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Malik SS, Mubarik S, Aftab A, Khan R, Masood N, Asif M, Bano R. Correlation of MSH2 exonic deletions and protein downregulation with breast cancer biomarkers and outcome in Pakistani women/patients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:3066-3077. [PMID: 32902747 DOI: 10.1007/s11356-020-10717-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Mismatch repair (MMR) pathway is one of the underlying mechanisms of predisposition to breast cancer (BC). The present study explored the association of MSH2 exonic deletions, respective survival analysis, protein structure prediction, transcription profiling, and expression analysis with BC risk. Genotyping analysis of 493 BC cases and 387 controls confirmed the association of two MSH2 exonic deletions, i.e., exon 3 (OR:6.4, CI = 3.4-12.1) and 9 (OR:7.8, CI = 4.1-14.8) with BC risk. In order to confirm the phenotypic-genotypic relationship, we have performed MSH2 transcriptomic (p < 0.05) and protein expression analysis (OR:30, CI = 4-230) which further confirmed its downregulation/loss in BC biopsy samples highlighting potential role in the onset of breast carcinogenesis. Additionally, we have presented that MSH2 mutations can alter the expression profile of other BC associated biomarkers like ER, PR, CK-7, GATA-3, and E-cadherin. Subsequently, the effect of exonic deletions on secondary structure of protein has shown missing of beta and alpha helices in their protein products via in-silico analysis. However, loss of exon 3 results in the altered core protein structure leading to dysfunction protein, possible cause of BC development. No association of MSH2 exonic deletions with survival statistics was observed conceivably due to the shorter follow-up time. Thus, our results at genetic, transcriptomic, and proteomic levels confirmed the downregulated MSH2, emphasizing its potential contribution in MMR mechanisms for breast tumorigenesis. In conclusion, MSH2 deficiency may cause breast cancer development and progression.
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Affiliation(s)
- Saima Shakil Malik
- Department of Zoology, University of Gujrat, Gujrat, Pakistan.
- Microbiology & Biotechnology Research Lab., Fatima Jinnah Women University, The Mall Rawalpindi, Rawalpindi, Punjab, Pakistan.
| | - Sumaira Mubarik
- Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ayesha Aftab
- Department of Biological Sciences, International Islamic University, Sector H10, Islamabad, Pakistan
| | - Ranjha Khan
- The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Huangshan Road, Hefei, 230027, Anhui, China
| | - Nosheen Masood
- Microbiology & Biotechnology Research Lab., Fatima Jinnah Women University, The Mall Rawalpindi, Rawalpindi, Punjab, Pakistan
| | - Muhammad Asif
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Razia Bano
- Breast Clinic, Combined Military Hospital, Rawalpindi, Pakistan
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Karschnia P, Erson-Omay EZ, Huttner AJ, Kaulen LD, Duran D, Fulbright RK, Günel M, Baehring JM. Genomic alterations in Turcot syndrome: Insights from whole exome sequencing. J Neurol Sci 2020; 417:117056. [PMID: 32739502 DOI: 10.1016/j.jns.2020.117056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/23/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Philipp Karschnia
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States of America; Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States of America; Department of Neurosurgery, Ludwig Maximilians University School of Medicine, Munich, Germany.
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States of America.
| | - Anita J Huttner
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States of America.
| | - Leon D Kaulen
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States of America.
| | - Daniel Duran
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States of America.
| | - Robert K Fulbright
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, United States of America.
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States of America.
| | - Joachim M Baehring
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States of America; Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States of America.
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Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women. Int J Mol Sci 2019; 20:ijms20194828. [PMID: 31569399 PMCID: PMC6801521 DOI: 10.3390/ijms20194828] [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: 09/02/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/25/2022] Open
Abstract
This study suggests that two newly discovered variants in the MSH2 gene, which codes for a DNA mismatch repair (MMR) protein, can be associated with a high risk of breast cancer. While variants in the MSH2 gene are known to be linked with an elevated cancer risk, the MSH2 gene is not a part of the standard kit for testing patients for elevated breast cancer risk. Here we used the results of genetic testing of women diagnosed with breast cancer, but who did not have variants in BRCA1 and BRCA2 genes. Instead, the test identified four variants with unknown significance (VUS) in the MSH2 gene. Here, we carried in silico analysis to develop a classifier that can distinguish pathogenic from benign mutations in MSH2 genes taken from ClinVar. The classifier was then used to classify VUS in MSH2 genes, and two of them, p.Ala272Val and p.Met592Val, were predicted to be pathogenic mutations. These two mutations were found in women with breast cancer who did not have mutations in BRCA1 and BRCA2 genes, and thus they are suggested to be considered as new bio-markers for the early detection of elevated breast cancer risk. However, before this is done, an in vitro validation of mutation pathogenicity is needed and, moreover, the presence of these mutations should be demonstrated in a higher number of patients or in families with breast cancer history.
