The influence of IL1RN VNTR polymorphism on HPV infection among some tribal communities.

Persistent infection of human Papillomavirus is the main etiological factor for cervical cancer. Austro-Asiatic tribes are early settlers in India and they have unique genetic variations compared to other people. The immunological response is crucial for the prevention of viral associated diseases. Interleukin-1 receptor antagonist (IL-1RN) is considered being an important regulator of host immune surveillance. A total of 45 Santali tribal women and 10 Kora tribal women were enrolled in the present study and demographic variables were recorded during collection. Genomic DNA was extracted from cervical/vaginal swab samples. IL1RN variable number of tandem repeats (VNTR) polymorphisms and HPV types were determined by PCR-based assay. Association between IL1RN VNTR polymorphisms with the HPV infections among the tribal communities was determined by logistic regression analysis. HPV18 prevalence was significantly higher among tribal women. We observed that the polymorphism A2*A2 (p = 0.022; odds ratio [OR] (95% confidence interval [CI]) = 0.16 (0.03-0.86)] were more resistant to oncogenic HPV infection. Use of oral contraceptives was associated with higher relative risk (p = 0.008; OR [95% CI] = 5.39 [1.47-19.8]) for oncogenic HPV18 positivity among the tribal women. The A2 allele homozygosity of IL1RN VNTR was identified to be associated with the protection from oncogenic HPV infection among various tribal communities of West Bengal and therefore may be a useful marker of host immune response among them.

Identification of novel genetic and epigenetic regulators of different tissue types of cervical cancer.

OBJECTIVES: The study aimed to find differential gene mutations, DNA methylation, and expression profiles among different categories of cervical cancer samples. METHODS: The study was based on freely available gene mutations, promoter methylation, and gene expression status of The Cancer Genome Atlas (TCGA) cervical cancer samples and adjacent normal tissues in the Genomic Data Commons (GDC) portal. The association of CpG island methylation with gene expression was determined through negative correlation analysis. RESULTS: We identified that the ErbB signaling pathway and proteoglycans pathway was significantly associated with adenocarcinoma cervical cancers patients. In these pathways, missense mutation especially S310F in the ERBB2 gene as well as G12D and A146T in the KRAS gene were significantly associated with adenocarcinoma cases. Furthermore, a comparison of SCC cases with adjacent control tissues revealed differential hypermethylation of two CpG positions of the KAAG1 gene and differential downregulation of NPY1R and NPY5R genes in cervical squamous cell carcinoma compared to cervical adenocarcinoma cases and adjacent normal tissues. Specifically, the hypermethylation of the promoter region of the KAAG1 gene might be responsible for the carcinogenesis of cervical squamous cells exclusively and methylation marks can be reversible by the widely used drug, azacytidine. In contrast, adenocarcinoma cervical cancer cases may be treated with floxuridine which is successfully utilized for other tissue-specific adenocarcinoma cases. CONCLUSIONS: These results provide valuable insight into the differential molecular markers among the categories of cervical cancer, which helps our ability to classify these cancers and for targeted therapy.

Insight of nitric oxide signaling: A potential biomarker with multifaceted complex mechanism in colorectal carcinogenesis.

Colorectal carcinogenesis (CRC) is the most important health concerns throughout the World as the tumour cells rapidly spread and abruptly grow in colon and rectum to further organs. Several etiological factors are associated with colorectal carcinogenesis. During invasion and proliferation of tumour cells, various mechanistic molecular pathways are involved in the cells. Nitric Oxide pathway (NO) is one of the important cellular mechanisms associated with tumour cells initiation, invasion and progression. Epidemiological evidences suggest that NO has potential role in development of cancer. The multidisciplinary action of NO on the initiation of cancer depends on several factors including cell type, metastasis stage, and organs involved. This review emphasizes the biological significance of NO in each step of cancer metastasis, its controversial effects for carcinogenesis including initiation, invasion and progression.

Molecular mechanistic pathway of colorectal carcinogenesis associated with intestinal microbiota.

