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Al Sharhan NA, Messaoudi SA, Babu SR, Chaudhary AB, Alsharm AA, Alrefaei AF, Kadasah S, Abu-Elmagd M, Assidi M, Buhmeida A, Carracedo Á, Almawi WY. Utility of Circulating Cell-Free DNA in Assessing Microsatellite Instability and Loss of Heterozygosity in Breast Cancer Using Human Identification Approach. Genes (Basel) 2022; 13:590. [PMID: 35456396 PMCID: PMC9027523 DOI: 10.3390/genes13040590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
The diagnostic and prognostic utility of circulating cell-free DNA (cfDNA) in breast cancer (BC) patients was recently reported. Here, we investigated the use of cfDNA to examine microsatellite instability (MSI) and loss of heterozygosity (LOH) for early BC diagnosis. cfDNA and genomic DNA from 41 female BC patients and 40 healthy controls were quantified using NanoDrop spectrophotometry and real-time PCR. The stability of genomic and cfDNA was assessed using a high-resolution AmpFlSTR MiniFiler human identification kit. Significant increases in cfDNA plasma concentrations were observed in BC patients compared to controls. The genotype distribution of the eight autosomal short tandem repeat (STR) loci D7S820, D13S317, D21S11, D2S1338, D18S51, D16S539, FGA, and CSF1PO were in Hardy-Weinberg equilibrium. Significant differences in the allele frequencies of D7S820 allele-8, D21S11 allele-29, allele-30.2, allele-32.2, and CSF1PO allele-11 were seen between BC patients and controls. LOH and MSI were detected in 36.6% of the cfDNA of patients compared to genomic DNA. This study highlights the utility of plasma-derived cfDNA for earlier, less invasive, and cost-effective cancer diagnosis and molecular stratification. It also highlights the potential value of cfDNA in molecular profiling and biomarkers discovery in precision and forensic medicine.
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Affiliation(s)
- Norah A. Al Sharhan
- Department of Biopharmaceutical, Laboratories and Research Sector, Saudi Food and Drug Authority, Riyadh 3292, Saudi Arabia;
| | - Safia A. Messaoudi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 14812, Saudi Arabia; (S.A.M.); (S.R.B.); (A.B.C.)
| | - Saranya R. Babu
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 14812, Saudi Arabia; (S.A.M.); (S.R.B.); (A.B.C.)
| | - AbdulRauf B. Chaudhary
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 14812, Saudi Arabia; (S.A.M.); (S.R.B.); (A.B.C.)
- Surgery Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Abdullah A. Alsharm
- Medical Oncology Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia;
| | | | - Sultan Kadasah
- Department of Biology, Faculty of Sciences, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Muhammad Abu-Elmagd
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.-E.); (M.A.); (A.B.)
- Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.-E.); (M.A.); (A.B.)
- Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdelbaset Buhmeida
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.-E.); (M.A.); (A.B.)
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), CIBERER, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Wassim Y. Almawi
- Faculté des Sciences de Tunis, Université de Tunis—El Manar, Tunis 1068, Tunisia
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Tozzo P, Chiara Frigo A, Caenazzo L. Pitfalls in interpreting autosomal InDel markers profiling: A study on mutations in tumoural specimens. Forensic Sci Int Genet 2020; 51:102429. [PMID: 33248349 DOI: 10.1016/j.fsigen.2020.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/03/2020] [Accepted: 11/13/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, Via Falloppio 50, 35121 Padova, Italy.
| | - Anna Chiara Frigo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Falloppio 50, 35121 Padova, Italy
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, Via Falloppio 50, 35121 Padova, Italy
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Barcelos D, Funabashi K, Mazloum S, Fernandes M, Cardili L. STR technique for the detection of contamination by exogenous DNA in paraffin blocks and histological slides. SURGICAL AND EXPERIMENTAL PATHOLOGY 2019. [DOI: 10.1186/s42047-019-0050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractGastrointestinal Stromal Tumors (GIST) present different types of mutations that may or may not be sensitive to specific target therapy. The laboratory procedure required to prepare histological sections traditionally demands multiple steps, making the process prone to contamination by exogenous genetic material (DNA). An eventual contamination of the biological sample with exogenous DNA may jeopardize subsequent analysis of mutations. The Short Tandem Repeat (STR) technique is frequently used in forensic science fields and presents a potential application in surgical pathology, especially in situations of suspected sample exchange. In the present study, the objective is to verify the possible contamination by exogenous DNA in gastric GIST samples and to evaluate if the presence of contamination can interfere in the detection of the mutations of interest. We assessed eight gastric GISTs by the Sanger sequencing and STR sequence analyses. Seven samples presented more than one profile, a result interpreted as contamination. Our results indicate that exogenous DNA contamination occurred in most of the samples studied and that this was more frequent in samples obtained from the slides than those obtained from the block. The presence of contamination did not inhibit the detection of the mutations of interest for a specific target therapy. Furthermore, the histologic block revealed to be more advantageously when compared to the slide for molecular pathology diagnosis.
