua, Italy; (S.P.); (L.D.)
- Soft-Tissue, Peritoneum and Melanoma Surgical Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Chiara Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy;
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15
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Molecular landscape of Hereditary Melanoma. Crit Rev Oncol Hematol 2021; 164:103425. [PMID: 34245855 DOI: 10.1016/j.critrevonc.2021.103425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 05/20/2021] [Accepted: 07/04/2021] [Indexed: 12/27/2022] Open
Abstract
Melanoma is considered the most lethal skin cancer and its incidence has increased during the past decades. About 10 % of cases are classified as hereditary melanoma. Genetic predisposition usually manifests itself clinically as early onset and multiple cutaneous melanomas. Several genes have been identified as involved to melanoma susceptibility, some of them still with unknown clinical relevance. Beyond melanoma, the affected families are also more prone to develop other malignancies, such as pancreatic cancer. The identification of risk families and involved genes is of great importance, since different forms of oncological surveillance are recommended. However, well established guidelines to standardize both the selection of individuals and the genetic panel to be requested are still lacking. Given the importance of the genetic counseling and testing in the context of clinical suspicion of hereditary melanoma, this paper aims to review the literature regarding genetic panel indications worldwide.
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16
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Blumhagen RZ, Schwartz DA, Langefeld CD, Fingerlin TE. Identification of Influential Variants in Significant Aggregate Rare Variant Tests. Hum Hered 2021; 85:1-13. [PMID: 33567433 PMCID: PMC8353006 DOI: 10.1159/000513290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Studies that examine the role of rare variants in both simple and complex disease are increasingly common. Though the usual approach of testing rare variants in aggregate sets is more powerful than testing individual variants, it is of interest to identify the variants that are plausible drivers of the association. We present a novel method for prioritization of rare variants after a significant aggregate test by quantifying the influence of the variant on the aggregate test of association. METHODS In addition to providing a measure used to rank variants, we use outlier detection methods to present the computationally efficient Rare Variant Influential Filtering Tool (RIFT) to identify a subset of variants that influence the disease association. We evaluated several outlier detection methods that vary based on the underlying variance measure: interquartile range (Tukey fences), median absolute deviation, and SD. We performed 1,000 simulations for 50 regions of size 3 kb and compared the true and false positive rates. We compared RIFT using the Inner Tukey to 2 existing methods: adaptive combination of p values (ADA) and a Bayesian hierarchical model (BeviMed). Finally, we applied this method to data from our targeted resequencing study in idiopathic pulmonary fibrosis (IPF). RESULTS All outlier detection methods observed higher sensitivity to detect uncommon variants (0.001 < minor allele frequency, MAF > 0.03) compared to very rare variants (MAF <0.001). For uncommon variants, RIFT had a lower median false positive rate compared to the ADA. ADA and RIFT had significantly higher true positive rates than that observed for BeviMed. When applied to 2 regions found previously associated with IPF including 100 rare variants, we identified 6 polymorphisms with the greatest evidence for influencing the association with IPF. DISCUSSION In summary, RIFT has a high true positive rate while maintaining a low false positive rate for identifying polymorphisms influencing rare variant association tests. This work provides an approach to obtain greater resolution of the rare variant signals within significant aggregate sets; this information can provide an objective measure to prioritize variants for follow-up experimental studies and insight into the biological pathways involved.
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Affiliation(s)
- Rachel Z Blumhagen
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA,
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA,
| | - David A Schwartz
- School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
- School of Medicine, University of Colorado, Aurora, Colorado, USA
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17
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Co-Occurrence of Hotspot Point Mutation and Novel Deletion Mutation of TERT Promoter in Solid Variant Papillary Thyroid Carcinoma in a Patient with Synchronous Esophageal Cancer. Diagnostics (Basel) 2020; 11:diagnostics11010004. [PMID: 33375021 PMCID: PMC7822032 DOI: 10.3390/diagnostics11010004] [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: 10/27/2020] [Revised: 12/10/2020] [Accepted: 12/20/2020] [Indexed: 11/17/2022] Open
Abstract
(1) Introduction: Telomerase reverse transcriptase (TERT) promoter mutations are associated with unfavorable clinical outcomes in papillary thyroid carcinomas (PTCs). Two substitution mutations, C228T (c.1-124C>T) and C250T (c.1-146C>T), make up most of the mutations and occur in a mutually exclusive manner. (2) Case presentation: A 72-year-old man was initially referred to a tertiary hospital for treatment of esophageal cancer. Preoperative imaging revealed a 3.2 cm thyroid nodule pathologically diagnosed as PTC on needle biopsy. The patient underwent thyroid lobectomy with esophagectomy and was finally diagnosed with synchronous solid variant PTC (SVPTC) and esophageal squamous cell carcinoma. Sanger sequencing using DNA from the thyroid tumor showed an indel mutation, c.1-132_1-124delinsT, composed of a deletion (c.1-132_1-125del) as well as a hotspot mutation (c.1-124C>T(C228T)) in the TERT promoter. (3) Conclusions: This is the first report of PTC harboring a novel deletion along with a hotspot mutation in the TERT promoter in a patient with synchronous esophageal squamous cell carcinoma.
