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Background: The Ring Finger 43 (RNF43) is a tumor suppressor gene that negatively regulates the Wnt/β-catenin signaling. The p.G659fs is a recurrent RNF43 C-terminal truncating variant frequent in colorectal cancer (CRC) patients. We aimed to identify this hotspot variant in CRC patients and assessed the relationship between the mutation, clinical characteristics, and tumor β-catenin localization. Materials and Methods: Formalin-fixed, paraffin-embedded tissue samples of upfront, surgically resected, sporadic colorectal adenocarcinoma cases were selected. The p.G659fs mutation was determined by capillary sequencing with sequence-specific primers. Tissue microarray and immunohistochemistry were employed to analyze nuclear β-catenin expression and the expression of mismatch repair (MMR) proteins, respectively. In addition, clinical details were retrieved from the hospital medical records and data were analyzed. Results: The RNF43 p.G659fs mutation was observed in 8% of CRC patients. In total, 25% of tumors showed a loss of immunostaining for one or more MMR proteins and 14.6% of tumors showed positive nuclear β-catenin staining. The p.G659fs variant was significantly enriched in MMR-deficient tumors (P = 0.04). Importantly, no correlation was observed between the variant and nuclear β-catenin localization (P = 0.48), indicating a Wnt-independent role of this variant in CRC tumors. Conclusions: To the best of our knowledge, this is the first study from North India to show the involvement of RNF43 p.G659fs variant in CRC patients. The mutation correlated with MMR protein deficiency and seems to be conferring tumorigenicity independent of the Wnt pathway. [ABSTRACT FROM AUTHOR]

Background: Oral cancer is alarming disease in the developing countries like India. DNA repair capacity may affect by genetic polymorphisms in DNA repair genes and thus may cause to cancer. XRCC3 involves in homologous recombination repair pathway and repair DNA damage and crosslinks while, NBS1 participate in repair of double strand DNA break and starts the cell-cycle checkpoint signaling. Aims and Objectives: This study was to conducted to find the association of XRCC3, NBS1 polymorphisms with oral disease. Materials and Methods: This study included 230 patients of precancerous oral lesions (Leukoplakia 70, Oral Sub mucous fibrosis 90, Lichen Planus 70), 72 oral cancer and 300 healthy control samples and genotyping was done by PCR-RFLP methods. Chi-square test was used for calculation of genotype and allele frequencies. Odds ratio and P values were calculated with Epi-Info programme (http://wwwn.cdc.gov/epiinfo/). Results: TT genotype of XRCC3 was associated with high risk of precancerous lesions and oral cancerous lesions (P value=0.0001, OR=9.68, 95% CI=2.82-33.21; and P value=0.0001, OR=13.10, 95% CI=3.38-50.73 respectively). We did not observe any interactions of XRCC3 polymorphism with demographic parameters in influencing the risk of oral diseases. Variant allele genotypes (CG, GG) of NBS1 (C>G) polymorphism showed protective association with Oral submucous fibrosis (OSMF), lichen planus as well as oral cancer (OR=0.31, OR=0.01; OR=0.39, OR=0.03; OR=0.43, OR=0.31 respectively). Particularly, tobacco chewer with CG & GG genotypes were at decrease risk of oral diseases (P value=0.02, OR=0.32, 95% CI=0.12-0.80). Compared to CC/CC combined genotype CG/CC, CG/CT, GG/CC and CG/CT genotypes decreased the risk of oral disease (OR=0.05, 0.47, 0.26 & 0.14 respectively). Conclusion: This study concludes that SNP in XRCC3, NBS1 affects susceptibility to oral disease. [ABSTRACT FROM AUTHOR]

Background: About 12%–15% of sporadic colorectal cancers (CRCs) display a defect in the DNA mismatch repair (MMR) system resulting in microsatellite instability (MSI). Many authors have described certain clinicopathological predictors of MSI and confirmed with ancillary studies. The purpose of this study was to determine the clinicopathological features and their association with MMR deficiency (dMMR) among CRC patients. Materials and Methods: A cross-sectional study was designed among patients presented with CRC. A predesigned proforma was used to document the particulars of the patient along with histological parameters to be assessed. Cases were analyzed for dMMR using MLH1 and MSH2 immunostains and categorized into dMMR and MMR-proficient. The association of clinicopathological features with MMR status was statistically analyzed. Results: Sixty-four CRC cases were analyzed in the study. Thirteen out of 64 cases showed dMMR. Most of the dMMR tumors were located in the right-sided colon (P < 0.001). Three patients with a family history of CRC exclusively had dMMR (P = 0.01). Mucinous (P = 0.04), signet ring cell differentiation (P = 0.04), and lack of dirty necrosis (P < 0.001) showed a significant difference between deficient and proficient MMR categories. Gender, mean tumor-infiltrating lymphocytes per hpf, Crohn's-like reaction, and tumor stage did not show any significant difference between the two categories. Conclusions: Clinicopathological features such as family history, tumor location, tumor size, histologic type, tumor differentiation, mucinous, signet ring cell component, and dirty necrosis are associated with MMR status in CRC. [ABSTRACT FROM AUTHOR]

