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Lawrence P, Chabane M, Abrouk L, Thiesson A, Berthé D, Diarra AB, Bengaly K, Traoré B, Kassogué D, Durand G, Voegele C, Le Calvez-Kelm F, Steenkeste N, Hainaut P, Kouriba B, Gormally E. First Molecular Characterization of Chronic Hepatitis B Carriers in Timbuktu, Mali. Diagnostics (Basel) 2023; 13:375. [PMID: 36766478 PMCID: PMC9913942 DOI: 10.3390/diagnostics13030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
In Mali, hepatocellular carcinoma (HCC) is the third and sixth most common cancer in men and women, respectively. Mali comprises several distinct climato-ecological zones. Most studies to date have been conducted in the sub-Sahelian zone of southern Mali, including the capital city Bamako. In this part of the country, the main risk factors for HCC are chronic hepatitis B virus (HBV) carriage and dietary exposure to aflatoxins, a well-known hepatocarcinogen. Data are scarce for other ecological zones, but our preliminary data from 721 blood donors in the area of Timbuktu, presented in this study, suggest that chronic HBV carriage is also endemic in the northern Saharan zone of Mali. For further study, 29 healthy HBV chronic carrier volunteers were recruited from the blood transfusion center in Timbuktu. Successful viral genotyping in 20 volunteers revealed HBV genotype E in 13 cases and D in 7 cases, suggesting that this geographical and anthropological transition zone may also represent a transition zone between HBV genotypes that dominate sub-Saharan and northern Africa, respectively. Sequencing of circulating cell-free plasma DNA (cfDNA) from donors did not reveal the presence of the TP53 R249S mutation in these donors, a marker of dietary exposure to aflatoxins in sub-Saharan Africa. These results suggest that the geo-epidemiological distribution of the risk factors for HCC is not uniform across Mali, but is dependent upon climatic, socioeconomic and anthropological factors that might have an impact on patterns of chronic liver disease and cancer.
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Affiliation(s)
- Philip Lawrence
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
| | | | - Lucie Abrouk
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
| | - Adrien Thiesson
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
| | | | - Amadou B. Diarra
- Centre National de Transfusion Sanguine (CNTS, National Blood Bank), Bamako BPE1520, Mali
| | - Karim Bengaly
- Centre d’Infectiologie Charles Mérieux, Bamako BPE2283, Mali
| | - Brehima Traoré
- Centre d’Infectiologie Charles Mérieux, Bamako BPE2283, Mali
| | | | - Geoffroy Durand
- International Agency for Research on Cancer, 69008 Lyon, France
| | | | | | | | - Pierre Hainaut
- Institute of Advanced Biosciences, INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38700 La Tronche, France
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux, Bamako BPE2283, Mali
| | - Emmanuelle Gormally
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
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Cell-Free-DNA-Based Copy Number Index Score in Epithelial Ovarian Cancer-Impact for Diagnosis and Treatment Monitoring. Cancers (Basel) 2021; 14:cancers14010168. [PMID: 35008332 PMCID: PMC8750971 DOI: 10.3390/cancers14010168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The prognosis of ovarian cancer is dependent on the tumor stage and the development of chemotherapy resistance. Using low-coverage cell-free tumor DNA sequencing, we were able to determine the chromosomal instability (CI) of tumors that are frequently found in patients with primary advanced and recurrent high-grade ovarian cancer from a blood sample. We were able to show that the CI could be used for the reliable detection of ovarian cancer in comparison to healthy controls. Moreover, we showed that the CI was significantly associated with the prognostic and predictive clinical measures in primary and recurrent ovarian cancer. The high diagnostic accuracy of the tumor CI derived from cfDNA analysis might lead to the optimization of main prognostic determinants in patients with ovarian cancer. As the CI is a characteristic feature in high-grade ovarian cancer, no upfront tumor tissue analysis is required to identify genomic alterations for targeted sequencing of cfDNA, if the herein described low-coverage sequencing and CNI-Score determination is used. Abstract Background: Chromosomal instability, a hallmark of cancer, results in changes in the copy number state. These deviant copy number states can be detected in the cell-free DNA (cfDNA) and provide a quantitative measure of the ctDNA levels by converting cfDNA next-generation sequencing results into a genome-wide copy number instability score (CNI-Score). Our aim was to determine the role of the CNI-Score in detecting epithelial ovarian cancer (EOC) and its role as a marker to monitor the response to treatment. Methods: Blood samples were prospectively collected from 109 patients with high-grade EOC. cfDNA was extracted and analyzed using a clinical-grade assay designed to calculate a genome-wide CNI-Score from low-coverage sequencing data. Stored data from 241 apparently healthy controls were used as a reference set. Results: Comparison of the CNI-Scores of primary EOC patients versus controls yielded sensitivities of 91% at a specificity of 95% to detect OC, respectively. Significantly elevated CNI-Scores were detected in primary (median: 87, IQR: 351) and recurrent (median: 346, IQR: 1891) blood samples. Substantially reduced CNI-Scores were detected after primary debulking surgery. Using a cut-off of 24, a diagnostic sensitivity of 87% for primary and recurrent EOC was determined at a specificity of 95%. CNI-Scores above this threshold were detected in 21/23 primary tumor (91%), 36/42 of platinum-eligible recurrent (85.7%), and 19/22 of non-platinum-eligible recurrent (86.3%) samples, respectively. Conclusion: ctDNA-quantification based on genomic instability determined by the CNI-Score was a biomarker with high diagnostic accuracy in high-grade EOC. The applied assay might be a promising tool for diagnostics and therapy monitoring, as it requires no a priori information about the tumor.
