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Jasmine F, Argos M, Khamkevych Y, Islam T, Rakibuz-Zaman M, Shahriar M, Shea CR, Ahsan H, Kibriya MG. Molecular Profiling and the Interaction of Somatic Mutations with Transcriptomic Profiles in Non-Melanoma Skin Cancer (NMSC) in a Population Exposed to Arsenic. Cells 2024; 13:1056. [PMID: 38920684 PMCID: PMC11201393 DOI: 10.3390/cells13121056] [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: 05/01/2024] [Revised: 05/31/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Exposure to inorganic arsenic (As) is recognized as a risk factor for non-melanoma skin cancer (NMSC). We followed up with 7000 adults for 6 years who were exposed to As. During follow-up, 2.2% of the males and 1.3% of the females developed basal cell carcinoma (BCC), while 0.4% of the male and 0.2% of the female participants developed squamous cell carcinoma (SCC). Using a panel of more than 400 cancer-related genes, we detected somatic mutations (SMs) in the first 32 NMSC samples (BCC = 26 and SCC = 6) by comparing paired (tissue-blood) samples from the same individual and then comparing them to the SM in healthy skin tissue from 16 participants. We identified (a) a list of NMSC-associated SMs, (b) SMs present in both NMSC and healthy skin, and (c) SMs found only in healthy skin. We also demonstrate that the presence of non-synonymous SMs in the top mutated genes (like PTCH1, NOTCH1, SYNE1, PKHD1 in BCC and TP53 in SCC) significantly affects the magnitude of differential expressions of major genes and gene pathways (basal cell carcinoma pathways, NOTCH signaling, IL-17 signaling, p53 signaling, Wnt signaling pathway). These findings may help select groups of patients for targeted therapy, like hedgehog signaling inhibitors, IL17 inhibitors, etc., in the future.
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Affiliation(s)
- Farzana Jasmine
- Institute for Population and Precision Health (IPPH), University of Chicago, Chicago, IL 60637, USA; (F.J.)
| | - Maria Argos
- Epidemiology & Biostatistics, Global Health, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Yuliia Khamkevych
- Institute for Population and Precision Health (IPPH), University of Chicago, Chicago, IL 60637, USA; (F.J.)
| | - Tariqul Islam
- UChicago Research Bangladesh (URB), University of Chicago, Dhaka 1230, Bangladesh
| | | | - Mohammad Shahriar
- Institute for Population and Precision Health (IPPH), University of Chicago, Chicago, IL 60637, USA; (F.J.)
| | - Christopher R. Shea
- Division of Dermatology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Habibul Ahsan
- Institute for Population and Precision Health (IPPH), University of Chicago, Chicago, IL 60637, USA; (F.J.)
- Department of Public Health Sciences, Biological Science Division, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G. Kibriya
- Institute for Population and Precision Health (IPPH), University of Chicago, Chicago, IL 60637, USA; (F.J.)
- Department of Public Health Sciences, Biological Science Division, University of Chicago, Chicago, IL 60637, USA
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Selvam K, Sivapragasam S, Poon GMK, Wyrick JJ. Detecting recurrent passenger mutations in melanoma by targeted UV damage sequencing. Nat Commun 2023; 14:2702. [PMID: 37169747 PMCID: PMC10175485 DOI: 10.1038/s41467-023-38265-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Sequencing of melanomas has identified hundreds of recurrent mutations in both coding and non-coding DNA. These include a number of well-characterized oncogenic driver mutations, such as coding mutations in the BRAF and NRAS oncogenes, and non-coding mutations in the promoter of telomerase reverse transcriptase (TERT). However, the molecular etiology and significance of most of these mutations is unknown. Here, we use a new method known as CPD-capture-seq to map UV-induced cyclobutane pyrimidine dimers (CPDs) with high sequencing depth and single nucleotide resolution at sites of recurrent mutations in melanoma. Our data reveal that many previously identified drivers and other recurrent mutations in melanoma occur at CPD hotspots in UV-irradiated melanocytes, often associated with an overlapping binding site of an E26 transformation-specific (ETS) transcription factor. In contrast, recurrent mutations in the promoters of a number of known or suspected cancer genes are not associated with elevated CPD levels. Our data indicate that a subset of recurrent protein-coding mutations are also likely caused by ETS-induced CPD hotspots. This analysis indicates that ETS proteins profoundly shape the mutation landscape of melanoma and reveals a method for distinguishing potential driver mutations from passenger mutations whose recurrence is due to elevated UV damage.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.
- Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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Non-Melanoma Skin Cancer: A Genetic Update and Future Perspectives. Cancers (Basel) 2022; 14:cancers14102371. [PMID: 35625975 PMCID: PMC9139429 DOI: 10.3390/cancers14102371] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Non-melanoma skin cancer (NMSC) is the main type of cancer in the Caucasian population, and the number of cases continues to rise. Research mostly focuses on clinical characteristics analysis, but genetic features are crucial to malignancies’ establishment and advance. We aim to explore the genetic basics of skin cancer, surrounding microenvironment interactions, and regulation mechanisms to provide a broader perspective for new therapies’ development. Abstract Skin cancer is one of the main types of cancer worldwide, and non-melanoma skin cancer (NMSC) is the most frequent within this group. Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the most common types. Multifactorial features are well-known for cancer development, and new hallmarks are gaining relevance. Genetics and epigenetic regulation play an essential role in cancer susceptibility and progression, as well as the variety of cells and molecules that interact in the tumor microenvironment. In this review, we provide an update on the genetic features of NMSC, candidate genes, and new therapies, considering diverse perspectives of skin carcinogenesis. The global health situation and the pandemic have been challenging for health care systems, especially in the diagnosis and treatment of patients with cancer. We provide innovative approaches to overcome the difficulties in the current clinical dynamics.
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Conversion of a Non-Cancer-Selective Promoter into a Cancer-Selective Promoter. Cancers (Basel) 2022; 14:cancers14061497. [PMID: 35326649 PMCID: PMC8946048 DOI: 10.3390/cancers14061497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/11/2022] [Accepted: 03/03/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The rat progression elevated gene-3 (PEG-3) promoter displays cancer-selective expression, whereas the rat growth arrest and DNA damage inducible gene-34 (GADD34) promoter lacks cancer specificity. PEG-3 and GADD34 minimal promoters display strong sequence homology except for two single point mutations. Since mutations are prevalent in many gene promoters resulting in significant alterations in promoter specificity and activity, we have explored the relevance of these two nucleotide alterations in determining cancer-selective gene expression. We demonstrate that these two point mutations are required to transform a non-cancer-specific promoter (pGADD) into a cancer-selective promoter (pGAPE). Additionally, we found GATA2 transcription factor binding sites in the GAPE-Prom, which regulates pGAPE activity selectively in cancer cells. This newly created pGAPE has all the necessary elements making it an appropriate genetic tool to noninvasively deliver imaging agents to follow tumor growth and progression to metastasis and for generating conditionally replicating adenoviruses that can express and deliver their payload exclusively in cancer. Abstract Progression-elevated gene-3 (PEG-3) and rat growth arrest and DNA damage-inducible gene-34 (GADD34) display significant sequence homology with regulation predominantly transcriptional. The rat full-length (FL) and minimal (min) PEG-3 promoter display cancer-selective expression in rodent and human tumors, allowing for cancer-directed regulation of transgenes, viral replication and in vivo imaging of tumors and metastases in animals, whereas the FL- and min-GADD34-Prom lack cancer specificity. Min-PEG-Prom and min-GADD34-Prom have identical sequences except for two single-point mutation differences (at −260 bp and +159 bp). Engineering double mutations in the min-GADD34-Prom produce the GAPE-Prom. Changing one base pair (+159) or both point mutations in the min-GADD34-Prom, but not the FL-GADD34-Prom, results in cancer-selective transgene expression in diverse cancer cells (including prostate, breast, pancreatic and neuroblastoma) vs. normal counterparts. Additionally, we identified a GATA2 transcription factor binding site, promoting cancer specificity when both min-PEG-Prom mutations are present in the GAPE-Prom. Taken together, introducing specific point mutations in a rat min-GADD34-Prom converts this non-cancer-specific promoter into a cancer-selective promoter, and the addition of GATA2 with existing AP1 and PEA3 transcription factors enhances further cancer-selective activity of the GAPE-Prom. The GAPE-Prom provides a genetic tool to specifically regulate transgene expression in cancer cells.