The colon rectal portion of gastrointestinal tract (GI) is full of microorganisms with different complex community that plays important role in maintaining homeostasis. But now-a-days different literature indicated that microbiota cause development of colorectal cancer (CRC) with a disease and ultimately aggravates to death. The mechanism inside the colo-rectal portion of GI tract is not fully well-known and bacterial contribution inside it is also fully unclear. Therefore, there is certain evidence trying a target about the unclear mechanism between intestinal microbiota and CRC. Different reports revealed that colo-rectal microorganisms is playing a great role in inducing the onset and progression of CRC with different dynamic mechanisms viz. acceleration of chronic inflammatory state, the biosynthesis of genotoxins that interfere with cell cycle regulation, the production of toxic metabolites, or heterocyclic amine activation of pro-diet carcinogenic compounds. There is growing evidence that individuals with colonic adenomas and carcinomas harbor a distinct microbiota. Alterations to the gut microbiota may allow the outgrowth of bacterial populations that induce genomic mutations or exacerbate tumor-promoting inflammation. While cancer is largely considered to be a disease of genetic and environmental factors, increasing evidence has demonstrated a role for the microbiota in shaping inflammatory environments and promoting tumor growth and spread. Despite all these advances, different studies depicted the relationship between microbiota and CRC in humans and animal models and aid in developing alternate therapeutic approach based on gut microbiota manipulations. Alteration of the microbiota may be a useful to preventing and altering the trajectory of colorectal cancer. Therefore, the aim of the study is to identify the possible mechanistic mechanism regarding host-microbiota interaction in colorectal carcinogenesis.

Molecular signature of nitric oxide on major cancer hallmarks of colorectal carcinoma.

Colorectal cancer (CRC) is the one of the most important diseases throughout the world. Several aetiological risk factors, viz. sedentary life style, smoking, alcohol intake, less physical activity, red meat, and microbiota, are associated with the development of CRC. Molecular pathophysiology of CRC implies inflammation, metastasis, apotosis and angiogenesis. Inflammation involves interaction between various immune cells, inflammatory cells, chemokines, cytokines, and pro-inflammatory mediators, such as cyclooxygenase (COX) and lipoxygenase (LOX) pathways, which may lead to signalling towards, tumour cell proliferation, growth, and invasion whereas nitric oxide (NO) has been associated with metastasis, apoptosis, and angiogenesis. Therefore, this review emphasises on the potential molecular mechanisms associated with NO with alteration of cancer biomarkers during development of colorectal carcinogenesis.

Impact of viral and host DNA methylations on HPV16-related cervical cancer pathogenesis.

Epigenetic alterations within human papillomavirus (HPV) and host cellular genomes are known to occur during cervical carcinogenesis. Our objective was to analyse the influence of (1) methylation within two immunostimulatory CpG motifs within HPV16 E6 and E7 genes around the viral late promoter and their correlation, if any, with expression deregulation of host receptor (TLR9) and DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and (2) global DNA methylation levels within CpGs of the repetitive Alu sequences, on cervical cancer (CaCx) pathogenesis. Significantly higher proportions of CaCx samples portrayed methylation in immunostimulatory CpG motifs, compared to HPV16-positive non-malignant samples, with cases harbouring episomal HPV16 showing decreased methylation compared to those with viral integration. A significant linear trend of TLR9 upregulation was recorded in the order of HPV-negative controls < HPV16-positive non-malignant samples < HPV16-positive CaCx cases. TLR9 upregulation in cases with episomal HPV16 was again higher among those with non-methylated immunostimulatory CpG motifs. Comparison of cases with HPV-negative controls revealed that DNMT3A was significantly downregulated only among integrated cases, DNMT3B was significantly overexpressed among both categories of cases, although at variable levels, while DNMT1 failed to show any deregulated expression among the cases. Global host DNA hypomethylation, also showed a significant linear increasing trend through the progressive CaCx development stages mentioned above and was most prominently higher among cases with episomal HPV16 as opposed to viral integration. Thus, HPV16 and host methylations appear to influence CaCx pathogenesis, with differential molecular signatures among CaCx cases with episomal and integrated HPV16.

Molecular Heterogeneity of Cervical Cancer Among Different Ethnic/Racial Populations.