Objectives: The prevalence of microsatellite instability (MSI) subtype among all colon cancers in India is about 30 %, approximately two times more than that of western population suggesting different molecular pathogeneses., Methods: A NanoString analysis-based Pan cancer differential expression (DE) profile was determined in a primary cohort of early-stage CRC (tumor=10, normal=7), and correlated against MSI status. Using RT-PCR, tumor-specific DE genes were validated in another cohort of MSI-high CRC (n=15)., Results: Among the most differentially expressed genes, AXIN2 , ETV4, and RNF43 were tumor cell-specific signals, while a set of genes including COL11A1 , COMP , INHBA , SPP1 , MMP3 , TLR2 , and others were immune cell-specific signals, that had a differential expression between MSI and MSS groups. When overlapped with The Cancer Genome Atlas (TCGA) studies using the Tumor immune estimation resource tool (TIMER), and protein-protein interaction analysis by STRING.db, these genes were segregated to representative tumor cells and immune cells. On validation, the tumor-specific gene signals were inversely associated with TLR4 expression., Conclusions: The differential expression distribution of AXIN2 , ETV4 , and RNF43 among tumor and immune cells, suggests more than one pathological subset in the MSI-H subgroup of early-stage CRC in the Indian population., (© 2024 Walter de Gruyter GmbH, Berlin/Boston.)

Oral squamous cell carcinoma (OSCC) is a common cancer of the oral cavity in India. Cigarette smoking and chewing tobacco are known risk factors associated with OSCC. However, genomic alterations in OSCC with varied tobacco consumption history are not well-characterized. In this study, we carried out whole-exome sequencing to characterize the mutational landscape of OSCC tumors from subjects with different tobacco consumption habits. We identified several frequently mutated genes, including TP53 , NOTCH1 , CASP8 , RYR2 , LRP2 , CDKN2A , and ATM. TP53 and HRAS exhibited mutually exclusive mutation patterns. We identified recurrent amplifications in the 1q31, 7q35, 14q11, 22q11, and 22q13 regions and observed amplification of EGFR in 25% of samples with tobacco consumption history. We observed genomic alterations in several genes associated with PTK6 signaling. We observed alterations in clinically actionable targets including ERBB4 , HRAS , EGFR , NOTCH1 , NOTCH4 , and NOTCH3. We observed enrichment of signature 29 in 40% of OSCC samples from tobacco chewers. Signature 15 associated with defective DNA mismatch repair was enriched in 80% of OSCC samples. NOTCH1 was mutated in 36% of samples and harbored truncating as well as missense variants. We observed copy number alterations in 67% of OSCC samples. Several genes associated with non-receptor tyrosine kinase signaling were affected in OSCC. These molecules can serve as potential candidates for therapeutic targeting in OSCC. [ABSTRACT FROM AUTHOR]

In India, over the past 50 years, aquaculture practices of species such as those used for Clarias batrachus were developed without adequate regulatory oversight. In these situations, it is important to consider the influence that genetic factors can have on such vulnerable aquaculture species. Population genetic structure can be evaluated through the use of neutral molecular markers, and this can aid in predicting the risk of the demise of populations and for framing management strategies to conserve remaining populations. The study presented here reports on the genetic status of C. batrachus populations through the analysis of data collected using 22 microsatellite markers from seven natural and one hatchery population. The mean values for observed heterozygosity across loci within populations ranged from 0.242 to 0.485. Measures of genetic differentiation were low overall, with mean values for FST of 0.270, FIS of 0.113 and FIT of 0.353. An AMOVA analysis revealed that percentages of variation among and within populations were 27.16 and 6.86, respectively, and Bayesian clustering analyses showed a population subdivision consisting of five clusters with admixture of haplotypes from other populations leading to genetic bottleneck. We also examined how hatchery management factors leading to excessive exchanges of fish between river systems through could impact the structure of the C. batrachus populations. Overall, this study shows how the systematic use of molecular markers can facilitate the development of management policies for these populations and for the development of a comprehensive set of rules for hatcheries and aquaculture practices, including avoidance of excessive homozygosity by avoiding repeated use of feral broodstock and their interrogation. [ABSTRACT FROM AUTHOR]

