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farrukh S, Baig S, Hussain R, Imad R, kulsoom O, Yousaf Rana M. Identification of polymorphic alleles in TERC and TERT gene reprogramming the telomeres of newborn and legacy with parental health. Saudi J Biol Sci 2024; 31:103897. [PMID: 38192544 PMCID: PMC10772381 DOI: 10.1016/j.sjbs.2023.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
Telomere and telomerase genes (TERC and TERT) highlighted many novel genetic polymorphisms related to common diseases. This study explored the polymorphic alleles of TERC and TERT gene in parents-newborn (triad) and its association with telomere length (TL) and parental diseases (mother: Gestational Diabetes Mellitus (GDM), Preeclampsia, fathers: Diabetes, Hypertension). In this cross-sectional study, the blood samples (n = 612) were collected from parents-newborn triad (204 each) for TL (T/S ratio) quantification by using qPCR, and gene (TERC and TERT) polymorphism was detected by Sanger sequencing. The correlation analysis was used to find an association between paternal TL (T/S ratio) and newborn TL. The multivariate linear regression was applied to determine the effect of parents genes and diseases on newborn TL. A positive association (r = 0.42,0.39) (p < 0.0001) among parents and newborn TL was observed. In the diseased group, both TERC (rs10936599) and TERT (rs2736100) genes had a high frequency of allele C in newborns (OR = 0.94, P = 0.90, OR = 4.24, P = 0.012). However, among parents, TERT gene [Mother CC (B = 0.575; P = 0.196), Father CC (B = -0.739; P = 0.071)] was found significant contributing factor for Newborn TL. Diseased parents with T/T and A/C genotypes had longer newborn TL (2.82 ± 2.43, p < 0.022; 1.80 ± 1.20, p < 0.00) than the C/C genotype. Therefore, the study, confirmed that major allele C of TERC and TERT genes is associated with smaller TL in diseased parents-newborns of the targeted population.
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Affiliation(s)
- Sadia farrukh
- Department of Biochemistry, Ziauddin University, Karachi, Pakistan
- Department of Community Health Sciences, The Agha Khan University, Karachi, Pakistan
| | - Saeeda Baig
- Department of Biochemistry, Ziauddin University, Karachi, Pakistan
| | - Rubina Hussain
- Department Gynecology and obstetrician, Ziauddin university and hospitals, Karachi, Pakistan
| | - Rehan Imad
- Department of Molecular medicine, Ziauddin University Karachi, Pakistan
| | - Ome kulsoom
- Department Gynecology and obstetrician, Ziauddin hospital, Karachi, Pakistan
| | - Mehreen Yousaf Rana
- Department Gynecology and obstetrician, Ziauddin hospital, Karachi, Pakistan
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Farrukh S, Baig S. Parental telomeres implications on immune senescence of newborns. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL IMMUNOLOGY 2023; 12:81-86. [PMID: 38022874 PMCID: PMC10658162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Telomere, the biological chronometer, and its effect on the immune system considerably varies among individuals. During pregnancy, multiple risk factors affect telomere reprogramming during fetal life which can lead to health disparities in newborns. These changes may cause a long-term impact on the telomere genetics of the newborn and become a reason for lifelong health implications and immune senescence. Therefore, telomere shortening in parents due to genetic variation may act as a hallmark of immune senescence and aging in their newborns.
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Affiliation(s)
- Sadia Farrukh
- Department of Biochemistry, Ziauddin University Karachi, Pakistan
| | - Saeeda Baig
- Department of Biochemistry, Ziauddin University Karachi, Pakistan
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Bhat KG, Guleria VS, J RK, Rastogi G, Sharma V, Sharma A. Preliminary genome wide screening identifies new variants associated with coronary artery disease in Indian population. Am J Transl Res 2022; 14:5124-5131. [PMID: 35958505 PMCID: PMC9360888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
AIM Coronary artery disease (CAD) is a major health problem in developed and developing nations. Development of CAD involves a complex interaction between genetics and lifestyle factors. Individuals with high-risk genetic predisposition along with poor lifestyle are more inclined to the development of CAD. Advancement in genotyping technologies and increase in genome wide studies has provided a platform to identify new risk factors associated with CAD and associated complexities. METHODOLOGY In this study we performed genome wide screening in 76 well-defined CAD cases and 77 control samples in Indian population. Interestingly, new variants are identified in three genes viz, VLDLR, IFITM2 and C2CD4C. RESULTS The odds ratios observed for variant rs1869592 (VLDLR), rs1059091 (IFITMI) and rs7247159 (C2CD4C) were 2.6 (1.4-4.8 95% CI), 1.9 (95% CI 1.2-3.1) and 2.1 (1.2-3.7 95% CI), respectively with significant P value <0.01. These variants that are associated with pathogenesis of CAD were not previously reported in literature. Moreover, we anticipate that these variants will be further validated using a larger sample size.