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Luo M, Ding J, Li Y, Tang H, Qi P, Ma J, Wang J, Chen G, Pu Z, Li W, Li Z, Harwood W, Lan X, Deng M, Lu Z, Wei Y, Zheng Y, Jiang Q. A single-base change at a splice site in Wx-A1 caused incorrect RNA splicing and gene inactivation in a wheat EMS mutant line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2097-2109. [PMID: 30993362 DOI: 10.1007/s00122-019-03340-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
An EMS-induced single-base mutation at a splice site caused abnormal RNA splicing and resulted in the gene inactivation and the lack of Wx-A1 protein in a wheat EMS mutant line. An EMS-mutagenized population was generated using common wheat cv. SM126 consisting of 10,600 M2 plants. One Wx-A1 null mutant was identified through analyses of 390 grains produced from 130 M2 plants using electrophoresis analyses. The Wx-A1 sequences of parental line SM126 and M2-31 mutant were determined as 2781 bp, and there was only one SNP mutation between them. The SNP was a mutation from G to A at nucleotide sequence position 2168 bp (G2168A) downstream of the start codon which was located at the splicing site within the eighth intron. All 52 cDNA transcripts were found to be incorrectly spliced and can be summarized as five types of variations. The deletion of the exon and the exclusion of intron were structural features in abnormal splicing RNA. Together with the prediction of potential splice regulatory motifs, the mutation G2168A happened within the 5' splice site of the eighth intron and destroyed the splice donor site from GU to AU, which may have brought about a barrier against correct RNA splice, and generated abnormal mRNA, which was the mechanism of the inactivation of Wx-A1 in M2-31. The lack of Wx-A1 has resulted in changes in starch properties in the M2-31 mutant, with the reduction in amylose and starch contents. The increased grains hardness was observed in M2-31, which may be related to the lower expression level of Pinb-D1 gene. As the waxy wheat foods have a lot of advantages, the null waxy genes will be widely applied in breeding waxy wheat for varied amylose contents.
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Affiliation(s)
- Mi Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jinjin Ding
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yu Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhien Pu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhongyi Li
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT, 2601, Australia
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhenxiang Lu
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, T1J 4B1, Canada
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Ghatak S, Lalnunhlimi S, Lalrohlui F, Pautu JL, Zohmingthanga J, Kunnumakkara AB, Kumar NS. Novel AKT1 mutations associated with cell-cycle abnormalities in gastric carcinoma. Per Med 2018; 15:79-86. [PMID: 29714127 DOI: 10.2217/pme-2017-0053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AIM The aim of this study is to identify the AKT1 gene mutation driven pathogenicity in gastric cancer for Mizo population. METHODS 50 diffuse-type gastric tumors were analyzed for AKT1 exon 2 and 14 mutations. Cell-cycle aberration was analyzed in the AKT1-mutated samples and the stability of the protein as well as exonic splicing enhancer motifs were examined. RESULTS The novel mutations, 15553T >A and 25376C >G might affect the exonic splicing enhancers and silencers. Significant decline was observed in the S-phase population in the tumor cells with 15553T >A and 15579G >C mutations suggesting the arrest of G1 phase. CONCLUSION The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.
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Affiliation(s)
- Souvik Ghatak
- Department of Biotechnology, Mizoram University, Aizawl - 796004, Mizoram, India
| | - Sylvine Lalnunhlimi
- Department of Biotechnology, Mizoram University, Aizawl - 796004, Mizoram, India
| | - Freda Lalrohlui
- Department of Biotechnology, Mizoram University, Aizawl - 796004, Mizoram, India
| | - Jeremy L Pautu
- Mizoram State Cancer Institute, Zemabawk, Aizawl - 796017, Mizoram, India
| | - John Zohmingthanga
- Department of Pathology, Civil Hospital Aizawl, Aizawl - 796001, Mizoram, India
| | - Ajaikumar B Kunnumakkara
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
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Takahashi K, Sato N, Sugawara T, Kato A, Sato T, Shimizu D, Tamura D, Kito M, Makino K, Shirasawa H, Miura H, Sato W, Kumazawa Y, Sato A, Terada Y. Clinical characteristics of Lynch-like cases collaterally classified by Lynch syndrome identification strategy using universal screening in endometrial cancer. Gynecol Oncol 2017; 147:388-395. [PMID: 28847642 DOI: 10.1016/j.ygyno.2017.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/11/2017] [Accepted: 08/12/2017] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Lynch syndrome (LS), an autosomal-dominant inherited disorder, increases the risk for LS-associated cancers (LS-AC). Molecular LS assessment for all cases is referred to as universal screening (U/S) and is recommended for endometrial cancer (EC) and colorectal cancer. Lynch-like cases (LL) lack LS-pathogenic mutations despite being suspected as LS by U/S, but have been poorly investigated in EC. The aim of this study was to capture the features of LL in EC and to devise LL management in EC. METHODS U/S, consisting of immunohistochemistry and reflex methylation analysis, was applied to 348 Asian ECs, and sporadic cancer (SC) cases were screened out. Genetic testing was offered to "suspected-LS" cases selected by U/S. The features of the LS, LL, and SC groups were recorded and compared. RESULTS U/S screened 306 ECs as SC. The recurrence rates of suspected-LS and SC cases were 14.3% (6/42) and 26.5% (81/306), respectively. Of the 42 suspected-LS cases, 10 were identified as LS, 17 were classified as LL, and 15 did not undergo genetic testing. In the LS group, the frequency of personal history (50%) and family history (100%) of LS-AC were prominent. Of note, the prevalence of family history of LS-AC and gastric cancer was significantly higher in the LL group than in the SC group (76.5% vs. 38.6% and 47.1% vs. 25.2%, respectively). CONCLUSIONS Herein, we report the features of LL classified by LS identification via U/S in Asian EC. LL should be candidates for tailored surveillance based on regionality and family history.