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18
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Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes. Biomedicines 2020; 8:biomedicines8100404. [PMID: 33050356 PMCID: PMC7601281 DOI: 10.3390/biomedicines8100404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
Cutaneous melanoma is the deadliest skin malignity with a rising prevalence worldwide. Patients carrying germline mutations in melanoma-susceptibility genes face an increased risk of melanoma and other cancers. To assess the spectrum of germline variants, we analyzed 264 Czech melanoma patients indicated for testing due to early melanoma (at <25 years) or the presence of multiple primary melanoma/melanoma and other cancer in their personal and/or family history. All patients were analyzed by panel next-generation sequencing targeting 217 genes in four groups: high-to-moderate melanoma risk genes, low melanoma risk genes, cancer syndrome genes, and other genes with an uncertain melanoma risk. Population frequencies were assessed in 1479 population-matched controls. Selected POT1 and CHEK2 variants were characterized by functional assays. Mutations in clinically relevant genes were significantly more frequent in melanoma patients than in controls (31/264; 11.7% vs. 58/1479; 3.9%; p = 2.0 × 10−6). A total of 9 patients (3.4%) carried mutations in high-to-moderate melanoma risk genes (CDKN2A, POT1, ACD) and 22 (8.3%) patients in other cancer syndrome genes (NBN, BRCA1/2, CHEK2, ATM, WRN, RB1). Mutations in high-to-moderate melanoma risk genes (OR = 52.2; 95%CI 6.6–413.1; p = 3.2 × 10−7) and in other cancer syndrome genes (OR = 2.3; 95%CI 1.4–3.8; p = 0.003) were significantly associated with melanoma risk. We found an increased potential to carry these mutations (OR = 2.9; 95%CI 1.2–6.8) in patients with double primary melanoma, melanoma and other primary cancer, but not in patients with early age at onset. The analysis revealed affected genes in Czech melanoma patients and identified individuals who may benefit from genetic testing and future surveillance management of mutation carriers.
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19
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The Role of Noncoding Variants in Heritable Disease. Trends Genet 2020; 36:880-891. [PMID: 32741549 DOI: 10.1016/j.tig.2020.07.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
The genetic basis of disease has largely focused on coding regions. However, it has become clear that a large proportion of the noncoding genome is functional and harbors genetic variants that contribute to disease etiology. Here, we review recent examples of inherited noncoding alterations that are responsible for Mendelian disorders or act to influence complex traits. We explore both rare and common genetic variants and discuss the wide range of mechanisms by which they affect gene regulation to promote disease. We also debate the challenges and progress associated with identifying and interpreting the functional and clinical significance of genetic variation in the context of the noncoding regulatory landscape.
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20
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Abstract
The incidence of cutaneous melanoma continues to increase in pale skinned peoples in Europe and elsewhere. Epidemiological studies identified genetically determined phenotypes such as pale skin, freckles and red hair, and sunburn as risk factors for this cancer. The development of many melanocytic naevi is also genetically determined and a strong melanoma risk phenotype. Not surprisingly then, genome wide association studies have identified pigmentation genes as common risk genes, and to a lesser extent, genes associated with melanocytic naevi. More unexpectedly, genes associated with telomere length have also been identified as risk genes. Higher risk susceptibility genes have been identified, particularly CDKN2A as the most common cause, and very rarely genes such as CDK4, POT1, TERT and other genes in coding for proteins in the shelterin complex are found to be mutated. Familial melanoma genes are associated with an increased number of melanocytic naevi but not invariably and the atypical naevus phenotype is therefore an imperfect marker of gene carrier status. At a somatic level, the most common driver mutation is BRAF, second most common NRAS, third NF1 and increasing numbers of additional rarer mutations are being identified such as in TP53. It is of note that the BRAF and NRAS mutations are not C>T accepted as characteristic of ultraviolet light induced mutations.
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21
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Toussi A, Mans N, Welborn J, Kiuru M. Germline mutations predisposing to melanoma. J Cutan Pathol 2020; 47:606-616. [PMID: 32249949 DOI: 10.1111/cup.13689] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/11/2022]
Abstract
Nearly 15% of melanomas occur in patients with a family history and a subset of these patients have a germline mutation in a melanoma predisposing gene. CDKN2A mutations are responsible for the majority of hereditary melanoma, but many other susceptibility genes have been discovered in recent years, including CDK4, TERT, ACD, TERF2IP, POT1, MITF, MC1R, and BAP1. Additionally, melanoma risk is increased in mixed cancer syndromes caused by mutations in PTEN, BRCA2, BRCA1, RB1, and TP53. While early onset, multiple tumors, and family cancer history remain the most valuable clinical clues for hereditary melanoma, characteristic epithelioid cytology of melanocytic tumors may suggest an underlying BAP1 mutation. Herein, we review the clinical and histopathologic characteristics of melanocytic tumors associated with these germline mutations and discuss the role of genetic counseling.
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Affiliation(s)
- Atrin Toussi
- Department of Dermatology, University of California, Davis, Sacramento, California, USA
| | - Nicole Mans
- Hereditary Cancer Program, Comprehensive Cancer Center, University of California, Davis, Sacramento, California, USA
| | - Jeanna Welborn
- Hereditary Cancer Program, Comprehensive Cancer Center, University of California, Davis, Sacramento, California, USA
| | - Maija Kiuru
- Department of Dermatology, University of California, Davis, Sacramento, California, USA.,Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
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22
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Insights into Genetic Susceptibility to Melanoma by Gene Panel Testing: Potential Pathogenic Variants in ACD, ATM, BAP1, and POT1. Cancers (Basel) 2020; 12:cancers12041007. [PMID: 32325837 PMCID: PMC7226507 DOI: 10.3390/cancers12041007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
The contribution of recently established or candidate susceptibility genes to melanoma missing heritability has yet to be determined. Multigene panel testing could increase diagnostic yield and better define the role of candidate genes. We characterized 273 CDKN2A/ARF and CDK4-negative probands through a custom-designed targeted gene panel that included CDKN2A/ARF, CDK4, ACD, BAP1, MITF, POT1, TERF2IP, ATM, and PALB2. Co-segregation, loss of heterozygosity (LOH)/protein expression analysis, and splicing characterization were performed to improve variant classification. We identified 16 (5.9%) pathogenic and likely pathogenic variants in established high/medium penetrance cutaneous melanoma susceptibility genes (BAP1, POT1, ACD, MITF, and TERF2IP), including two novel variants in BAP1 and 4 in POT1. We also found four deleterious and five likely deleterious variants in ATM (3.3%). Thus, including potentially deleterious variants in ATM increased the diagnostic yield to about 9%. Inclusion of rare variants of uncertain significance would increase the overall detection yield to 14%. At least 10% of melanoma missing heritability may be explained through panel testing in our population. To our knowledge, this is the highest frequency of putative ATM deleterious variants reported in melanoma families, suggesting a possible role in melanoma susceptibility, which needs further investigation.