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Nasrollahzadeh D, Roshandel G, Delhomme TM, Avogbe PH, Foll M, Saidi F, Poustchi H, Sotoudeh M, Malekzadeh R, Brennan P, Mckay J, Hainaut P, Abedi-Ardekani B. TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation. Int J Mol Sci 2021; 22:5627. [PMID: 34073316 PMCID: PMC8197963 DOI: 10.3390/ijms22115627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/17/2021] [Indexed: 12/30/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11-3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC.
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Affiliation(s)
- Dariush Nasrollahzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Gholamreza Roshandel
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan 49177-44563, Iran;
| | - Tiffany Myriam Delhomme
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Patrice Hodonou Avogbe
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Matthieu Foll
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Farrokh Saidi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - James Mckay
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm 1209 CNRS 5309 UGA, 38700 Grenoble, France;
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
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Zvereva M, Pisarev E, Hosen I, Kisil O, Matskeplishvili S, Kubareva E, Kamalov D, Tivtikyan A, Manel A, Vian E, Kamalov A, Ecke T, Calvez-Kelm FL. Activating Telomerase TERT Promoter Mutations and Their Application for the Detection of Bladder Cancer. Int J Mol Sci 2020; 21:E6034. [PMID: 32839402 PMCID: PMC7503716 DOI: 10.3390/ijms21176034] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 01/10/2023] Open
Abstract
This review summarizes state-of-the-art knowledge in early-generation and novel urine biomarkers targeting the telomerase pathway for the detection and follow-up of bladder cancer (BC). The limitations of the assays detecting telomerase reactivation are discussed and the potential of transcription-activating mutations in the promoter of the TERT gene detected in the urine as promising simple non-invasive BC biomarkers is highlighted. Studies have shown good sensitivity and specificity of the urinary TERT promoter mutations in case-control studies and, more recently, in a pilot prospective cohort study, where the marker was detected up to 10 years prior to clinical diagnosis. However, large prospective cohort studies and intervention studies are required to fully validate their robustness and assess their clinical utility. Furthermore, it may be interesting to evaluate whether the clinical performance of urinary TERT promoter mutations could increase when combined with other simple urinary biomarkers. Finally, different approaches for assessment of TERT promoter mutations in urine samples are presented together with technical challenges, thus highlighting the need of careful technological validation and standardization of laboratory methods prior to translation into clinical practice.
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Affiliation(s)
- Maria Zvereva
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- International Agency for Research on Cancer (IARC), 69372 Lyon, France;
| | - Eduard Pisarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Ismail Hosen
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Olga Kisil
- Gause Institute of New Antibiotics, 119021 Moscow, Russia;
| | - Simon Matskeplishvili
- Medical Research and Education Center, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.M.); (D.K.); (A.T.); (A.K.)
| | - Elena Kubareva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia;
| | - David Kamalov
- Medical Research and Education Center, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.M.); (D.K.); (A.T.); (A.K.)
| | - Alexander Tivtikyan
- Medical Research and Education Center, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.M.); (D.K.); (A.T.); (A.K.)
| | | | - Emmanuel Vian
- Department of Urology, Protestant Clinic of Lyon, 69300 Lyon, France;
| | - Armais Kamalov
- Medical Research and Education Center, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.M.); (D.K.); (A.T.); (A.K.)
| | - Thorsten Ecke
- Department of Urology, HELIOS Hospital Bad Saarow, D-15526 Bad Saarow, Germany;
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