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Nawrocka PM, Galka-Marciniak P, Urbanek-Trzeciak MO, M-Thirusenthilarasan I, Szostak N, Philips A, Susok L, Sand M, Kozlowski P. Profile of Basal Cell Carcinoma Mutations and Copy Number Alterations - Focus on Gene-Associated Noncoding Variants. Front Oncol 2021; 11:752579. [PMID: 34900699 PMCID: PMC8656283 DOI: 10.3389/fonc.2021.752579] [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: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Basal cell carcinoma (BCC) of the skin is the most common cancer in humans, characterized by the highest mutation rate among cancers, and is mostly driven by mutations in genes involved in the hedgehog pathway. To date, almost all BCC genetic studies have focused exclusively on protein-coding sequences; therefore, the impact of noncoding variants on the BCC genome is unrecognized. In this study, with the use of whole-exome sequencing of 27 tumor/normal pairs of BCC samples, we performed an analysis of somatic mutations in both protein-coding sequences and gene-associated noncoding regions, including 5'UTRs, 3'UTRs, and exon-adjacent intron sequences. Separately, in each region, we performed hotspot identification, mutation enrichment analysis, and cancer driver identification with OncodriveFML. Additionally, we performed a whole-genome copy number alteration analysis with GISTIC2. Of the >80,000 identified mutations, ~50% were localized in noncoding regions. The results of the analysis generally corroborated the previous findings regarding genes mutated in coding sequences, including PTCH1, TP53, and MYCN, but more importantly showed that mutations were also clustered in specific noncoding regions, including hotspots. Some of the genes specifically mutated in noncoding regions were identified as highly potent cancer drivers, of which BAD had a mutation hotspot in the 3'UTR, DHODH had a mutation hotspot in the Kozak sequence in the 5'UTR, and CHCHD2 frequently showed mutations in the 5'UTR. All of these genes are functionally implicated in cancer-related processes (e.g., apoptosis, mitochondrial metabolism, and de novo pyrimidine synthesis) or the pathogenesis of UV radiation-induced cancers. We also found that the identified BAD and CHCHD2 mutations frequently occur in melanoma but not in other cancers via The Cancer Genome Atlas analysis. Finally, we identified a frequent deletion of chr9q, encompassing PTCH1, and unreported frequent copy number gain of chr9p, encompassing the genes encoding the immune checkpoint ligands PD-L1 and PD-L2. In conclusion, this study is the first systematic analysis of coding and noncoding mutations in BCC and provides a strong basis for further analyses of the variants in BCC and cancer in general.
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Affiliation(s)
- Paulina Maria Nawrocka
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Natalia Szostak
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Laura Susok
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Michael Sand
- Department of Dermatology, Venereology and Allergology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany.,Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, Essen, Germany Department of Plastic, Reconstructive and Aesthetic Surgery, St. Josef Hospital, Essen, Germany
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Martin-Gorgojo A, Gilaberte Y, Nagore E. Vitamin D and Skin Cancer: An Epidemiological, Patient-Centered Update and Review. Nutrients 2021; 13:4292. [PMID: 34959844 PMCID: PMC8709188 DOI: 10.3390/nu13124292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The current vitamin D deficiency epidemic is accompanied by an increase in endemic skin cancer. There are still multiple controversies. This review aims to give practical recommendations regarding vitamin D among people at risk or with a personal history of skin cancer. METHODS Narrative review including human research articles published between 2011 and 2021, elaborated bearing in mind an epidemiological, patient-centered approach. RESULTS Ultraviolet (UV) exposure (neither artificial nor natural) is not the ideal source to synthesize vitamin D. There is conflicting epidemiological evidence regarding vitamin D, non-melanoma skin cancer (NMSC), and cutaneous melanoma (CMM), confounded by the effect of sun exposure and other factors. CONCLUSIONS Current evidence is controversial, and there are no widely applicable strategies. We propose three practical recommendations. Firstly, sun protection recommendations should be kept among people at risk or with a personal history of skin cancer. Secondly, vitamin D should preferably be sourced through diet. In patients with melanoma or at risk of cutaneous cancer, serum vitamin D checks are warranted to detect and avoid its insufficiency.