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Affiliation(s)
| | | | - Ratheesh Kumar J
- Department of Cardiology, Army Hospital (R&R)New Delhi-110010, India
| | - Garima Rastogi
- NMC Genetics India Pvt. Ltd.Gurugram 122001, Haryana, India
| | - Varun Sharma
- NMC Genetics India Pvt. Ltd.Gurugram 122001, Haryana, India
| | - Anuka Sharma
- NMC Genetics India Pvt. Ltd.Gurugram 122001, Haryana, India
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Mushtaq I, Bhat GR, Rah B, Besina S, Zahoor S, Wani MA, Shah MA, Bashir S, Farooq M, Rather RA, Afroze D. Telomere Attrition With Concomitant hTERT Overexpression Involved in the Progression of Gastric Cancer May Have Prognostic and Clinical Implications in High-Risk Population Group From North India. Front Oncol 2022; 12:919351. [PMID: 35912187 PMCID: PMC9326504 DOI: 10.3389/fonc.2022.919351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Genetic instabilities exacerbated by the dysfunction of telomeres can lead to the development of cancer. Nearly 90% of all human malignancies are linked with telomere dysregulation and overexpression of telomerase, an enzyme that catalyzes the synthesis of telomeric DNA repeats at the ends of chromosomes. The burden of gastric cancer continues to inflict a deterring impact on the global health scenario, accounting for over one million new cases in 2020. The disease is asymptomatic in its early stages of progression, which is attributed to the poor prognosis and overall surge in mortality rate worldwide. Exploiting telomere physiology can provide extensive mechanistic insight into telomere-associated gastric cancer progression and its use as a target in a variety of therapeutic interventions. In this study, we aimed to evaluate the clinical implications of c-Myc, human telomerase reverse transcriptase (hTERT) expression, and telomere length in patients with gastric cancer. A total of 57 gastric cancer cases and adjacent controls were included in the study. RT-PCR and immunohistochemistry were used to assess the expression levels of c-Myc and hTERT. The relative telomere length was measured by MMQPCR using the Cawthon method. Our results indicated that the shorter telomere and increased hTERT expression were associated with gastric cancer progression. The study also highlighted the role of short telomeres and increased expression of hTERT in gastric cancer progression and its association with various etiological risk factors, transcriptional activators, and overall survival among the ethnic Kashmiri population of North India.
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Affiliation(s)
- Ifra Mushtaq
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Gh Rasool Bhat
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Bilal Rah
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Syed Besina
- Department of Pathology, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Sheikh Zahoor
- Department of Surgical Oncology, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Muneer A. Wani
- Department of General Surgery, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Mubashir A. Shah
- Department of General Surgery, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Sadaf Bashir
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Muzamil Farooq
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Rafiq A. Rather
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
| | - Dil Afroze
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Srinagar, India
- *Correspondence: Dil Afroze,
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Bhatt SP, Misra A, Pandey RM, Upadhyay AD. Shortening of leucocyte telomere length is independently correlated with high body mass index and subcutaneous obesity (predominantly truncal), in Asian Indian women with abnormal fasting glycemia. BMJ Open Diabetes Res Care 2022; 10:10/4/e002706. [PMID: 35835478 PMCID: PMC9289012 DOI: 10.1136/bmjdrc-2021-002706] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION Leucocyte telomere length (LTL) is linked to accelerate aging and premature mortality. In this research, we aimed to explore the relations between biochemical and anthropometry markers and LTL in Asian Indian women with abnormal fasting glycemia (impaired fasting glucose). RESEARCH DESIGN AND METHODS In this study, 797 pre-diabetic women (obese, 492; non-obese, 305) were recruited. Demographic and clinical profiles, anthropometry, and fasting blood glucose were evaluated. LTL was quantified by a quantitative PCR. LTL was expressed as the relative telomere length or telomere repeat:single copy gene (T:S) ratio. The subjects were separated into quartiles according to the LTL. RESULTS The average LTL was significantly decreased with increasing age. The average LTL was significantly shorter in obese women with abnormal fasting glycemia (p<0.05). R-squared (R2) statistic for multivariable linear model after adjusted for age, family income, education and hypertension showed that LTL was inversely correlated with body mass index (BMI), waist and hip circumference, waist-hip and waist-to-height ratio, truncal skinfolds (subscapular, and subscapular/triceps ratio, central and total skinfolds), fat mass (kg) and % body fat. The relationship between obesity measures and LTL (using the LTL quartile 1 as reference) identified central skinfolds (R2=0.92, p<0.0001), Σ4SF (R2=0.90, p<0.0001), BMI (R2=0.93, p<0.0001) and % body fat (R2=0.91, p<0.0001) as independent predictors of LTL. CONCLUSIONS Besides age, obesity and subcutaneous adiposity (predominantly truncal) are major contributors to telomere shortening in Asian Indian women with abnormal fasting glycemia (impaired fasting glucose).