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23
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McNally EJ, Luncsford PJ, Armanios M. Long telomeres and cancer risk: the price of cellular immortality. J Clin Invest 2019; 129:3474-3481. [PMID: 31380804 PMCID: PMC6715353 DOI: 10.1172/jci120851] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The distribution of telomere length in humans is broad, but it has finite upper and lower boundaries. Growing evidence shows that there are disease processes that are caused by both short and long telomere length extremes. The genetic basis of these short and long telomere syndromes may be linked to mutations in the same genes, such as the telomerase reverse transcriptase (TERT), but through differential effects on telomere length. Short telomere syndromes have a predominant degenerative phenotype marked by organ failure that most commonly manifests as pulmonary fibrosis and are associated with a relatively low cancer incidence. In contrast, insights from studies of cancer-prone families as well as genome-wide association studies (GWAS) have identified both rare and common variants that lengthen telomeres as being strongly associated with cancer risk. We have hypothesized that these cancers represent a long telomere syndrome that is associated with a high penetrance of cutaneous melanoma and chronic lymphocytic leukemia. In this Review, we will synthesize the clinical and human genetic observations with data from mouse models to define the role of telomeres in cancer etiology and biology.
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Affiliation(s)
| | | | - Mary Armanios
- Department of Oncology
- Telomere Center
- Sidney Kimmel Comprehensive Cancer Center, and
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Toland AE. POT1 pathogenic variants: not all telomere pathway genes are equal in risk of hereditary cutaneous melanoma. Br J Dermatol 2019; 181:14-15. [PMID: 31259399 DOI: 10.1111/bjd.17728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, U.S.A
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25
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Potrony M, Puig-Butille J, Ribera-Sola M, Iyer V, Robles-Espinoza C, Aguilera P, Carrera C, Malvehy J, Badenas C, Landi M, Adams D, Puig S. POT1 germline mutations but not TERT promoter mutations are implicated in melanoma susceptibility in a large cohort of Spanish melanoma families. Br J Dermatol 2019; 181:105-113. [PMID: 30451293 PMCID: PMC6526091 DOI: 10.1111/bjd.17443] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Germline mutations in telomere-related genes such as POT1 and TERT predispose individuals to familial melanoma. OBJECTIVES To evaluate the prevalence of germline mutations in POT1 and TERT in a large cohort of Spanish melanoma-prone families (at least two affected first- or second-degree relatives). METHODS Overall, 228 CDKN2A wild-type melanoma-prone families were included in the study. Screening of POT1 was performed in one affected person from each family and TERT was sequenced in one affected patient from 202 families (26 families were excluded owing to DNA exhaustion/degradation). TERT promoter sequencing was extended to an additional 30 families with CDKN2A mutation and 70 patients with sporadic multiple primary melanoma (MPM) with a family history of other cancers. RESULTS We identified four families with potentially pathogenic POT1 germline mutations: a missense variant c.233T>C (p.Ile78Thr); a nonsense variant c.1030G>T (p.Glu344*); and two other variants, c.255G>A (r.125_255del) and c.1792G>A (r.1791_1792insAGTA, p.Asp598Serfs*22), which we confirmed disrupted POT1 mRNA splicing. A TERT promoter variant of unknown significance (c.-125C>A) was detected in a patient with MPM, but no germline mutations were detected in TERT promoter in cases of familial melanoma. CONCLUSIONS Overall, 1·7% of our CDKN2A/CDK4-wild type Spanish melanoma-prone families carry probably damaging mutations in POT1. The frequency of TERT promoter germline mutations in families with melanoma in our population is extremely rare.
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Affiliation(s)
- Miriam Potrony
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - J.A. Puig-Butille
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - M. Ribera-Sola
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - V. Iyer
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - C.D. Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Mexico
- Experimental Cancer Genetics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - P. Aguilera
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cristina Carrera
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - J. Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - C. Badenas
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - M.T. Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - D.J. Adams
- Experimental Cancer Genetics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
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Wong K, Robles-Espinoza CD, Rodriguez D, Rudat SS, Puig S, Potrony M, Wong CC, Hewinson J, Aguilera P, Puig-Butille JA, Bressac-de Paillerets B, Zattara H, van der Weyden L, Fletcher CDM, Brenn T, Arends MJ, Quesada V, Newton-Bishop JA, Lopez-Otin C, Bishop DT, Harms PW, Johnson TM, Durham AB, Lombard DB, Adams DJ. Association of the POT1 Germline Missense Variant p.I78T With Familial Melanoma. JAMA Dermatol 2019; 155:604-609. [PMID: 30586141 PMCID: PMC6506889 DOI: 10.1001/jamadermatol.2018.3662] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
Importance The protection of telomeres 1 protein (POT1) is a critical component of the shelterin complex, a multiple-protein machine that regulates telomere length and protects telomere ends. Germline variants in POT1 have been linked to familial melanoma, and somatic mutations are associated with a range of cancers including cutaneous T-cell lymphoma (CTCL). Objective To characterize pathogenic variation in POT1 in families with melanoma to inform clinical management. Design, Setting, and Participants In this case study and pedigree evaluation, analysis of the pedigree of 1 patient with melanoma revealed a novel germline POT1 variant (p.I78T, c.233T>C, chromosome 7, g.124870933A>G, GRCh38) that was subsequently found in 2 other pedigrees obtained from the GenoMEL Consortium. Main Outcomes and Measures (1) Identification of the POT1 p.I78T variant; (2) evaluation of the clinical features and characteristics of patients with this variant; (3) analysis of 3 pedigrees; (4) genomewide single-nucleotide polymorphism genotyping of germline DNA; and (5) a somatic genetic analysis of available nevi and 1 melanoma lesion. Results The POT1 p.I78T variant was found in 3 melanoma pedigrees, all of persons who self-reported as being of Jewish descent, and was shown to disrupt POT1-telomere binding. A UV mutation signature was associated with nevus and melanoma formation in POT1 variant carriers, and somatic mutations in driver genes such as BRAF, NRAS, and KIT were associated with lesion development in these patients. Conclusions and Relevance POT1 p.I78T is a newly identified, likely pathogenic, variant meriting screening for in families with melanoma after more common predisposition genes such as CDKN2A have been excluded. It could also be included as part of gene panel testing.