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Affiliation(s)
| | - Yolanda Gilaberte
- Dermatology Department, Hospital Universitario Miguel Servet, IIS Aragon, 50009 Zaragoza, Spain;
| | - Eduardo Nagore
- Dermatology Department, Universidad Catolica de Valencia, 46001 Valencia, Spain;
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7
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Onodera S, Morita N, Nakamura Y, Takahashi S, Hashimoto K, Nomura T, Katakura A, Kosaki K, Azuma T. Novel alterations in IFT172 and KIFAP3 may induce basal cell carcinoma. Orphanet J Rare Dis 2021; 16:443. [PMID: 34674729 PMCID: PMC8529737 DOI: 10.1186/s13023-021-02033-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Basal cell carcinoma (BCC) is the most commonly occurring neoplasm in patients with Gorlin syndrome. It is widely accepted that multiple basal cell carcinomas simultaneously develop in middle-aged patients with this syndrome. However, the presence of driver genes other than the PTCH1 in Gorlin syndrome has not been explored. This study aimed to identify common gene mutations other than PTCH1 in simultaneously occurring basal cell carcinomas in patients with Gorlin syndrome via exome sequencing analysis. Methods Next-generation sequencing analysis was performed using four basal cell carcinoma samples, one dental keratinocyte sample, and two epidermoid cyst samples, which were surgically resected from one patient with Gorlin syndrome on the same day. Results Overall, 282 somatic mutations were identified in the neoplasms. No additional somatic mutations in PTCH1, PTCH2, TP53, and SMO were identified. However, enrichment analysis showed that multiple genes, such as IFT172 and KIFAP3, could regulate ciliary functions important for Hedgehog signaling. Conclusion The development of BCCs in patients with Gorlin syndrome may be triggered by mutations that cause substantial dysfunction of cilia.
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Affiliation(s)
- Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, 2-9-18, Kanda Misakichou, Chiyoda, Tokyo, 101-0061, Japan.
| | - Nana Morita
- Department of Oral Medicine and Hospital Dentistry, Tokyo Dental College, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan.,Department of Dentistry, Oral and Maxillofacial Surgery, Tama-Hokubu Medical Center, Tokyo Metropolitan Health and Medical Treatment Corporation, 1-7-1, aoba-cho, Higashimurayama, Tokyo, 189-8511, Japan
| | - Yuriko Nakamura
- Department of Oral Oncology, Oral and Maxillofacial Surgery, Tokyo Dental College, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Shinichi Takahashi
- Department of Dermatology, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Kazuhiko Hashimoto
- Division of Surgical Pathology, Clinical Laboratory, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Takeshi Nomura
- Department of Oral Oncology, Oral and Maxillofacial Surgery, Tokyo Dental College, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Akira Katakura
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, 2-9-18, Kanda Misakichou, Chiyoda, Tokyo, 101-0061, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 2-15-45, Mita, Minatoku, Tokyo, 108-8345, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, 2-9-18, Kanda Misakichou, Chiyoda, Tokyo, 101-0061, Japan.
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Villani R, Murigneux V, Alexis J, Sim SL, Wagels M, Saunders N, Soyer HP, Parmentier L, Nikolaev S, Fink JL, Roy E, Khosrotehrani K. Subtype-Specific Analyses Reveal Infiltrative Basal Cell Carcinomas Are Highly Interactive with their Environment. J Invest Dermatol 2021; 141:2380-2390. [PMID: 33865912 DOI: 10.1016/j.jid.2021.02.760] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Little is known regarding the molecular differences between basal cell carcinoma (BCC) subtypes, despite clearly distinct phenotypes and clinical outcomes. In particular, infiltrative BCCs have poorer clinical outcomes in terms of response to therapy and propensity for dissemination. In this project, we aimed to use exome sequencing and RNA sequencing to identify somatic mutations and molecular pathways leading to infiltrative BCCs. Using whole-exome sequencing of 36 BCC samples (eight infiltrative) combined with previously reported exome data (58 samples), we determine that infiltrative BCCs do not contain a distinct somatic variant profile and carry classical UV-induced mutational signatures. RNA sequencing on both datasets revealed key differentially expressed genes, such as POSTN and WISP1, suggesting increased integrin and Wnt signaling. Immunostaining for periostin and WISP1 clearly distinguished infiltrative BCCs, and nuclear β-catenin staining patterns further validated the resulting increase in Wnt signaling in infiltrative BCCs. Of significant interest, in BCCs with mixed morphology, infiltrative areas expressed WISP1, whereas nodular areas did not, supporting a continuum between subtypes. In conclusion, infiltrative BCCs do not differ in their genomic alteration in terms of initiating mutations. They display a specific type of interaction with the extracellular matrix environment regulating Wnt signaling.
