Multiple single nucleotide polymorphism analysis and association of specific genotypes in FHIT, SAMD4A, and ANKRD17 in Indian patients with oral cancer

D’Souza, Wendy; Pradhan, Sangram K.; Saranath, Dhananjaya

doi:10.1002/hed.24798

Cited by 6 publications

(9 citation statements)

References 27 publications

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“…The 260/280 ratio of the DNA was assessed and DNA quantified using NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific). Genotyping was performed using allelic discrimination Real‐Time PCR assay with SYBR Select Master Mix on a StepOne Plus Real‐Time PCR system (Applied Biosystems, CA) as previously described . Thirteen SNPs in seven transcription factor genes associated with proliferation, differentiation, and apoptosis were analyzed.…”

Section: Methodsmentioning

confidence: 99%

“…Genotyping was performed using allelic discrimination Real-Time PCR assay with SYBR Select Master Mix on a StepOne Plus Real-Time PCR system (Applied Biosystems, CA) as previously described. 11,20 Thirteen SNPs in seven transcription factor genes associated with proliferation, differentiation, and apoptosis were analyzed. As a measure of quality control, 5% of samples were randomly selected and repeated with 100% concordance.…”

Section: Genotypingmentioning

confidence: 99%

“…A similar situation is seen in Asian countries with less than 15% mortality due to tobacco in oral cancer . An inherent role of the genomic constitution is considered as a predisposition or protective factor in oral carcinogenesis . The complex multifactorial molecular landscape of oral cancer encompasses somatic mutations, deregulated expression, epigenetic regulation via DNA methylation, histone modification, and microRNAs, and genomic variants …”

Section: Introductionmentioning

confidence: 99%

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Single nucleotide polymorphisms in transcription factor genes associated with susceptibility to oral cancer

Shah

Saranath

Pradhan

2019

J of Cellular Biochemistry

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Oral cancer is a major public health concern in the Asian countries predominated by India which accounts for 33.81% of the annual global oral cancer burden. The well‐established high‐risk factors associated with oral cancer include tobacco, areca nut, alcohol consumption, and high‐risk human papilloma virus types 16/18. Additionally, in the past two decades, the critical role of the genomic constitution of individuals in oral cancer susceptibility has emerged. Accumulating evidence indicates the association of several single nucleotide polymorphisms (SNPs) with oral cancer risk. Thus in the current study, we assessed the association of thirteen SNPs in seven transcription factor genes along with HBB (a control SNP) to identify high‐risk genotypes associated with increased oral cancer risk in an Indian cohort of tobacco habitués. Fourteen SNPs were investigated in 500 patients with oral cancer and 500 clinically healthy long‐term tobacco users as controls of Indian ethnicity. Allelic discrimination real‐time polymerase chain reaction was the method of choice for genotyping the samples. Logistic regression analysis was performed and the association of SNPs with oral cancer risk was estimated using odds ratio (OR) and 95% confidence interval (CI). We observed five SNPs—rs2051526 (ETV6), rs6021247 (NFATC2), rs3757769 (SND1), rs7085532 (TCF7L2), and rs7778413 (SND1) indicating increased oral cancer risk with OR ranging from 1.61 to 34.60. Further, as a proof of concept, the coinheritance of high‐risk genotypes in rs6021247 (NFATC2) GG (OR, 2.77; CI, 2.09‐3.69) and rs7778413 (SND1) CC (OR, 34.60; CI, 17.32‐69.13) reflected further increase in the risk with OR‐49.94 (CI, 16.25‐153.48). The present study indicates the association of transcription factor SNPs with increased oral cancer risk constituting “predictive biomarkers” in oral cancers.