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Affiliation(s)
- Surya Prakash Bhatt
- Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, Delhi, India
- Metabolic Research Unit, Diabetes Foundation (India), Safdarjung Development Area (SDA), New Delhi, Delhi, India
- Metabolic Research Unit, National Diabetes Obesity and Cholesterol Foundation (N-DOC), SDA, New Delhi, Delhi, India
| | - Anoop Misra
- Metabolic Research Unit, Diabetes Foundation (India), Safdarjung Development Area (SDA), New Delhi, Delhi, India
- Metabolic Research Unit, National Diabetes Obesity and Cholesterol Foundation (N-DOC), SDA, New Delhi, Delhi, India
- Diabetes and Metabolic Unit, Fortis C-DOC Center of Excellence for Diabetes, Metabolic Diseases, and Endocrinology, New Delhi, Delhi, India
| | - Ravindra Mohan Pandey
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Ashish Datt Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, Delhi, India
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Rai S, Badarinath ARS, George A, Sitaraman S, Bronson SC, Anandt S, Babu KT, Moses A, Saraswathy R, Hande MP. Association of telomere length with diabetes mellitus and idiopathic dilated cardiomyopathy in a South Indian population: A pilot study. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 874-875:503439. [PMID: 35151422 DOI: 10.1016/j.mrgentox.2021.503439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Telomere shortening has been associated with ageing and with many age-related diseases including cancer, coronary artery disease, heart failure and diabetes. We sought to investigate the link between telomere shortening and age-related diseases like type 2 diabetes mellitus (DM) (without any complications: DM; with neuropathic complication: DN) and idiopathic dilated cardiomyopathy (IDCM) in south Indian population. We compared telomere lengths of blood lymphocytes taken from patients with associated age-related diseases, namely DM (n = 47), DN (n = 52) and IDCM (n = 34) and controls (n = 46). In addition, we evaluated the relationship between echocardiographic left ventricular ejection fraction (LVEF), left ventricular end diastolic and systolic diameters (LVEDd and LVESd) and telomere length in IDCM patients. Telomere length negatively correlated with age in the cohorts with diabetes and IDCM, and in controls. Average telomere length in diabetes and IDCM patients was significantly shorter than that of controls either before or after adjustments for age and sex. Duration of diabetes in patients with type 2 diabetes did not correlate with telomere length. No correlation was found between the length of telomeres and echocardiography parameters like LVEF, LVEDd and LVESd in IDCM patients. Though echocardiographic characteristics of IDCM did not correlate with telomere length, telomere shortening was found to be accelerated in diabetes (both DM and DN) and IDCM in a south Indian population. Neuropathic complication in diabetes had no effect on telomere shortening. While telomere shortening is a cause or a consequence of diabetic and cardiac pathology remains further investigation, the current study substantiates the usefulness of telomere length measurements as a marker in conjunction with other biochemical markers of age-related diseases.