The study aimed to find differential gene mutation profile and gene expression status among different ethnic/racial human populations relevant for cervical cancer pathogenesis. The study was based on freely available datasets of The Cancer Genome Atlas (TCGA) of cervical cancer samples in Genomic Data Commons (GDC) data portal. We identified that choline metabolism in cancer and Ras signaling pathways were significantly associated with the Hispanic and Latino group of cervical cancer patients. In these pathways, mutations in the PIK3CA gene, especially E545K, were significantly associated with the Hispanic and LATINO group. We found that AFF3 gene mutation was associated with downregulation of its expression only among the White racial category of cervical cancer cases. Additionally, hypomethylation of the CpG position in the S shore region of the PM20D1 gene was associated with overexpression among the Asian category of cervical cancer cases. Heterogeneity of the molecular profile of AFF3 and PM20D1 gene among racial groups reflects the potential of differential targeted therapy of cervical cancer.

Predominance of genomically defined A lineage of HPV16 over D lineage in Indian patients from eastern India with squamous cell carcinoma of the cervix in association with distinct oncogenic phenotypes.

Human papillomavirus type-16 (HPV16) is classified into lineages, A, B, C and D and 10 sub-lineages portraying variable infectivity, persistence, and cytological outcomes, however, with geographical variations. Our objective was to delineate the distinctive features of lineages among cervical squamous cell carcinoma (SCC) in the eastern region of India. A total of 145 SCC cases and 24 non-malignant specimens, harboring episomal HPV16, were included. The presence of higher proportion of lineage A over D was observed among SCC cases (86.89% A1, 8.97% D1 and 4.14% D2), while only A1 sub-lineage viruses were found among control specimens. Among the A1 viruses, an association of variants in the E5 (Y44L, I65V), E6 (L83V) genes and LCR: C7577T with SCC, with combined Odd's ratio (95% CI) of 20.5(4.61-91.25) was observed. Network analyses revealed the presence of 10 clades of lineage A viruses comprising of 64 HPV16 genomes harboring the risk alleles. High episomal HPV16 DNA copy numbers (adjusted p-value= 0.0271) and E7 mRNA expression (p-value=0.000017) predominated in SCC with lineage A, over D. Our study highlights the distinctive modalities of oncogenicity among different HPV16 lineages.

Implication of therapeutic outcomes associated with molecular characterization of paediatric aplastic anaemia.

OBJECTIVES: Severe aplastic anemia is characterized by a hypocellular bone marrow and peripheral cytopenia. Mesenchymal stem cells (MSCs) play a crucial role in haematopoietic stem cells (HSCs) development and the development of microenvironment suitable for hematopoiesis. Molecular characterization of telomere maintenance pathway and gene expression profiling of MSCs can be important for the therapeutic interventions among paediatric aplastic anaemia patients. METHODS: The study involved paediatric aplastic anaemia patients (n = 10) and age matched paediatric healthy donors (n = 8). Peripheral blood samples were collected from the individuals. Average leucocyte telomere length and gene expression of the telomere maintenance genes were determined by quantitative real time PCR. Microarray based gene expression profiles (GSE33812) of MSCs for five paediatric aplastic anaemia patients were analyzed compared to five healthy controls and the data was downloaded from the GEO database. RESULTS: The telomere length was significantly shorter among paediatric AA patients compared to age matched healthy donors. Interestingly, one subgroup (n = 2) of paediatric AA patients has moderate telomere length comparable to age matched healthy donors. Based on the gene expression analysis of telomere maintenance pathway, TERF2 was significantly downregulated among paediatric patients with shorter telomere length but not among paediatric patients with moderate telomere length. Gene expression profiling of MSCs revealed three differentially expressed genes (GAS2L3, MK167 and TMSB15A) among the patients and was associated with therapeutic outcome. CONCLUSION: Telomere length estimation and gene expression patterns of the MSCs and telomere length maintenance pathway may serve as a potential biomarker and could be associated with therapeutic choice of paediatric aplastic anaemia patients.

Recent advances of Blood telomere length (BTL) shortening: A potential biomarker for development of cancer.