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Detecting genetic hypermutability of gastrointestinal tumor by using a forensic STR kit. Front Med 2019; 14:101-111. [PMID: 31368030 DOI: 10.1007/s11684-019-0698-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/13/2019] [Indexed: 12/11/2022]
Abstract
Growing evidence suggests that somatic hypermutational status and programmed cell death-1 overexpression are potential predictive biomarkers indicating treatment benefits from immunotherapy using immune checkpoint inhibitors. However, biomarker-matched trials are still limited, and many of the genomic alterations remain difficult to target. To isolate the potential somatic hypermutational tumor from microsatellite instability low/microsatellite stability (MSI-L/MSS) cases, we employed two commercial kits to determine MSI and forensic short tandem repeat (STR) alternations in 250 gastrointestinal (GI) tumors. Three types of forensic STR alternations, namely, allelic loss, Aadd, and Anew, were identified. 62.4% (156/250) of the patients with GI exhibited STR alternation, including 100% (15/15) and 60% (141/235) of the microsatellite high instability and MSI-L/MSS cases, respectively. 30% (75/250) of the patients exhibited STR instability with more than 26.32% (26.32%-84.21%) STR alternation. The cutoff with 26.32% of the STR alternations covered all 15 MSI cases and suggested that it might be a potential threshold. Given the similar mechanism of the mutations of MSI and forensic STR, the widely used forensic identifier STR kit might provide potential usage for identifying hypermutational status in GI cancers.
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Cui Z, Pan X, Wang Q. LOH detected by microsatellite markers reveals the clonal origin of recurrent laryngeal squamous cell carcinoma. PLoS One 2014; 9:e111857. [PMID: 25365429 PMCID: PMC4218824 DOI: 10.1371/journal.pone.0111857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/30/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The question of whether "recurrent" laryngeal carcinoma is truly a new tumour with a clonal origin that differs from that of the primary tumour has remained unanswered. The objective of this study was to determine whether recurrent tumours have the same genetic basis as primary tumours, as the answer to this question is important for the development of treatment strategies. MATERIALS AND METHODS Matched samples consisting of primary tumour, recurrent tumour and normal tissue were obtained from the same patient. A total of 37 patients with laryngeal cancer were examined for loss of heterozygosity (LOH) on the 3p, 5p, 7q, 8p, 9p, 13p, 17p and 18q chromosomal arms using PCR to amplify microsatellite markers. All patients were routinely followed up and 5-year survival rates were calculated using directly calculating method and Kaplan-Meier's method. RESULTS A total of 28 out of 37 (75.6%) patients showed LOH at a minimum of one locus, and 19 out of 37 (51.3%) patients showed LOH at two loci. Primary and recurrent tumours in each patient showed identical allelic loss patterns and incidence rates. Patients without LOH had a longer average time to recurrence than patients with LOH (P<0.05). Additionally, patients with LOH had a longer average smoking duration prior to surgery than patients without LOH (P<0.05). The 5-year survival rates were 32.14%in patients with LOH versus 44.4% in patients without LOH. CONCLUSIONS The data indicate that primary and recurrent tumours have the same clonal origin. This result implies that we failed to radically resect the primary tumours and/or micrometastases in these patients. Consequently, some form of adjunctive therapy may be necessary. Additionally, the data indicate that the recurrence of laryngeal squamous cell carcinoma is closely related to chromosomal aberrations (specifically LOH).
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Affiliation(s)
- Zhaoyang Cui
- Department of Otorhinolaryngology, Shandong Provincial Qianfoshan Hospital, Clinical Medical College of Shandong University, Jinan, China
- * E-mail:
| | - Xinliang Pan
- Department of Otorhinolaryngology, Qilu Hospital, Shandong University, Jinan, China
| | - Qirong Wang
- Department of Otorhinolaryngology, Shandong Provincial Qianfoshan Hospital, Clinical Medical College of Shandong University, Jinan, China
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