1
|
Ibrahim MB, Flanagan J, Ibrahim T, Rouleau E. Unraveling noncoding DNA variants and epimutations: a paradigm shift in hereditary cancer research. Future Oncol 2024:1-10. [PMID: 38722139 DOI: 10.2217/fon-2023-0665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/11/2024] [Indexed: 06/12/2024] Open
Abstract
Exhaustive efforts have been dedicated to uncovering genomic aberrations linked to cancer susceptibility. Noncoding sequence variants and epigenetic alterations significantly influence gene regulation and could contribute to cancer development. However, exploring noncoding regions in hereditary cancer susceptibility demands cutting-edge methodologies for functionally characterizing genomic discoveries. Additionally, comprehending the impact on cancer development of variants in noncoding DNA and the epigenome necessitates integrating diverse data through bioinformatic analyses. As novel technologies and analytical methods continue to advance, this realm of research is rapidly gaining traction. Within this mini-review, we delve into future research domains concerning aberrations in noncoding DNA regions, such as pseudoexons, promoter variants and cis-epimutations.
Collapse
Affiliation(s)
- Maria Baz Ibrahim
- Department of Oncogenetics & Tumor Biology, Paul Brousse Hospital, Villejuif, France
| | - James Flanagan
- Department of Surgery & Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Tony Ibrahim
- International Department of Medical Oncology, Gustave Roussy, 94805, Villejuif, France
| | - Etienne Rouleau
- Department of Biology & Pathology-Cancer Genetics Laboratory, Gustave Roussy, 94805, Villejuif, France
| |
Collapse
|
2
|
Vazquez E, Lipovka Y, Cervantes-Arias A, Garibay-Escobar A, Haby MM, Queiroga FL, Velazquez C. Canine Mammary Cancer: State of the Art and Future Perspectives. Animals (Basel) 2023; 13:3147. [PMID: 37835752 PMCID: PMC10571550 DOI: 10.3390/ani13193147] [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: 07/21/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Mammary cancer is the most frequently diagnosed neoplasia in women and non-spayed female dogs and is one of the leading causes of death in both species. Canines develop spontaneous mammary tumors that share a significant number of biological, clinical, pathological and molecular characteristics with human breast cancers. This review provides a detailed description of the histological, molecular and clinical aspects of mammary cancer in canines; it discusses risk factors and currently available diagnostic and treatment options, as well as remaining challenges and unanswered questions. The incidence of mammary tumors is highly variable and is impacted by biological, pathological, cultural and socioeconomic factors, including hormonal status, breed, advanced age, obesity and diet. Diagnosis is mainly based on histopathology, although several efforts have been made to establish a molecular classification of canine mammary tumors to widen the spectrum of treatment options, which today rely heavily on surgical removal of tumors. Lastly, standardization of clinical study protocols, development of canine-specific biological tools, establishment of adequate dog-specific disease biomarkers and identification of targets for the development of new therapies that could improve survival and have less adverse effects than chemotherapy are among the remaining challenges.
Collapse
Affiliation(s)
- Eliza Vazquez
- Department of Chemistry-Biology, University of Sonora, Blvd. Luis Encinas y Rosales s/n, Hermosillo 83000, Mexico; (E.V.); (Y.L.); (A.G.-E.); (M.M.H.)
| | - Yulia Lipovka
- Department of Chemistry-Biology, University of Sonora, Blvd. Luis Encinas y Rosales s/n, Hermosillo 83000, Mexico; (E.V.); (Y.L.); (A.G.-E.); (M.M.H.)
| | - Alejandro Cervantes-Arias
- Department of Small Animal Medicine and Surgery, Small Animal Teaching Hospital, The National University of Mexico (UNAM), Ciudad Universitaria, Investigación Científica 3000, Coyoacán, Mexico City 04360, Mexico;
| | - Adriana Garibay-Escobar
- Department of Chemistry-Biology, University of Sonora, Blvd. Luis Encinas y Rosales s/n, Hermosillo 83000, Mexico; (E.V.); (Y.L.); (A.G.-E.); (M.M.H.)
| | - Michelle M. Haby
- Department of Chemistry-Biology, University of Sonora, Blvd. Luis Encinas y Rosales s/n, Hermosillo 83000, Mexico; (E.V.); (Y.L.); (A.G.-E.); (M.M.H.)
| | - Felisbina Luisa Queiroga
- CECAV—Animal and Veterinary Research Center, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - Carlos Velazquez
- Department of Chemistry-Biology, University of Sonora, Blvd. Luis Encinas y Rosales s/n, Hermosillo 83000, Mexico; (E.V.); (Y.L.); (A.G.-E.); (M.M.H.)