Background: Single Nucleotide Polymorphisms (SNPs) at DNA repair genes are considered as potential biomarkers of radio-sensitivity. The coastal belt of Kerala in south west India has a patchy distribution of monazite in its beach sand that contains Th-232 and its decay products. Thus, radiation levels in this area vary from <1.0mGy to 45.0mGy/year. The areas with external gamma radiation dose >1.5mGy/year are considered as High-Level Natural Radiation Areas (HLNRA) and ≤ 1.5mGy/year are Normal Level Natural Radiation Area (NLNRA). Objective: In the present study, an attempt was made to evaluate the influence of chronic low dose radiation exposure on DNA repair gene polymorphisms in NLNRA and HLNRA population of Kerala coast. Materials and methods: Genomic DNA was isolated from venous blood samples of 246 random, healthy individuals (NLNRA, N = 104; HLNRA, N = 142) and genotyping of five SNPs such as X-ray repair cross complementing 1(XRCC1 Arg399Gln), X-ray repair cross complementing 3 (XRCC3 Thr241Met], Protein kinase, DNA-activated, catalytic subunit (PRKDC) (X-ray repair cross-complementing group 7, XRCC7 G/T), nei like DNA glycosylase 1 (NEIL1 G/T) and DNA ligase 1 (LIG1 A/C) was carried out using PCR based restriction fragment length polymorphism (PCR-RFLP) followed by silver staining. Results: Our results showed no significant difference in genotype frequencies in HLNRA vs NLNRA at three of the five SNPs studied i.e. XRCC1 Arg399Gln (χ2(2) = 5.85, p =.054), XRCC3 Thr241Met (χ2(1) = 0.71, p =.339), PRKDC (XRCC7 G/T) (χ2(2) = 3.72, p =.156), whereas significant difference was observed at NEIL1 G/T (χ2(2) =8.71, p =.013) and LIG1 A/C (χ2(2) = 7.66, p =.022). The odds of heterozygote to homozygote genotypes in HLNRA relative to NLNRA at XRCC1 Arg399Gln (OR = 1.96, 95% CI: 1.13–3.40), XRCC3 Thr241Met (OR = 0.73, 95% CI: 0.41–1.31), PRKDC (XRCC7 G/T), (OR = 0.81; 95% CI: 0.48–1.38), NEIL1 G/T (OR = 0.54; 95% CI: 0.31–0.96) and LIG1 A/C (OR = 1.62; 95% CI: 0.97–2.69) was also not significantly different in HLNRA vs NLNRA, except at XRCC1 and NEIL1. Conclusion: The genotype frequencies at three of these SNPs i.e. XRCC1 Arg399Gln, XRCC3 Thr241Met and PRKDC (XRCC7 G/T) were similar, whereas NEIL1 G/T and LIG1 A/C showed significant difference between HLNRA and NLNRA population. However, further research using more number of SNPs in a larger cohort is required in this study area. [ABSTRACT FROM AUTHOR]

Background: Microsatellite instability (MSI) accounts for 15-20% of colorectal cancer (CRC) and is considered to have favorable stage-adjusted prognosis compared to Microsatellite stable (MSS) CRCs. Determination of MSI in stage II CRC is important for management decisions regarding adjuvant chemotherapy administration. The aim of this study was to determine the prognostic and predictive significance of MSI in stage 2 CRC in the Indian scenario.Materials and Methods: A total of 195 patients who underwent curative surgery for stage II CRC from 2010 to 2017 were included. MSI testing by immunohistochemistry (DNA MisMatch Repair proteins) was performed in all. Various clinicopathological factors and disease-free survival and overall survival were assessed between MSI and MSS groups. The effect of treatment in terms of survival benefits with adjuvant therapy in the MSI group was also assessed.Results: 27.1% of the CRCs' showed MSI. Younger age (<50 years), family history of cancer, synchronous/metachronous malignancies, proximal (right sided) location, poor morphological tumour differentiation, mucin production, and presence of peritumoral (Crohn's-like) lymphocytic response showed statistically significant association with MSI. Majority (56%) of our patients showed combined loss of MLH1 and PMS2. Overall, survival among the MSI patients was significantly higher (76.6 ± 4.149 months) than the MSS patients (65.05 ± 3.555)P= 0.04. MSI patients did not show any differences in survival with or without treatment.Conclusion: This study highlights the distinct clinicopathological features of MSI-related CRC and the relevance of MSI testing of stage II CRC for management decisions and prognostication. [ABSTRACT FROM AUTHOR]