Telomeres, the specific DNA-protein structures remains at both ends of each chromosome and are crucial in the maintenance of chromosome integrity and genomic stability with protection of the chromosome from damage and degradation.. Increasing evidences suggest the correlation between telomere length and the development of cancers, but the findings remain obscure. Generally, the average length of telomere repeats at the ends of chromosomes that gives a clue in providing indirect information about their mitotic history. It plays immense role in preventing genome from nucleolytic degradation, unnecessary recombination, repair, and interchromosomal fusion. It has major role in storing the information in the genome. Telomere attrition during successive cell divisions induces chromosomal instability and contributes significantly to genomic rearrangements that can result in tumorigenesis. Convincing evidence documented that a meagre portion of telomeric DNA is expelled out during mitotic stage of cell division. But accelerated shortening telomere length at critical level triggers senescence and/or apoptosis. Various harmful agents with bad lifestyles are responsible in inducing shortening of telomere length with damage of DNA resulting to occurrence of disease with shortening of lifespan. Besides, telomerases, the specialized polymerase that synthesizes new telomere repeats and is strongly associated with cancer facilitating malignant transformation. Therefore, in the study, it is highlighted that the telomeres may play diverse roles in different cancers whereas shortening of telomere length may be risk factors for the development of tumors.

Integrated analysis of global gene and microRNA expression profiling associated with aplastic anaemia.

AIMS: Aplastic anaemia is a rare disorder characterized by peripheral pancytopenia and hypocellular bone marrow. Recent advancement of miRNA technologies, new promising therapy using small molecule inhibitors was suggested as efficient treatment option. Therefore, the study was undertaken to identify the significantly altered miRNA (miR-1202-upregulation) among aplastic anaemia patients compared to healthy controls by global miRNA expression profiling of bone marrow. MATERIALS AND METHODS: miRNA and gene expression profiles for all the categories of aplastic anaemia patients and healthy controls were generated using Affymetrix probes. KEY FINDINGS: The study was based on freely available miRNA and host gene expression in NCBI GEO dataset. Microarray based gene expression profiling (GSE3807) revealed that RAPGEF5 and MANEA genes were significantly downregulated among aplastic anaemia patients compared to healthy controls and the expression of these genes were again upregulated after application of therapy among those patients compared to pre-therapy condition. RAPGEF5 was involved in Rap1 and Ras signaling pathways those were significantly enriched among aplastic anaemia patients and could be relevant for that phenotype. Microarray based miRNA expression profiling (GSE82095) also identified that miR-1202 was significantly upregulated among aplastic anaemia patients compared to controls and can potentially target RAPGEF5 and MANEA genes based on target prediction of miRNAs. SIGNIFICANCE: Thus synthetic miRNA inhibitors of miR-1202 can be used as a possible therapeutic agent to target miR-1202 and this inhibition can lead to its corresponding target gene upregulation for reversal of disease phenotype.

Cervical cancer subtypes harbouring integrated and/or episomal HPV16 portray distinct molecular phenotypes based on transcriptome profiling of mRNAs and miRNAs.

Heterogeneity in cervical cancers (CaCx) in terms of HPV16 physical status prompted us to investigate the mRNA and miRNA signatures among the different categories of CaCx samples. We performed microarray-based mRNA expression profiling and quantitative real-time PCR-based expression analysis of some prioritised miRNAs implicated in cancer-related pathways among various categories of cervical samples. Such samples included HPV16-positive CaCx cases that harboured either purely integrated HPV16 genomes (integrated) and those that harboured episomal viral genomes, either pure or concomitant with integrated viral genomes (episomal), which were compared with normal cervical samples that were either HPV negative or positive for HPV16. The mRNA expression profile differed characteristically between integrated and episomal CaCx cases for enriched biological pathways. miRNA expression profiles also differed among CaCx cases compared with controls (upregulation-miR-21, miR-16, miR-205, miR-323; downregulation-miR-143, miR-196b, miR-203, miR-34a; progressive upregulation-miR-21 and progressive downregulation-miR-143, miR-34a, miR-196b and miR-203) in the order of HPV-negative controls, HPV16-positive non-malignant samples and HPV16-positive CaCx cases. miR-200a was upregulated in HPV16-positive cervical tissues irrespective of histopathological status. Expression of majority of the predicted target genes was negatively correlated with their corresponding miRNAs, irrespective of the CaCx subtypes. E7 mRNA expression correlated positively with miR-323 expression among episomal cases and miR-203, among integrated cases. miR-181c expression was downregulated only among the episomal CaCx cases and negatively correlated with protein coding transcript of the proliferative target gene, CKS1B of the significantly enriched "G2/M DNA Damage Checkpoint Regulation" pathway among CaCx cases. Thus, the two CaCx subtypes are distinct entities at the molecular level, which could be differentially targeted for therapy. In fact, availability of a small molecule inhibitor of CKS1B, suggests that drugging CKS1B could be a potential avenue of treating the large majority of CaCx cases harbouring episomal HPV16.