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Affiliation(s)
- Kim Wong
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, England
| | - Carla Daniela Robles-Espinoza
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, England
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro, Qro, Mexico
| | - David Rodriguez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Saskia S. Rudat
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, England
| | - Susana Puig
- Melanoma Unit, Department of Dermatology, Hospital Clínic de Barcelona, IDIBAPS, Barcelona University, Barcelona, Spain
- Centre of Biomedical Research on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Miriam Potrony
- Melanoma Unit, Department of Dermatology, Hospital Clínic de Barcelona, IDIBAPS, Barcelona University, Barcelona, Spain
- Centre of Biomedical Research on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Chi C. Wong
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, England
| | - James Hewinson
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, England
| | - Paula Aguilera
- Melanoma Unit, Department of Dermatology, Hospital Clínic de Barcelona, IDIBAPS, Barcelona University, Barcelona, Spain
- Centre of Biomedical Research on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Joan Anton Puig-Butille
- Centre of Biomedical Research on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Barcelona University, Barcelona, Spain
| | - Brigitte Bressac-de Paillerets
- Gustave Roussy, Université Paris-Saclay, Département de Biologie et Pathologie Médicales, Villejuif, France
- INSERM U1186, Université Paris-Saclay, Villejuif, France
| | - Hélène Zattara
- Département de Génétique, APHM, CHU Timone-Enfants, Marseille, France
| | | | | | - Thomas Brenn
- Pathology Department, Western General Hospital, Edinburgh, Scotland
| | - Mark J. Arends
- Pathology Department, Western General Hospital, Edinburgh, Scotland
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Julia A. Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, England
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación en Red de Cáncer (CIBERONC), Madrid, Spain
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, England
| | - Paul W. Harms
- Department of Pathology, University of Michigan, Ann Arbor
| | | | | | | | - David J. Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, England
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Rossi M, Pellegrini C, Cardelli L, Ciciarelli V, Di Nardo L, Fargnoli MC. Familial Melanoma: Diagnostic and Management Implications. Dermatol Pract Concept 2019; 9:10-16. [PMID: 30775140 PMCID: PMC6368081 DOI: 10.5826/dpc.0901a03] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background An estimated 5%-10% of all cutaneous melanoma cases occur in families. This review describes susceptibility genes currently known to be involved in melanoma predisposition, genetic testing of familial melanoma patients, and management implications. Results CDKN2A is the major high-penetrance susceptibility gene with germline mutations identified in 20%-40% of melanoma families. A positive CDKN2A mutation status has been associated with a high number of affected family members, multiple primary melanomas, pancreatic cancer, and early age at melanoma onset. Mutations in the other melanoma predisposition genes-CDK4, BAP1, TERT, POT1, ACD, TERF2IP, and MITF-are rare, overall contributing to explain a further 10% of familial clustering of melanoma. The underlying genetic susceptibility remains indeed unexplained for half of melanoma families. Genetic testing for melanoma is currently recommended only for CDKN2A and CDK4, and, at this time, the role of multigene panel testing remains under debate. Individuals from melanoma families must receive genetic counseling to be informed about the inclusion criteria for genetic testing, the probability of an inconclusive result, the genetic risk for melanoma and other cancers, and the debatable role of medical management. They should be counseled focusing primarily on recommendations on appropriate lifestyle, encouraging skin self-examination, and regular dermatological screening. Conclusions Genetic testing for high-penetrance melanoma susceptibility genes is recommended in melanoma families after selection of the appropriate candidates and adequate counseling of the patient. All patients and relatives from melanoma kindreds, irrespective of their mutation status, should be encouraged to adhere to a correct ultraviolet exposure, skin self-examination, and surveillance by physicians.