Background: Three molecular pathways are described as the genetic basis of colorectal tumorigenesis. Among these, microsatellite instability (MSI) has shown greatest promise in serving as a biomarker to determine disease aggression by tumour biology, recurrence, and response to chemotherapy., Methodology: This prospective observational pilot study included patients of colorectal cancers, in a population subset coming to a tertiary care hospital in northern India, who were operated with curative or palliative intent over a period of one year and followed up for a maximum of 55 months. The post-operative pathological assessment was done for MSI status using PCR technique, and an attempt was made to evaluate its correlation with conventional clinical and histological parameters, early recurrences, disease-free survival and overall survival in comparison to MSS type tumours in sporadic cases of colorectal malignancies., Results: Out of 38 patients of colorectal cancer, 26 were included in the study. Male to female ratio was 7:6 (n=14:12). Mean age of presentation was 48±14.2 years. Incidence of MSI was n=4 (15.4%). On subgroup analysis, age of presentation (p=0.044) and evidence of perineural invasion (p=0.017) was found to have significant statistical association with MSI tumour biology. Recurrence was seen in seven of the seventeen patients who previously had no synchronous or metastatic disease (41.2%). The mean disease-free survival for MSS was 21.32 months and was 25.25 months for MSI group which was statistically insignificant (p = 0.277). Out of four MSI tumour biology patients one was alive and without recurrence at 47 months. While the other two were alive and without recurrence till 27 months of follow-up.   Conclusion: Age and perineural invasion showed statistically significant association with MSI tumour biology. Due to the small sample size statistical significance was not established with site, recurrence rate, DFS and OS.

This study investigated genomic differences in Australian and Indian Pseudomonas aeruginosa isolates from keratitis (infection of the cornea). Overall, the Indian isolates were resistant to more antibiotics, with some of those isolates being multi-drug resistant. Acquired genes were related to resistance to fluoroquinolones, aminoglycosides, beta-lactams, macrolides, sulphonamides, and tetracycline and were more frequent in Indian (96%) than in Australian (35%) isolates (p = 0.02). Indian isolates had large numbers of gene variations (median 50,006, IQR = 26,967–50,600) compared to Australian isolates (median 26,317, IQR = 25,681–33,780). There were a larger number of mutations in the mutL and uvrD genes associated with the mismatch repair (MMR) system in Indian isolates, which may result in strains losing their efficacy for DNA repair. The number of gene variations were greater in isolates carrying MMR system genes or exoU. In the phylogenetic division, the number of core genes were similar in both groups, but Indian isolates had larger numbers of pan genes (median 6518, IQR = 6040–6935). Clones related to three different sequence types—ST308, ST316, and ST491—were found among Indian isolates. Only one clone, ST233, containing two strains was present in Australian isolates. The most striking differences between Australian and Indian isolates were carriage of exoU (that encodes a cytolytic phospholipase) in Indian isolates and exoS (that encodes for GTPase activator activity) in Australian isolates, large number of acquired resistance genes, greater changes to MMR genes, and a larger pan genome as well as increased overall genetic variation in the Indian isolates. [ABSTRACT FROM AUTHOR]