Prevalence and age-wise distribution of Human Papillomavirus type 16/18 infections among hospital screened women of a peri-urban area in West Bengal: Impact of socio-demographic factors.

BACKGROUND: We undertook the current study on cervical Human Papillomavirus (HPV) prevalence along with cytology in women visiting the Gynecology Out-patient Department of a hospital for common gynecological ailments, subsequent to our earlier population-based study on HPV prevalence from India. METHODS: We analyzed data on cervical-cytology (Pap smears) and PCR-based molecular detection of HPV infection along with socio-demographic variables (N = 696). RESULTS: We identified 36.84% HPV-positive women amongst whom, HPV16 and 18 together predominated (79.37%) over other HPV types (20.63%). Contrarily, only 6.4% women revealed abnormal cytological lesions, of which, 46.51% were HPV-positive and 95% of such women harbored HPV16/18, while 5% harbored other HPV types. Individuals with normal cytology portrayed 36.09% HPV infections, of which, 77.97% were HPV16/18-positive and 22.03% harbored other HPV types. Overall HPV prevalence decreased significantly (ptrend  = 0.047) with increase in age, but HPV16/18 infections were significantly over-represented compared to the other HPV types across all age-groups. Specifically, HPV16 prevalence increased (p trend < 0.01) with increase in severity of cervical lesions. HPV16 prevalence did not differ between the Hindus and Muslims but HPV18 was significantly higher among the cytologically normal Muslim women (24.14%, p = 0.02), compared to the Hindus (11.91%), specifically among those ≥ 30 years of age. There was a significant (p < 0.05) overrepresentation of HPV16 prevalence among women who were users of oral contraceptive-pills, irrespective of cytology. CONCLUSIONS: Our study highlights the need for HPV16/18-based screening of cervical cancers in India considering the immense socio-cultural and genetic diversity at the population level.

Molecular insight of arsenic-induced carcinogenesis and its prevention.

Population of India and Bangladesh and many other parts of the world are badly exposed to arsenic through drinking water. Due to non-availability of safe drinking water, they are dependent on arsenic-contaminated water. Generally, poverty level is high in those areas with lack of proper nutrition. Arsenic is considered to be an environmental contaminant and widely distributed in the environment due to its natural existence and anthropogenic applications. Contamination of arsenic in both human and animal could occur through air, soil, and other sources. Arsenic exposure mainly occurs in food materials through drinking water with high levels of arsenic in it. High levels of arsenic in groundwater have been found to be associated with various health-related problems including arsenicosis, skin lesions, cardiovascular diseases, reproductive problems, psychological, neurological, immunotoxic, and carcinogenesis. The mechanism of arsenic toxicity consists in its transformation in metaarsenite, which acylates protein sulfhydryl groups, affect on mitochondria by inhibiting succinic dehydrogenase activity and can uncouple oxidative phosphorylation with production of active oxygen species by tissues. A variety of dietary antioxidant supplements are useful to protect the carcinogenetic effects of arsenic. They play crucial role for counteracting oxidative damage and protect carcinogenesis by chelating with heavy metal moiety. Phytochemicals and chelating agents will be beneficial for combating heavy metal-induced carcinogenesis through its biopharmaceutical properties.

Potential biomarkers associated with oxidative stress for risk assessment of colorectal cancer.

Cells are continuously threatened by the damage caused by reactive oxygen/nitrogen species (ROS/RNS), which are produced during physiological oxygen metabolism. In our review, we will summarize the latest reports on the role of oxidative stress and oxidative stress-induced signaling pathways in the etiology of colorectal cancer. The differences in ROS generation may influence the levels of oxidized proteins, lipids, and DNA damage, thus contributing to the higher susceptibility of colon. Reactive species (RS) of various types are formed and are powerful oxidizing agents, capable of damaging DNA and other biomolecules. Increased formation of RS can promote the development of malignancy, and the "normal" rates of RS generation may account for the increased risk of cancer development in the aged. In this review, we focus on the role of oxidative stress in the etiology of colorec-tal cancer and discuss free radicals and free radical-stimulated pathways in colorectal carcinogenesis.