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Affiliation(s)
- Shivam Rai
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - A R S Badarinath
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Alex George
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India; Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, India
| | - Sneha Sitaraman
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Stephen Charles Bronson
- Institute of Diabetology, Madras Medical College & Rajiv Gandhi Government General Hospital, Chennai, Tamil Nadu, India
| | | | - K Thirumal Babu
- Heartline Clinic and Research Centre, Vellore, Tamil Nadu, India
| | - Anand Moses
- Institute of Diabetology, Madras Medical College & Rajiv Gandhi Government General Hospital, Chennai, Tamil Nadu, India
| | - Radha Saraswathy
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
| | - M Prakash Hande
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Tacheva T, Zienolddiny S, Dimov D, Vlaykova D, Vlaykova T. The leukocyte telomere length, single nucleotide polymorphisms near TERC gene and risk of COPD. PeerJ 2021; 9:e12190. [PMID: 34824901 PMCID: PMC8590800 DOI: 10.7717/peerj.12190] [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: 02/19/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by irreversible airflow obstruction and is associated with chronic local and systemic inflammation and oxidative stress. The enhanced oxidative stress and inflammation have been reported to affect telomere length (TL). Furthermore, a number of SNPs at loci encoding the main components of the telomerase genes, TERT and TERC have been shown to correlate with TL. We aimed to explore the leukocyte TL and genotypes for single nucleotide polymorphisms, rs12696304 (C > G) and rs10936599 (C > T) near TERC in COPD cases and matched healthy controls using q-PCR technologies. Successful assessment of TL was performed for 91 patients and 88 controls. The patients had shorter TL (17919.36 ± 1203.01 bp) compared to controls (21 271.48 ± 1891.36 bp) although not significant (p = 0.137). The TL did not associate with the gender, age, spirometric indexes, smoking habits but tended to correlate negatively with BMI (Rho = − 0.215, p = 0.076) in the controls, but not in COPD patients. The genotype frequencies of the SNPs rs12696304 and rs10936599 were compared between patients and controls and the odds ratios (OR) for developing COPD were calculated. The carriers of the common homozygous (CC) genotypes of the SNPs had higher risk for COPD, compared to carriers of the variants alleles (rs12696304 CG+GG vs. CC; OR: 0.615, 95% CI [0.424–0.894], p = 0.011 and for rs10936599 CT+TT vs. CC OR = 0.668, 95% CI [0.457–0.976], p = 0.044). Analysis on the combined effects of the TERCrs12696304 (C > G) and rs10936599 (C > T) genotypes, CC/CC genotype combination was associated with higher risk for COPD (p < 0.0001) and marginally lower FEV1% pr. in patients with GOLD II (p = 0.052). There was no association between the SNP genotypes and TL. In summary, our results suggest that COPD patients may have shorter TL, and rs12696304 and rs10936599 near TERC may affect the risk of COPD independently of TL.
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Affiliation(s)
- Tanya Tacheva
- Department of Medical Chemistry and Biochemistry, Medical Faculty, Trakia University, Stara Zagora, Bulgaria
| | - Shanbeh Zienolddiny
- Section for Toxicology and Biological Work Environment, National Institute of Occupational Health, Oslo, Norway
| | - Dimo Dimov
- Department of Medical Chemistry and Biochemistry, Medical Faculty, Trakia University, Stara Zagora, Bulgaria
| | - Denitsa Vlaykova
- Department of Medical Chemistry and Biochemistry, Medical Faculty, Trakia University, Stara Zagora, Bulgaria
| | - Tatyana Vlaykova
- Department of Medical Chemistry and Biochemistry, Medical Faculty, Trakia University, Stara Zagora, Bulgaria.,Department of Medical Biochemistry, Medical University - Plovdiv, Plovdiv, Bulgaria
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Zeid D, Mooney-Leber S, Seemiller LR, Goldberg LR, Gould TJ. Terc Gene Cluster Variants Predict Liver Telomere Length in Mice. Cells 2021; 10:2623. [PMID: 34685603 PMCID: PMC8533930 DOI: 10.3390/cells10102623] [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: 08/27/2021] [Revised: 09/19/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Variants in a gene cluster upstream-adjacent to TERC on human chromosome 3, which includes genes APRM, LRRC31, LRRC34 and MYNN, have been associated with telomere length in several human populations. Currently, the mechanism by which variants in the TERC gene cluster influence telomere length in humans is unknown. Given the proximity between the TERC gene cluster and TERC (~0.05 Mb) in humans, it is speculated that cluster variants are in linkage disequilibrium with a TERC causal variant. In mice, the Terc gene/Terc gene cluster are also located on chromosome 3; however, the Terc gene cluster is located distantly downstream of Terc (~60 Mb). Here, we initially aim to investigate the interactions between genotype and nicotine exposure on absolute liver telomere length (aTL) in a panel of eight inbred mouse strains. Although we found no significant impact of nicotine on liver aTL, this first experiment identified candidate single nucleotide polymorphisms (SNPs) in the murine Terc gene cluster (within genes Lrrc31, Lrriq4 and Mynn) co-varying with aTL in our panel. In a second experiment, we tested the association of these Terc gene cluster variants with liver aTL in an independent panel of eight inbred mice selected based on candidate SNP genotype. This supported our initial finding that Terc gene cluster polymorphisms impact aTL in mice, consistent with data in human populations. This provides support for mice as a model for telomere dynamics, especially for studying mechanisms underlying the association between Terc cluster variants and telomere length. Finally, these data suggest that mechanisms independent of linkage disequilibrium between the Terc/TERC gene cluster and the Terc/TERC gene mediate the cluster's regulation of telomere length.