Introduction: Colorectal cancer is the third most common cancer in men and second most common in women globally. In the present study, we aimed to analyse the proportion of patients with loss of immunostaining for mismatch repair (MMR) proteins in all newly diagnosed stage II cases of colorectal cancer for the purpose of prognostication, for determination of further chemotherapeutic strategy and for familial screening., Method: From January 2014 to December 2015, 62 consecutive newly diagnosed cases of stage II colorectal cancer were included in the study. Details of each patient related to their demographic profile and tumour profile were recorded. All the cases were grossed and staged according to College of American Pathologist (CAP) guidelines. The expression of MMR proteins (which was earlier validated on normal as well as tumour tissue) in FFPE tumour tissue using IHC for mut L homologue 1 (MLH1), mut S homologue 2 (MSH2), mut S homologue 6 (MSH6) and post-meiotic segregation increased 2 (PMS2) was studied. Information regarding stage, treatment, clinical outcome and overall survival was retrieved when available., Results: Out of a total of 371 cases, 62 (16.7%) cases were of stage II CRC, out of which 43 (12%) were treatment naive. Among the selected 62 cases, 26 (41.9%) demonstrated loss of MMR proteins and 36 (58.0%) cases had intact nuclear expression. Out of the cases with MMR loss, 38.4% showed loss of MLH1 and PMS2, 30.7% showed loss of MSH2 and MSH6, 26.9% showed isolated loss of PMS2 and 3.8% showed isolated loss of MSH6. Right-sided location (57.6%) was more common than left-sided (19.2%) and transverse colon (23.0%). Majority of the cases were moderately differentiated (65.3%) in morphology. There was no intratumoural infiltrate in most of the cases (53.8%), and only 3.8% cases showed marked intratumoural infiltrate. Also, peritumoural lymphocytic infiltrate was mild to moderate in most of the cases (26.9%) and marked Crohn's-like infiltrate was seen in only 7.6% cases., Conclusion: Our study shows that the routine evaluation of MMR proteins is achievable and essential for the purpose of prognostication, planning of treatment strategies and ascertaining a hereditary basis of CRC. The incidence of MMR protein loss was quite high in our study compared to other studies probably due to a difference in ethnicity. Though a right-sided predominance was supported, none of the typical morphological features of microsatellite instability (MSI) tumours were substantiated by our study, highlighting the lack of importance of histology for predicting MSI, and emphasising the point that MSI testing should be done as a routine procedure in all stage II CRC. A short follow-up was done for all our cases and comparison between the survival of the chemotherapy treated MSI cases versus those which were treatment naïve was performed and revealed that chemotherapy (CT) did not provide additional benefit to survival; MSI tumours in general are a better prognostic category and do not require additional chemotherapy.

Background: Colorectal cancer (CRC) is the fourth most common cancer in men and third most common cancer in women worldwide, with higher incidence reported in western countries. Over the last decade a remarkable 2-4 fold increase in CRC incidence has been observed in Asian countries like India. Lower prevalence of sporadic CRC cases in India have been linked to lifestyle, with an emphasis on a vegetarian diet. However, the incidence of hereditary CRCs in India have not been well documented. In the west hereditary CRCs i.e. Familial adenomatous polyposis (FAP) and Lynch syndrome or the Hereditary Nonpolyposis Colon Cancer (HNPCC) are common and account for 1% and 2-5% of the CRCs reported, respectively. We report a similar trend at a rural cancer center in western India (KCHRC, Goraj, Gujarat), where 70-75 CRC patients are seen annually. Methods: We have identified three families, one diagnosed with FAP and two with HNPCC. In order to identify the underlying germline mutation in each family, we sequenced the genomes of 3 families, one with FAP and two with reported HNPCC. Results: In The FAP family, we identified a novel heterozygous mutation in the APC (pSerPhefster6) gene in 3 affected members, all aged above 45 years. The mutation was also found in younger unaffected members of this family who have been appropriately counselled. Both HNPCC families had unique mutations in the MLH1 gene, a frequently mutated gene in HNPCC with a role in DNA mismatch repair. Conclusions: Thus far we have identified mutations in genes frequently reported in the west in both FAP and HNPCC. In FAP the region of mutation is APC but the mutation is unique. Further larger number of patients require to evaluate and compare to western countries. [ABSTRACT FROM AUTHOR]

Background: To determine the mismatch repair (MMR) protein loss in colorectal cancer (CRC) in north Indian patients and its clinicopathological correlation., Method: A prospective study on patients with colorectal cancer from a tertiary level hospital conducted between May 2014 and June 2015. MMR protein loss was determined using immunohistochemistry for MLH1, MSH2, PMS2 and MSH6., Results: 52 patients (38 male and 14 females) of CRC, with median age of 52.5 years who underwent resection form the study group. 18 (35%) patients were < 50 years of age. Family history of malignancy was present in 3 (6 %) patients. A total of 15 (29%) patients had loss of MMR protein of which 7 (46%) were < 50 years. Most common MMR loss was combined loss of MSH2 + MSH6 [6 (11.5%)] followed by isolated loss of PMS2 [5 (9.6%)]. MMR protein loss was more frequent in patients with right side colon cancer [12 (42%)] compared to left [3 (13%)] (p = 0.033). MMR protein loss was seen in 11 (34%) out of 32 patients fulfilling the revised Bethesda criteria compared to 4 (20%) out of 20 patients who did not fulfil the criteria (p = 0.352)., Conclusion: This study demonstrates high frequency of MMR protein loss in colorectal cancer in north Indian patients which was more common in right colon cancer. Many patients having MMR protein loss do not satisfy the revised Bethesda criteria and would have been missed if selective testing was done. Further research and larger studies are required to validate these findings and develop India specific clinical criteria., (Copyright© Authors.)