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Affiliation(s)
- Mariarita Rossi
- Department of Dermatology, DISCAB, University of L'Aquila, L'Aquila, Italy
| | | | - Ludovica Cardelli
- Department of Dermatology, DISCAB, University of L'Aquila, L'Aquila, Italy
| | - Valeria Ciciarelli
- Department of Dermatology, DISCAB, University of L'Aquila, L'Aquila, Italy
| | - Lucia Di Nardo
- Department of Dermatology, DISCAB, University of L'Aquila, L'Aquila, Italy.,Institute of Dermatology, Catholic University, Rome, Italy
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Potjer TP, Bollen S, Grimbergen AJEM, van Doorn R, Gruis NA, van Asperen CJ, Hes FJ, van der Stoep N. Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non-CDKN2A/CDK4 melanoma families. Int J Cancer 2019; 144:2453-2464. [PMID: 30414346 PMCID: PMC6590189 DOI: 10.1002/ijc.31984] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/12/2018] [Accepted: 10/25/2018] [Indexed: 02/01/2023]
Abstract
Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susceptibility genes using a custom‐designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (n = 3 BAP1, n = 15 MITF p.E318K; diagnostic yield 4.0%). Among the three identified BAP1‐families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes ACD and TERF2IP, but none in the POT1 gene. MC1R risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88–4.68, p <0.001). Several variants of interest were also identified in candidate melanoma susceptibility genes, in particular rare (pathogenic) variants in the albinism gene OCA2 were repeatedly found. We conclude that multigene panel testing for familial melanoma is appropriate considering the additional 4% diagnostic yield in non‐CDKN2A/CDK4 families. Our study shows that BAP1 and MITF are important genes to be included in such a diagnostic test. What's new? Germline mutations in CDKN2A are major contributors to familial melanoma. These mutations, however, are responsible for only 10 to 40 percent of genetic susceptibility in melanoma‐prone families. In this study, 30 established and candidate melanoma susceptibility genes were investigated for associations with the disease in patients from 451 non‐CDKN2A/CDK4 melanoma families. From the candidate gene panel, (likely) pathogenic variants in BAP1 and MITF were identified in several families, and potentially deleterious variants were identified in the shelterin complex genes ACD and TERF2IP. These genes appear to play a significant role in familial melanoma predisposition and are therefore promising candidates for incorporation into comprehensive genetic tests.
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Affiliation(s)
- Thomas P Potjer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Sander Bollen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
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Genome-wide linkage analysis in Spanish melanoma-prone families identifies a new familial melanoma susceptibility locus at 11q. Eur J Hum Genet 2018; 26:1188-1193. [PMID: 29706638 DOI: 10.1038/s41431-018-0149-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/23/2018] [Accepted: 03/27/2018] [Indexed: 12/20/2022] Open
Abstract
The main genetic factors for familial melanoma remain unknown in >75% of families. CDKN2A is mutated in around 20% of melanoma-prone families. Other high-risk melanoma susceptibility genes explain <3% of families studied to date. We performed the first genome-wide linkage analysis in CDKN2A-negative Spanish melanoma-prone families to identify novel melanoma susceptibility loci. We included 68 individuals from 2, 3, and 6 families with 2, 3, and at least 4 melanoma cases. We detected a locus with significant linkage evidence at 11q14.1-q14.3, with a maximum het-TLOD of 3.449 (rs12285365:A>G), using evidence from multiple pedigrees. The genes contained by the subregion with the strongest linkage evidence were: DLG2, PRSS23, FZD4, and TMEM135. We also detected several regions with suggestive linkage evidence (TLOD >1.9) (1q, 6p, 7p, 11q, 12p, 13q) including the region previously detected in melanoma-prone families from Sweden at 3q29. The family-specific analysis revealed three loci with suggestive linkage evidence for family #1: 1q31.1-q32.1 (max. TLOD 2.447), 6p24.3-p22.3 (max. TLOD 2.409), and 11q13.3-q21 (max. TLOD 2.654). Future next-generation sequencing studies of these regions may allow the identification of new melanoma susceptibility genetic factors.
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Characterization of melanoma susceptibility genes in high-risk patients from Central Italy. Melanoma Res 2018; 27:258-267. [PMID: 28146043 DOI: 10.1097/cmr.0000000000000323] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genetic susceptibility to cutaneous melanoma has been investigated in Italian high-risk melanoma patients from different geographical regions. CDKN2A, CDK4, and MC1R genes have been screened in most studies, MITF and POT1 were screened in only one study, and none analyzed the TERT promoter. We carried out a mutational analysis of CDKN2A, CDK4 exon 2, POT1 p.S270N, MITF exon 10, MC1R, and the TERT promoter in 106 high-risk patients with familial melanoma (FM) and sporadic multiple primary melanoma (spMPM) from Central Italy and evaluated mutations according to the clinicopathological characteristics of patients and lesions. In FM, CDKN2A mutations were detected in 8.3% of the families, including one undescribed exon 1β mutation (p.T31M), and their prevalence increased with the number of affected relatives within the family. MC1R variants were identified in 65% of the patients and the TERT rs2853669 promoter polymorphism was identified in 58% of the patients. A novel synonymous mutation detected in MITF exon 10 (c.861A>G, p.E287E), although predicted as a splice site mutation by computational tools, could not functionally be confirmed to alter splicing. For spMPM, 3% carried CDKN2A mutations, 79% carried MC1R variants, and 47% carried the TERT rs2853669 promoter polymorphism. MC1R variants were associated with fair skin type and light hair color both in FM and in spMPM, and with a reduction of age at diagnosis in FM patients. Mutations in CDK4 exon 2 and the POT1 p.S270N mutation were not detected. A low frequency of CDKN2A mutations and a high prevalence of MC1R variants characterize high-risk melanoma patients from Central Italy.