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Affiliation(s)
- Kazue Takahashi
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan.
| | - Naoki Sato
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Tae Sugawara
- Department of Obstetrics and Gynecology, Akita city General Hospital, Akita, Japan
| | - Aya Kato
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Toshiharu Sato
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Dai Shimizu
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Daisuke Tamura
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Masahiko Kito
- Department of Obstetrics and Gynecology, Noshiro Kosei Medical Center, Akita, Japan
| | - Kenichi Makino
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiromitsu Shirasawa
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroshi Miura
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Wataru Sato
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Yukiyo Kumazawa
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Akira Sato
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
| | - Yukihiro Terada
- Department of Obstetrics and Gynecology, Akita University Graduate School of Medicine, Akita, Japan
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Peña-Diaz J, Rasmussen LJ. Approaches to diagnose DNA mismatch repair gene defects in cancer. DNA Repair (Amst) 2015; 38:147-154. [PMID: 26708048 DOI: 10.1016/j.dnarep.2015.11.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 08/12/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
The DNA repair pathway mismatch repair (MMR) is responsible for the recognition and correction of DNA biosynthetic errors caused by inaccurate nucleotide incorporation during replication. Faulty MMR leads to failure to address the mispairs or insertion deletion loops (IDLs) left behind by the replicative polymerases and results in increased mutation load at the genome. The realization that defective MMR leads to a hypermutation phenotype and increased risk of tumorigenesis highlights the relevance of this pathway for human disease. The association of MMR defects with increased risk of cancer development was first observed in colorectal cancer patients that carried inactivating germline mutations in MMR genes and the disease was named as hereditary non-polyposis colorectal cancer (HNPCC). Currently, a growing list of cancers is found to be MMR defective and HNPCC has been renamed Lynch syndrome (LS) partly to include the associated risk of developing extra-colonic cancers. In addition, a number of non-hereditary, mostly epigenetic, alterations of MMR genes have been described in sporadic tumors. Besides conferring a strong cancer predisposition, genetic or epigenetic inactivation of MMR genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance of MMR gene alterations in human disease.
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Affiliation(s)
- Javier Peña-Diaz
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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Polyethylene Glycol Electrolyte Lavage Solution versus Colonic Hydrotherapy for Bowel Preparation before Colonoscopy: A Single Center, Randomized, and Controlled Study. Gastroenterol Res Pract 2014; 2014:541586. [PMID: 24995014 PMCID: PMC4068103 DOI: 10.1155/2014/541586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/15/2023] Open
Abstract
This single center, randomized, and controlled study aimed to compare the effectiveness and safety of polyethylene glycol electrolyte lavage (PEG-EL) solution and colonic hydrotherapy (CHT) for bowel preparation before colonoscopy. A total of 196 eligible outpatients scheduled for diagnostic colonoscopy were randomly assigned to the PEG-EL (n = 102) or CHT (n = 94) groups. Primary outcome measures included colonic cleanliness and adverse effects. Secondary outcome measures were patient satisfaction and preference, colonoscopic findings, ileocecal arrival rate, examiner satisfaction, and cecal intubation time. The results show that PEG-EL group was associated with significantly better colonic cleanliness than CHT group, fewer adverse effects, and increased examiner satisfaction. However, the CHT group had higher patient satisfaction and higher diverticulosis detection rates. Moreover, the results showed the same ileocecal arrival rate and patient preference between the two groups (P > 0.05). These findings indicate that PEG-EL is the preferred option in patients who followed the preparation instructions completely.
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