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Affiliation(s)
- Rehan Villani
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - Valentine Murigneux
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia; QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Josue Alexis
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia; Department of Plastic Surgery, Princess Alexandra Hospital, Metro South Health, Brisbane, Australia
| | - Seen-Ling Sim
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - Michael Wagels
- Department of Plastic Surgery, Princess Alexandra Hospital, Metro South Health, Brisbane, Australia
| | - Nicholas Saunders
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - H Peter Soyer
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia; Department of Dermatology, Princess Alexandra Hospital, Metro South Health, Brisbane, Australia
| | | | - Sergey Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - J Lynn Fink
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - Edwige Roy
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - Kiarash Khosrotehrani
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia; Department of Dermatology, Princess Alexandra Hospital, Metro South Health, Brisbane, Australia.
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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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10
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Abi Karam M, Kourie HR, Jalkh N, Mehawej C, Kesrouani C, Haddad FG, Feghaly I, Chouery E, Tomb R. Molecular profiling of basal cell carcinomas in young patients. BMC Med Genomics 2021; 14:187. [PMID: 34284772 PMCID: PMC8293576 DOI: 10.1186/s12920-021-01030-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 07/05/2021] [Indexed: 12/30/2022] Open
Abstract
Background Basal cell carcinoma (BCC) represents by far the most common non-melanoma skin cancer (NMSC) in the world with an increasing incidence of 3% to 10% per year, especially in patients under the age of 40. While variants in the sonic Hedgehog and cell cycle regulation pathways account for the majority of BCC cases in adults, the molecular etiology of BCC in young patients is unelucidated yet. This study aims to investigate the molecular profile of BCC in the young population. Methods 28 tumors belonging to 25 Lebanese patients under the age of 40, presenting different stages of BCC and diagnosed at Hôtel Dieu de France—Saint Joseph University Medical Center were included in this study. A selected panel of 150 genes involved in cancer was analyzed by Next Generation Sequencing (NGS) in the 28 included tumors. Results Genetic variants detected in more than 5% of the reads, with a sequencing depth ≥ 50x, were selected. Two hundred and two genetic variants in 48 different genes were detected, with an overall average sequencing depth of 1069x. Among the 28 studied tumors, 18 (64.3%) show variations in the PTCH1 gene, 6 (21.4%) in TP53 and 3 (10.7%) in SMO. Conclusions This is the first study reporting NGS-based analysis of BCC in a cohort of young patients. Our results highlight the involvement of the hedgehog and cell cycle regulation pathways in the genesis of BCC in the general population. The inclusion of a larger cohort of young patients is needed to confirm our findings. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01030-w.
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Affiliation(s)
- Marc Abi Karam
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon. .,Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.
| | - Nadine Jalkh
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Cybel Mehawej
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Carole Kesrouani
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.,Pathology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Fady Gh Haddad
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Iman Feghaly
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Roland Tomb
- Dermatology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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11
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Ko EK, Capell BC. Methyltransferases in the Pathogenesis of Keratinocyte Cancers. Cancers (Basel) 2021; 13:cancers13143402. [PMID: 34298617 PMCID: PMC8304454 DOI: 10.3390/cancers13143402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/13/2022] Open
Abstract
Recent evidence suggests that the disruption of gene expression by alterations in DNA, RNA, and histone methylation may be critical contributors to the pathogenesis of keratinocyte cancers (KCs), made up of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), which collectively outnumber all other human cancers combined. While it is clear that methylation modifiers are frequently dysregulated in KCs, the underlying molecular and mechanistic changes are only beginning to be understood. Intriguingly, it has recently emerged that there is extensive cross-talk amongst these distinct methylation processes. Here, we summarize and synthesize the latest findings in this space and highlight how these discoveries may uncover novel therapeutic approaches for these ubiquitous cancers.