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31
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Marques IJ, Moura MM, Cabrera R, Pinto AE, Simões-Pereira J, Santos C, Menezes FD, Montezuma D, Henrique R, Rodrigues Teixeira M, Leite V, Cavaco BM. Identification of somatic TERT promoter mutations in familial nonmedullary thyroid carcinomas. Clin Endocrinol (Oxf) 2017; 87:394-399. [PMID: 28502101 DOI: 10.1111/cen.13375] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/19/2017] [Accepted: 05/09/2017] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The genes causing familial nonmedullary thyroid carcinoma (FNMTC) identified to date are only involved in a small fraction of the families. Recently, somatic mutations in TERT promoter region and in EIF1AX gene were reported in thyroid tumours of undefined familial status. The aim of this study was to investigate the role of TERT and EIF1AX mutations in familial thyroid tumours. DESIGN The promoter region of TERT was sequenced in leucocyte DNA of the probands from 75 FNMTC families. In thyroid tumours from 54 familial cases, we assessed somatic TERT promoter, RAS and BRAF hotspot mutations, and the whole EIF1AX gene. RESULTS No potentially pathogenic germline variants were identified in TERT in the 75 FNMTC families' probands. In the 54 carcinomas, we identified five cases (9%) with hotspot somatic TERT promoter mutations. BRAF mutations were found in 41% of the tumours. All TERT-positive samples were also positive for BRAF p.Val600Glu, and this co-occurrence was found to be statistically significant (P=.008). RAS mutations were detected in four tumours wild-type for TERT (7%). Evaluation of tumour mutation data together with the patients' clinicopathological features revealed a significant correlation between TERT plus BRAF mutations and advanced tumour stage (T4) (P=.020). No mutations were identified in EIF1AX. CONCLUSIONS The results of this study suggest that TERT promoter and EIF1AX mutations are not frequently involved in FNMTC aetiology. However, we show for the first time that TERT alterations are associated with familial thyroid tumour progression. Our data also suggest that TERT mutations are more often found in concomitance with BRAF mutations in advanced stages of FNMTC.
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Affiliation(s)
- Inês J Marques
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
- Chronic Diseases Research Centre (CEDOC), Universidade Nova de Lisboa, Lisboa, Portugal
- Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Margarida M Moura
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Rafael Cabrera
- Serviço de Anatomia Patológica, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - António E Pinto
- Serviço de Anatomia Patológica, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Joana Simões-Pereira
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
- Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
- Serviço de Endocrinologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Catarina Santos
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, Porto, Portugal
| | - Francisco D Menezes
- Serviço de Anatomia Patológica, Instituto Português de Oncologia do Porto Francisco Gentil, Porto, Portugal
| | - Diana Montezuma
- Serviço de Anatomia Patológica, Instituto Português de Oncologia do Porto Francisco Gentil, Porto, Portugal
| | - Rui Henrique
- Serviço de Anatomia Patológica, Instituto Português de Oncologia do Porto Francisco Gentil, Porto, Portugal
- Departamento de Patologia e Imunologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Manuel Rodrigues Teixeira
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, Porto, Portugal
- Departamento de Patologia e Imunologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Valeriano Leite
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
- Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
- Serviço de Endocrinologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
| | - Branca M Cavaco
- Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisboa, Portugal
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Melanocytic nevi and melanoma: unraveling a complex relationship. Oncogene 2017; 36:5771-5792. [PMID: 28604751 DOI: 10.1038/onc.2017.189] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/11/2022]
Abstract
Approximately 33% of melanomas are derived directly from benign, melanocytic nevi. Despite this, the vast majority of melanocytic nevi, which typically form as a result of BRAFV600E-activating mutations, will never progress to melanoma. Herein, we synthesize basic scientific insights and data from mouse models with common observations from clinical practice to comprehensively review melanocytic nevus biology. In particular, we focus on the mechanisms by which growth arrest is established after BRAFV600E mutation. Means by which growth arrest can be overcome and how melanocytic nevi relate to melanoma are also considered. Finally, we present a new conceptual paradigm for understanding the growth arrest of melanocytic nevi in vivo termed stable clonal expansion. This review builds upon the canonical hypothesis of oncogene-induced senescence in growth arrest and tumor suppression in melanocytic nevi and melanoma.
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33
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Malignant melanoma of sun-protected sites: a review of clinical, histological, and molecular features. J Transl Med 2017; 97:630-635. [PMID: 28092366 DOI: 10.1038/labinvest.2016.147] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/22/2016] [Accepted: 12/06/2016] [Indexed: 01/16/2023] Open
Abstract
In most cases of cutaneous melanoma, ultraviolet (UV) radiation is recognized as a prominent risk factor. Less is known regarding the mechanisms of mutagenesis for melanoma arising in sun-protected sites, such as acral and mucosal melanoma. Acral and mucosal melanoma share many common features, including a late age of onset, a broad radial growth phase with prominent lentiginous growth, the presence of field cancerization cells, and, in most cases, lack of a precursor nevus. In addition to early chromosomal instability, many of the same genes are also involved in these two distinct melanoma subtypes. To better understand non-UV-mediated pathogenesis in melanoma, we conducted a joint literature review of clinical, histological, and molecular features in acral and mucosal melanoma. We also reviewed the current literature regarding aberrations in KIT, PDGFRA, TERT, and other commonly involved genes. By comparing common features of these two subtypes, we suggest potential mechanisms underlying acral and/or mucosal melanoma and offer direction for future investigations.