Complete Genome Sequences of Eight Human Papillomavirus Type 16 Asian American and European Variant Isolates from Cervical Biopsies and Lesions in Indian Women.

Human papillomavirus type 16 (HPV16), a member of the Papillomaviridae family, is the primary etiological agent of cervical cancer. Here, we report the complete genome sequences of four HPV16 Asian American variants and four European variants, isolated from cervical biopsies and scrapings in India.

Bridging Links between Long Noncoding RNA HOTAIR and HPV Oncoprotein E7 in Cervical Cancer Pathogenesis.

Human Papillomavirus (HPV) type 16 oncoprotein E7 plays a major role in cervical carcinogenesis by interacting with and functionally inactivating various host regulatory molecules. Long noncoding RNA (lncRNA) HOTAIR is one such regulator that recruits chromatin remodelling complex PRC2, creating gene silencing H3K27 me3 marks. Hence, we hypothesized that HOTAIR could be a potential target of E7, in HPV16 related cervical cancers (CaCx). We identified significant linear trend of progressive HOTAIR down-regulation through HPV negative controls, HPV16 positive non-malignants and CaCx samples. Majority of CaCx cases portrayed HOTAIR down-regulation in comparison to HPV negative controls, with corresponding up-regulation of HOTAIR target, HOXD10, and enrichment of cancer related pathways. However, a small subset had significantly higher HOTAIR expression, concomitant with high E7 expression and enrichment of metastatic pathways. Expression of HOTAIR and PRC2-complex members (EZH2 and SUZ12), showed significant positive correlation with E7 expression in CaCx cases and E7 transfected C33A cell line, suggestive of interplay between E7 and HOTAIR. Functional inactivation of HOTAIR by direct interaction with E7 could also be predicted by in silico analysis and confirmed by RNA-Immunoprecipitation. Our study depicts one of the causal mechanisms of cervical carcinogenesis by HPV16 E7, through modulation of HOTAIR expression and function.

Differential expression of HPV16 L2 gene in cervical cancers harboring episomal HPV16 genomes: influence of synonymous and non-coding region variations.

We tested the hypothesis that (i) synonymous variations within the coding regions, and (ii) variations within the non-coding regions of HPV, influence cervical cancer (CaCx) pathogenesis under the impact of intact HPV16 genomes. Whole genome sequence analysis of HPV16 isolates within 70 CaCx cases and 25 non-malignant samples revealed that synonymous variations were significantly higher within the E6 (p = 0.014), E5 (p = 0.001) and L2 (p = 0.0002) genes of HPV16 isolates within cases, compared to isolates within non-malignant samples. All of the 25 (100%) humanized codons identified within L2 ORF of the samples analyzed, were harbored by CaCx cases, while 8 out of 25 (32%) were harbored by HPV16 positive non-malignant samples (p = 3.87105E-07). L2 (mRNA and protein) expression was evident only among cases with episomal viral genomes and L2 mRNA expression correlated significantly with E2 gene copy numbers suggesting expression from all episomal genomes. Among such cases, Asian American (AA) isolates portrayed all of the humanized codons (100%; 4-6/sample) recorded within L2, which was significantly higher (p = 2.02E-7) compared to the European (E) isolates (22.8%; none or 1-2/sample). Additionally, majority of E variant isolates within cases (54/57; 94.7%) portrayed a variation (T4228C) within the short non-coding region (NCR2) between E5 and L2 genes, which portrays a weak promoter activity specific for L2 mRNA expression. This resulted in loss of 9 out of 14 miRNA binding sites (hsa-miR-548 family), despite the significant overexpression of miR548a-5p and miR548d-5p among such cases (28.64 and 36.25 folds, respectively), in comparison to HPV negative control samples. The findings exemplify the biological relevance of sequence variations in HPV16 genomes and highlight that episomal HPV16 in CaCx cases employ multiple mechanisms to sustain L2 expression, thereby justifying the potential role of L2 in such cancers, as opposed to those harboring viral integration.