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Affiliation(s)
- Eun Kyung Ko
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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Abstract
A number of genes have been implicated in the pathogenesis of BCC in addition to the Hedgehog pathway, which is known to drive the initiation of this tumour. We performed in-depth analysis of 13 BCC-related genes (CSMD1, CSMD2, DPH3 promoter, PTCH1, SMO, GLI1, NOTCH1, NOTCH2, TP53, ITIH2, DPP10, STEAP4, TERT promoter) in 57 BCC lesions (26 superficial and 31 nodular) from 55 patients and their corresponding blood samples. PTCH1 and TP53 mutations were found in 71.9% and 45.6% of BCCs, respectively. A high mutation rate was also detected in CSMD1 (63.2%), NOTCH1 (43.8%) and DPP10 (35.1%), and frequent non-coding mutations were identified in TERT (57.9%) and DPH3 promoter (49.1%). CSMD1 mutations significantly co-occurred with TP53 changes (p = 0.002). A significant association was observed between the superficial type of BCC and PTCH1 (p = 0.018) and NOTCH1 (p = 0.020) mutations. In addition, PTCH1 mutations were significantly associated with intermittent sun exposure (p = 0.046) and the occurrence of single lesions (p = 0.021), while NOTCH1 mutations were more frequent in BCCs located on the trunk compared to the head/neck and extremities (p = 0.001). In conclusion, we provide further insights into the molecular alterations underlying the tumorigenic mechanism of superficial and nodular BCCs with a view towards novel rationale-based therapeutic strategies.
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Dratwa M, Wysoczańska B, Łacina P, Kubik T, Bogunia-Kubik K. TERT-Regulation and Roles in Cancer Formation. Front Immunol 2020; 11:589929. [PMID: 33329574 PMCID: PMC7717964 DOI: 10.3389/fimmu.2020.589929] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
Telomerase reverse transcriptase (TERT) is a catalytic subunit of telomerase. Telomerase complex plays a key role in cancer formation by telomere dependent or independent mechanisms. Telomere maintenance mechanisms include complex TERT changes such as gene amplifications, TERT structural variants, TERT promoter germline and somatic mutations, TERT epigenetic changes, and alternative lengthening of telomere. All of them are cancer specific at tissue histotype and at single cell level. TERT expression is regulated in tumors via multiple genetic and epigenetic alterations which affect telomerase activity. Telomerase activity via TERT expression has an impact on telomere length and can be a useful marker in diagnosis and prognosis of various cancers and a new therapy approach. In this review we want to highlight the main roles of TERT in different mechanisms of cancer development and regulation.
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Affiliation(s)
- Marta Dratwa
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Barbara Wysoczańska
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Tomasz Kubik
- Department of Computer Engineering, Faculty of Electronics, Wrocław University of Science and Technology, Wroclaw, Poland
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Fania L, Didona D, Morese R, Campana I, Coco V, Di Pietro FR, Ricci F, Pallotta S, Candi E, Abeni D, Dellambra E. Basal Cell Carcinoma: From Pathophysiology to Novel Therapeutic Approaches. Biomedicines 2020; 8:biomedicines8110449. [PMID: 33113965 PMCID: PMC7690754 DOI: 10.3390/biomedicines8110449] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022] Open
Abstract
Basal cell carcinoma (BCC) is the most common human cancer worldwide, and is a subtype of nonmelanoma skin cancer, characterized by a constantly increasing incidence due to an aging population and widespread sun exposure. Although the mortality from BCC is negligible, this tumor can be associated with significant morbidity and cost. This review presents a literature overview of BCC from pathophysiology to novel therapeutic approaches. Several histopathological BCC subtypes with different prognostic values have been described. Dermoscopy and, more recently, reflectance confocal microscopy have largely improved BCC diagnosis. Although surgery is the first-line treatment for localized BCC, other nonsurgical local treatment options are available. BCC pathogenesis depends on the interaction between environmental and genetic characteristics of the patient. Specifically, an aberrant activation of Hedgehog signaling pathway is implicated in its pathogenesis. Notably, Hedgehog signaling inhibitors, such as vismodegib and sonidegib, are successfully used as targeted treatment for advanced or metastatic BCC. Furthermore, the implementation of prevention measures has demonstrated to be useful in the patient management.
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Affiliation(s)
- Luca Fania
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
- Correspondence:
| | - Dario Didona
- Department of Dermatology and Allergology, Philipps University, 35043 Marburg, Germany;
| | - Roberto Morese
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Irene Campana
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Valeria Coco
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Francesca Romana Di Pietro
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Francesca Ricci
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Sabatino Pallotta
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Eleonora Candi
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier, 1, 00133 Rome, Italy
| | - Damiano Abeni
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
| | - Elena Dellambra
- Istituto Dermopatico dell’Immacolata-IRCCS, via dei Monti di Creta 104, 00167 Rome, Italy; (R.M.); (I.C.); (V.C.); (F.R.D.P.); (F.R.); (S.P.); (E.C.); (D.A.); (E.D.)
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