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O’Shea SJ, Robles-Espinoza CD, McLellan L, Harrigan J, Jacq X, Hewinson J, Iyer V, Merchant W, Elliott F, Harland M, Bishop DT, Newton-Bishop JA, Adams DJ. A population-based analysis of germline BAP1 mutations in melanoma. Hum Mol Genet 2017; 26:717-728. [PMID: 28062663 PMCID: PMC5409081 DOI: 10.1093/hmg/ddw403] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/19/2016] [Accepted: 11/21/2016] [Indexed: 01/08/2023] Open
Abstract
Germline mutation of the BRCA1 associated protein-1 (BAP1) gene has been linked to uveal melanoma, mesothelioma, meningioma, renal cell carcinoma and basal cell carcinoma. Germline variants have also been found in familial cutaneous melanoma pedigrees, but their contribution to sporadic melanoma has not been fully assessed. We sequenced BAP1 in 1,977 melanoma cases and 754 controls and used deubiquitinase assays, a pedigree analysis, and a histopathological review to assess the consequences of the mutations found. Sequencing revealed 30 BAP1 variants in total, of which 27 were rare (ExAc allele frequency <0.002). Of the 27 rare variants, 22 were present in cases (18 missense, one splice acceptor, one frameshift and two near splice regions) and five in controls (all missense). A missense change (S98R) in a case that completely abolished BAP1 deubiquitinase activity was identified. Analysis of cancers in the pedigree of the proband carrying the S98R variant and in two other pedigrees carrying clear loss-of-function alleles showed the presence of BAP1-associated cancers such as renal cell carcinoma, mesothelioma and meningioma, but not uveal melanoma. Two of these three probands carrying BAP1 loss-of-function variants also had melanomas with histopathological features suggestive of a germline BAP1 mutation. The remaining cases with germline mutations, which were predominantly missense mutations, were associated with less typical pedigrees and tumours lacking a characteristic BAP1-associated histopathological appearances, but may still represent less penetrant variants. Germline BAP1 alleles defined as loss-of-function or predicted to be deleterious/damaging are rare in cutaneous melanoma.
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Affiliation(s)
- Sally J. O’Shea
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Carla Daniela Robles-Espinoza
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Juriquilla 76230, Santiago de Querétaro, Qro, Mexico
| | - Lauren McLellan
- MISSION Therapeutics, Babraham Research Campus. Moneta (Building 280). Cambridge, UK
| | - Jeanine Harrigan
- MISSION Therapeutics, Babraham Research Campus. Moneta (Building 280). Cambridge, UK
| | - Xavier Jacq
- MISSION Therapeutics, Babraham Research Campus. Moneta (Building 280). Cambridge, UK
| | - James Hewinson
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Vivek Iyer
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Will Merchant
- Histopathology Department, Bexley Wing, St. James’s University Hospital, Leeds, UK
| | - Faye Elliott
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Julia A. Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - David J. Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
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Zhang T, Xu M, Makowski MM, Lee C, Kovacs M, Fang J, Willems E, Trent JM, Hayward NK, Vermeulen M, Brown KM. SDHD Promoter Mutations Ablate GABP Transcription Factor Binding in Melanoma. Cancer Res 2017; 77:1649-1661. [PMID: 28108517 DOI: 10.1158/0008-5472.can-16-0919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 11/22/2016] [Accepted: 01/06/2017] [Indexed: 11/16/2022]
Abstract
SDHD encodes subunit D of the succinate dehydrogenase complex, an integral membrane protein. Across cancer types, recurrent SDHD promoter mutations were reported to occur exclusively in melanomas, at a frequency of 4% to 5%. These mutations are predicted to disrupt consensus ETS transcription factor-binding sites and are correlated with both reduced SDHD gene expression and poor prognosis. However, the consequence of these mutations on SDHD expression in melanoma is still unclear. Here, we found that expression of SDHD in melanoma correlated with the expression of multiple ETS transcription factors, particularly in SDHD promoter wild-type samples. Consistent with the predicted loss of ETS transcription factor binding, we observed that recurrent hotspot mutations resulted in decreased luciferase activity in reporter assays. Furthermore, we demonstrated specific GABPA and GABPB1 binding to probes containing the wild-type promoter sequences, with binding disrupted by the SDHD hotspot promoter mutations in both quantitative mass spectrometry and band-shift experiments. Finally, using siRNA-mediated knockdown across multiple melanoma cell lines, we determined that loss of GABPA resulted in reduced SDHD expression at both RNA and protein levels. These data are consistent with a key role for GABPA/B1 as the critical ETS transcription factors deregulating SDHD expression in the context of highly recurrent promoter mutations in melanoma and warrant a detailed search for other recurrent promoter mutations that create or disrupt GABPA consensus sequences. Cancer Res; 77(7); 1649-61. ©2017 AACR.
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Affiliation(s)
- Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Matthew M Makowski
- Radboud Institute of Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Christine Lee
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Michael Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Jun Fang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Esther Willems
- Radboud Institute of Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Jeffrey M Trent
- The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michiel Vermeulen
- Radboud Institute of Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland.
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36
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Heidenreich B, Kumar R. TERT promoter mutations in telomere biology. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 771:15-31. [PMID: 28342451 DOI: 10.1016/j.mrrev.2016.11.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/10/2016] [Indexed: 02/07/2023]
Abstract
Telomere repeats at chromosomal ends, critical to genome integrity, are maintained through an elaborate network of proteins and pathways. Shelterin complex proteins shield telomeres from induction of DNA damage response to overcome end protection problem. A specialized ribonucleic protein, telomerase, maintains telomere homeostasis through repeat addition to counter intrinsic shortcomings of DNA replication that leads to gradual sequence shortening in successive mitoses. The biogenesis and recruitment of telomerase composed of telomerase reverse transcriptase (TERT) subunit and an RNA component, takes place through the intricate machinery that involves an elaborate number of molecules. The synthesis of telomeres remains a controlled and limited process. Inherited mutations in the molecules involved in the process directly or indirectly cause telomeropathies. Telomerase, while present in stem cells, is deactivated due to epigenetic silencing of the rate-limiting TERT upon differentiation in most of somatic cells with a few exceptions. However, in most of the cancer cells telomerase reactivation remains a ubiquitous process and constitutes one of the major hallmarks. Discovery of mutations within the core promoter of the TERT gene that create de novo binding sites for E-twenty-six (ETS) transcription factors provided a mechanism for cancer-specific telomerase reactivation. The TERT promoter mutations occur mainly in tumors from tissues with low rates of self-renewal. In melanoma, glioma, hepatocellular carcinoma, urothelial carcinoma and others, the promoter mutations have been shown to define subsets of patients with adverse disease outcomes, associate with increased transcription of TERT, telomerase reactivation and affect telomere length; in stem cells the mutations inhibit TERT silencing following differentiation into adult cells. The TERT promoter mutations cause an epigenetic switch on the mutant allele along with recruitment of pol II following the binding of GABPA/B1 complex that leads to mono-allelic expression. Thus, the TERT promoter mutations hold potential as biomarkers as well as future therapeutic targets.