| |
Collapse
|
3
|
Jasiak A, Koczkowska M, Stukan M, Wydra D, Biernat W, Izycka-Swieszewska E, Buczkowski K, Eccles MR, Walker L, Wasag B, Ratajska M. Analysis of BRCA1 and BRCA2 alternative splicing in predisposition to ovarian cancer. Exp Mol Pathol 2023; 130:104856. [PMID: 36791903 DOI: 10.1016/j.yexmp.2023.104856] [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: 08/08/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND The mRNA splicing is regulated on multiple levels, resulting in the proper distribution of genes' transcripts in each cell and maintaining cell homeostasis. At the same time, the expression of alternative transcripts can change in response to underlying genetic variants, often missed during routine diagnostics. AIM The main aim of this study was to define the frequency of aberrant splicing in BRCA1 and BRCA2 genes in blood RNA extracted from ovarian cancer patients who were previously found negative for the presence of pathogenic alterations in the 25 most commonly analysed ovarian cancer genes, including BRCA1 and BRCA2. MATERIAL AND METHODS Frequency and spectrum of splicing alterations in BRCA1 and BRCA2 genes were analysed in blood RNA from 101 ovarian cancer patients and healthy controls (80 healthy women) using PCR followed by gel electrophoresis and Sanger sequencing. The expression of splicing events was examined using RT-qPCR. RESULTS We did not identify any novel, potentially pathogenic splicing alterations. Nevertheless, we detected six naturally occurring transcripts, named BRCA1ΔE9-10, BRCA1ΔE11, BRCA1ΔE11q, and BRCA2ΔE3, BRCA2ΔE12 and BRCA2ΔE17-18 of which three (BRCA1ΔE11q, BRCA1ΔE11 and BRCA2ΔE3) were significantly higher expressed in the ovarian cancer cohort than in healthy controls (p ≤ 0.0001). CONCLUSIONS This observation indicates that the upregulation of selected naturally occurring transcripts can be stimulated by non-genetic mechanisms and be a potential systemic response to disease progression and/or treatment. However, this hypothesis requires further examination.
Collapse
Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland.
| | - Magdalena Koczkowska
- 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Stukan
- Department of Gynecologic Oncology, Gdynia Oncology Center, Pomeranian Hospitals, Gdynia, Poland; Department Oncological Propedeutics, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, Gdansk, Poland
| | | | - Kamil Buczkowski
- Department of Pathology & Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Logan Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
| |
Collapse
|
4
|
Blood-Based mRNA Tests as Emerging Diagnostic Tools for Personalised Medicine in Breast Cancer. Cancers (Basel) 2023; 15:cancers15041087. [PMID: 36831426 PMCID: PMC9954278 DOI: 10.3390/cancers15041087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Molecular diagnostic tests help clinicians understand the underlying biological mechanisms of their patients' breast cancer (BC) and facilitate clinical management. Several tissue-based mRNA tests are used routinely in clinical practice, particularly for assessing the BC recurrence risk, which can guide treatment decisions. However, blood-based mRNA assays have only recently started to emerge. This review explores the commercially available blood mRNA diagnostic assays for BC. These tests enable differentiation of BC from non-BC subjects (Syantra DX, BCtect), detection of small tumours <10 mm (early BC detection) (Syantra DX), detection of different cancers (including BC) from a single blood sample (multi-cancer blood test Aristotle), detection of BC in premenopausal and postmenopausal women and those with high breast density (Syantra DX), and improvement of diagnostic outcomes of DNA testing (variant interpretation) (+RNAinsight). The review also evaluates ongoing transcriptomic research on exciting possibilities for future assays, including blood transcriptome analyses aimed at differentiating lymph node positive and negative BC, distinguishing BC and benign breast disease, detecting ductal carcinoma in situ, and improving early detection further (expression changes can be detected in blood up to eight years before diagnosing BC using conventional approaches, while future metastatic and non-metastatic BC can be distinguished two years before BC diagnosis).
Collapse
|
5
|
Alenezi WM, Fierheller CT, Revil T, Serruya C, Mes-Masson AM, Foulkes WD, Provencher D, El Haffaf Z, Ragoussis J, Tonin PN. Case Review: Whole-Exome Sequencing Analyses Identify Carriers of a Known Likely Pathogenic Intronic BRCA1 Variant in Ovarian Cancer Cases Clinically Negative for Pathogenic BRCA1 and BRCA2 Variants. Genes (Basel) 2022; 13:genes13040697. [PMID: 35456503 PMCID: PMC9032308 DOI: 10.3390/genes13040697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/01/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Detecting pathogenic intronic variants resulting in aberrant splicing remains a challenge in routine genetic testing. We describe germline whole-exome sequencing (WES) analyses and apply in silico predictive tools of familial ovarian cancer (OC) cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants. Methods: WES data from 27 familial OC cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants and 53 sporadic early-onset OC cases were analyzed for pathogenic variants in BRCA1 or BRCA2. WES data from carriers of pathogenic BRCA1 or BRCA2 variants were analyzed for pathogenic variants in 10 other OC predisposing genes. Loss of heterozygosity analysis was performed on tumor DNA from variant carriers. Results: BRCA1 c.5407-25T>A intronic variant, identified in two affected sisters and one sporadic OC case, is predicted to create a new splice effecting transcription of BRCA1. WES data from BRCA1 c.5407-25T>A carriers showed no evidence of pathogenic variants in other OC predisposing genes. Sequencing the tumor DNA from the variant carrier showed complete loss of the wild-type allele. Conclusions: The findings support BRCA1 c.5407-25T>A as a likely pathogenic variant and highlight the importance of investigating intronic sequences as causal variants in OC families where the involvement of BRCA1 is highly suggestive.
Collapse
Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Department of Medical Laboratory Technology, Taibah University, Medina 42353, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
| | - Anne-Marie Mes-Masson
- Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada;
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Lady Davis Institute for Medical Research of the Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Department of Medical Genetics, McGill University Health Centre, Montreal, QC H3H 1P3, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 1G5, Canada
| | - Diane Provencher
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC H4A 3J1, Canada
| | - Zaki El Haffaf
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada; (D.P.); (Z.E.H.)
- Service de Médecine Génique, Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; (W.M.A.); (C.T.F.); (T.R.); (W.D.F.); (J.R.)
- Cancer Research Program, Centre for Translational Biology, The Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada;
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-(514)-934-1934 (ext. 44069)
| |
Collapse
|