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Section: Methodsmentioning

confidence: 99%

Section: Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Single nucleotide polymorphisms in transcription factor genes associated with susceptibility to oral cancer

Shah

Saranath

Pradhan

2019

J of Cellular Biochemistry

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“…Alcohol and smoked tobacco are the two key risk factors leading to oral cancer [ 76 , 77 ]. The researchers performed the single nucleotide polymorphism (SNP) analysis of rs1957358 in SAMD4A of 500 patients with oral cancer in India, and found that wild-type thymine (T) mutation to cytosine (C) significantly reduced the risk of oral cancer, such as rs1957358 TT mutation to rs1957358 TC, whereas rs1957358 TT reflected the increased risk [ 78 ]. This finding identifies SNPs with susceptibility to oral cancer in high risk populations and makes it possible to screen patients susceptible to oral cancer by SNP analysis.…”

Section: Samd4 and Related Diseasesmentioning

confidence: 99%

RNA binding protein SAMD4: current knowledge and future perspectives

Wang

Zhang

2023

Cell Biosci

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SAMD4 protein family is a class of novel RNA-binding proteins that can mediate post-transcriptional regulation and translation repression in eukaryotes, which are highly conserved from yeast to humans during evolution. In mammalian cells, SAMD4 protein family consists of two members including SAMD4A/Smaug1 and SAMD4B/Smaug2, both of which contain common SAM domain that can specifically bind to different target mRNAs through stem-loop structures, also known as Smaug recognition elements (SREs), and regulate the mRNA stability, degradation and translation. In addition, SAMD4 can form the cytoplasmic mRNA silencing foci and regulate the translation of SRE-containing mRNAs in neurons. SAMD4 also can form the cytosolic membrane-less organelles (MLOs), termed as Smaug1 bodies, and regulate mitochondrial function. Importantly, many studies have identified that SAMD4 family members are involved in various pathological processes including myopathy, bone development, neural development, and cancer occurrence and progression. In this review, we mainly summarize the structural characteristics, biological functions and molecular regulatory mechanisms of SAMD4 protein family members, which will provide a basis for further research and clinical application of SAMD4 protein family.

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“…Studies from our group defined mutations and polymorphisms of biologically functional genes including oncogenes, tumor suppressor genes, apoptotic genes, receptor genes and signal transduction genes in oral cancer [10][11][12][13][14][15]. With advances in technology, high throughput microarray based whole genome expression analysis and whole genome association studies (GWAS), confirmed by nucleotide sequencing and allele specific oligonucleotide assays for examination of the genome, we identified several SNPs associated with increased or decreased risk of developing oral cancer [16][17][18][19][20][21][22]. Several global studies have highlighted the role of specific SNPs in oral cancer predisposition and oral cancer [17,[23][24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Clinical Implications of Single Nucleotide Polymorphisms in Oral Cancer

Saranath¹

2022

MRD

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Background: Oral cancer is a high incidence cancer with well-established risk factors including tobacco, alcohol, areca nut, and HR-HPV 16/18. Additional risk factors such as Single Nucleotide Polymorphisms (SNPs) associated with genetic susceptibility, disease progression and prognosis. A comprehensive review of clinically relevant SNPs is synopsized in the current article. Methods:The PubMed repository was primarily used to retrieve articles using a combined keyword search. We selected 81 eligible studies examining association of SNPs with oral cancer, published in peer reviewed journals, between January 2000 and March 2022, with a focus on SNPs and prediction of oral cancer survival indicating response to therapy.Results: Twelve SNPs including ERCC5 rs17655, ERCC1 rs735482, TP53 rs1042522, MDM2 rs2279744, MTHFR rs1801133, MTHFR rs1801131, MSH2 rs3732183, MLH1 rs1800734, FADS1 rs174549, XPD rs13181, XPD rs1799793, and TGFBR1 rs33438 emerged as potential SNP markers for prediction of oral cancer survival and response to therapy. Conclusion:The risk-loci may be indicated potential biomarkers for early oral cancer detection, better patient prognosis and also serve as molecular targets for novel therapies.

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Multiple single nucleotide polymorphism analysis and association of specific genotypes in FHIT, SAMD4A, and ANKRD17 in Indian patients with oral cancer

Abstract: Our study identified SNPs with susceptibility to oral cancer in high-risk populations.

Cited by 6 publications

References 27 publications

Single nucleotide polymorphisms in transcription factor genes associated with susceptibility to oral cancer

Single nucleotide polymorphisms in transcription factor genes associated with susceptibility to oral cancer

RNA binding protein SAMD4: current knowledge and future perspectives

Clinical Implications of Single Nucleotide Polymorphisms in Oral Cancer

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