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Affiliation(s)
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center, 69120 Heidelberg, Germany.
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Helgadottir H, Höiom V. The genetics of uveal melanoma: current insights. APPLICATION OF CLINICAL GENETICS 2016; 9:147-55. [PMID: 27660484 PMCID: PMC5019476 DOI: 10.2147/tacg.s69210] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Uveal melanoma (UM) is the most common malignant eye tumor in adults affecting ~7,000 individuals per year worldwide. UM is a rare subtype of melanoma with distinct clinical and molecular features as compared to other melanoma subtypes. UMs lack the most typical cutaneous melanoma-associated mutations (BRAF, NRAS, and NF1) and are instead characterized by a different set of genes with oncogenic or loss-of-function mutations. By next-generation sequencing efforts on UM tumors, several driver genes have been detected. The most frequent ones are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1. In many cases, mutations in these genes appear in a mutually exclusive manner, have different risk of metastasis, and are consequently of prognostic importance. The majority of UM cases are sporadic but a few percentage of the cases occurs in families with an inherited predisposition for this malignancy. In recent years, germline mutations in the BAP1 gene have been found to segregate in an autosomal dominant pattern with numerous different cancer types including UM in cancer-prone families. This cancer syndrome has been denoted as the tumor predisposition syndrome.
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Affiliation(s)
- Hildur Helgadottir
- Department of Oncology and Pathology, Karolinska institutet; Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology and Pathology, Karolinska institutet
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38
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Abstract
Malignant melanoma is a rare, often fatal form of skin cancer with a complex multigenic etiology. The incidence of melanoma is increasing at an alarming rate. A number of heritable factors contribute to a patient's overall melanoma risk, including response to ultraviolet light, nevus number, and pigmentation characteristics, such as eye and hair color. Approximately 5%-10% of melanoma cases are familial, yet the majority of familial cases lack identifiable germ-line mutations in known susceptibility genes. Additionally, most familial melanomas lack germ-line mutations in genes that are commonly mutated in sporadic melanoma. Candidate and systematic genome-wide association studies have led to an improved understanding of the risk factors for melanoma and the identification of susceptibility genes. In this review, we provide an overview of the major risk factors and known genes implicated in familial melanoma susceptibility.
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Affiliation(s)
- Jason E Hawkes
- Department of Dermatology, University of Utah, Salt Lake City, UT
| | - Amanda Truong
- Department of Dermatology, University of Utah, Salt Lake City, UT
| | - Laurence J Meyer
- Department of Dermatology, University of Utah, Salt Lake City, UT; Veterans Administration Hospital, Salt Lake City, UT.
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39
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Lee M, Napier CE, Yang SF, Arthur JW, Reddel RR, Pickett HA. Comparative analysis of whole genome sequencing-based telomere length measurement techniques. Methods 2016; 114:4-15. [PMID: 27565742 DOI: 10.1016/j.ymeth.2016.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/17/2016] [Accepted: 08/20/2016] [Indexed: 12/30/2022] Open
Abstract
Telomeres are regions of repetitive DNA at the ends of human chromosomes that function to maintain the integrity of the genome. Telomere attrition is associated with cellular ageing, whilst telomere maintenance is a prerequisite for malignant transformation. Whole genome sequencing (WGS) captures sequence information from the entire genome, including the telomeres, and is increasingly being applied in research and in the clinic. Several bioinformatics tools have been designed to determine telomere content and length from WGS data, and include Motif_counter, TelSeq, Computel, qMotif, and Telomerecat. These tools utilise different approaches to identify, quantify and normalise telomeric reads; however, it is not known how they compare to one another. Here we describe the details and utility of each tool, and directly compare WGS telomere length output with laboratory-based telomere length measurements. In addition, we evaluate the accessibility, practicality, speed, and additional features of each tool. Each tool was tested using a range of telomere read extraction criteria, to determine the optimal parameters for the specific WGS read length. The aim of this article is to improve the accessibility of WGS telomere length measurement tools, which have the potential to be applied to WGS cohorts for clinical as well as research benefit.
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Affiliation(s)
- Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Sile F Yang
- Telomere Length Regulation Group, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.
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40
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Zhang T, Dutton-Regester K, Brown KM, Hayward NK. The genomic landscape of cutaneous melanoma. Pigment Cell Melanoma Res 2016; 29:266-83. [PMID: 26833684 DOI: 10.1111/pcmr.12459] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/25/2016] [Indexed: 12/31/2022]
Abstract
Somatic mutation analysis of melanoma has been performed at the single gene level extensively over the past several decades. This has provided considerable insight into the critical pathways controlling melanoma initiation and progression. During the last 5 yr, next-generation sequencing (NGS) has enabled even more comprehensive mutational screening at the level of multigene panels, exomes and genomes. These studies have uncovered many new and unexpected players in melanoma development. The recent landmark study from The Cancer Genome Atlas (TCGA) consortium describing the genomic architecture of 333 cutaneous melanomas provides the largest and broadest analysis to date on the somatic aberrations underlying melanoma genesis. It thus seems timely to review the mutational landscape of melanoma and highlight the key genes and cellular pathways that appear to drive this cancer.
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Affiliation(s)
- Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ken Dutton-Regester
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
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