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Affiliation(s)
- Dana Zeid
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
| | - Sean Mooney-Leber
- Department of Psychology, University of Wisconsin-Stevens Point, Stevens Point, WI 54481, USA;
| | - Laurel R. Seemiller
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
| | - Lisa R. Goldberg
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
| | - Thomas J. Gould
- Department of Biobehavioral Health, Penn State University, University Park, PA 16802, USA; (L.R.S.); (L.R.G.); (T.J.G.)
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Kroupa M, Rachakonda S, Vymetalkova V, Tomasova K, Liska V, Vodenkova S, Cumova A, Rossnerova A, Vodickova L, Hemminki K, Soucek P, Kumar R, Vodicka P. Telomere length in peripheral blood lymphocytes related to genetic variation in telomerase, prognosis and clinicopathological features in breast cancer patients. Mutagenesis 2020; 35:491-497. [PMID: 33367858 DOI: 10.1093/mutage/geaa030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/06/2020] [Indexed: 11/15/2022] Open
Abstract
Disruption of telomere length (TL) homeostasis in peripheral blood lymphocytes has been previously assessed as a potential biomarker of breast cancer (BC) risk. The present study addressed the relationship between lymphocyte TL (LTL), prognosis and clinicopathological features in the BC patients since these associations are insufficiently explored at present. LTL was measured in 611 BC patients and 154 healthy controls using the monochrome multiplex quantitative Polymerase Chain Reaction assay. In addition, we genotyped nine TL-associated single-nucleotide polymorphisms that had been identified through genome-wide association studies. Our results showed that the patients had significantly (P = 0.001, Mann-Whitney U-test) longer LTL [median (interquartile range); 1.48 (1.22-1.78)] than the healthy controls [1.27 (0.97-1.82)]. Patients homozygous (CC) for the common allele of hTERT rs2736108 or the variant allele (CC) of hTERC rs16847897 had longer LTL. The latter association remained statistically significant in the recessive genetic model after the Bonferroni correction (P = 0.004, Wilcoxon two-sample test). We observed no association between LTL and overall survival or relapse-free survival of the patients. LTL did not correlate with cancer staging based on Union for International Cancer Control (UICC), The tumor node metastasis (TNM) staging system classification, tumour grade or molecular BC subtypes. Overall, we observed an association between long LTL and BC disease and an association of the hTERC rs16847897 CC genotype with increased LTL. However, no association between LTL, clinicopathological features and survival of the patients was found.
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Affiliation(s)
- Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
| | - Sivaramakrishna Rachakonda
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov, Prague, Czech Republic
| | - Kristyna Tomasova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
| | - Vaclav Liska
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska, Prague, Czech Republic
| | - Andrea Cumova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov, Prague, Czech Republic
| | - Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov, Prague, Czech Republic
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Pavel Soucek
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
| | - Rajiv Kumar
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Husova, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov, Prague, Czech Republic
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Bakshi D, Nagpal A, Sharma V, Sharma I, Shah R, Sharma B, Bhat A, Verma S, Bhat GR, Abrol D, Sharma R, Vaishnavi S, Kumar R. MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population. BMC Cancer 2020; 20:861. [PMID: 32894086 PMCID: PMC7487711 DOI: 10.1186/s12885-020-07361-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
Background Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. Methods SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. Results The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08–2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136–5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123–0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46–0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. Conclusion It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.
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Affiliation(s)
- Divya Bakshi
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
| | - Ashna Nagpal
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Varun Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, India
| | - Indu Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, India
| | - Ruchi Shah
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Bhanu Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Sonali Verma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Gh Rasool Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Deepak Abrol
- Department of Radiotherapy, GMC, Kathua, J&K, India
| | - Rahul Sharma
- Department of Radiotherapy, GMC, Jammu, J&K, India
| | - Samantha Vaishnavi
- Department of Plant Sciences, Central University of Jammu, Jammu, J&K, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
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