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Thalassemia is the most common inherited hemoglobinopathy worldwide. Variation of clinical symptoms in this hemoglobinopathy entails differences in disease-onset and transfusion requirements. The aim of this study was to investigate the role of α-globin gene deletions in modulating the clinical heterogeneity of β-thalassemia (β-thal) syndromes. A total number 270 β-thal subjects were enrolled. Hematological parameters were recorded. β-Globin mutations were determined by amplified refractory mutation system-polymerase chain reaction (ARMS-PCR), gap-PCR and Sanger sequencing. α-Globin gene deletions were determined by multiplex PCR. Out of 270 β-thal subjects, 19 carried β

Differentiation of Crohn’s disease (CD) from intestinal tuberculosis (ITB) is a big challenge to gastroenterologists because of their indistinguishable features and insensitive diagnostic tools. A non-invasive biomarker is urgently required to distinguish ITB/CD patients particularly in India, a TB endemic region, where CD frequency is increasing rapidly due to urbanization. Among the three differentially expressed miRNAs obtained from small RNA transcriptomic profiling of ileocaecal/terminal ileal tissue of ITB/CD patients (n = 3), only two down-regulated miRNAs, miR-31-5p, and miR-215-5p showed comparable data in qRT-PCR. Out of which, only miR-215-5p was detectable in the patient’s plasma, but there was no significant difference in expression between ITB/CD. On the other hand, miR-375-3p, the pulmonary TB specific marker was found in higher amount in the plasma of ITB patients than CD while reverse expression was observed in the ileocaecal/terminal ileal tissues of the same patients. Next, using Bioplex pro-human cytokine 48-plex screening panel, only three chemokines, Eotaxin-1/CCL11, SDF-1α/CXCL12, and G-CSF have noted significantly different levels in the serum of ITB/CD patients. ROC analysis has revealed that compared to a single molecule, a combination of miR-375-3p + Eotaxin-1/CCL11 + SDF-1α /CXCL12 + G-CSF showed a better AUC of 0.83, 95% CI (0.69–0.96) with 100% specificity and positive predictive value while sensitivity, negative predictive value, and accuracy were 56%, 69%, and 78% respectively in distinguishing ITB from CD. This study suggests that a combination of plasma markers shows better potential in differentiating ITB from CD than a single marker and this panel of markers may be used for clinical management of ITB/CD patients.

Parkinson's disease (PD) is a progressive neurodegenerative disorder with a complex etiology. Presence of autosomal mutations in PARK7/DJ-1 gene has been associated with early-onset PD. Growing evidence has suggested that DJ-1 acts as a putative sensor of oxidative stress. Reduced levels of DJ-1 protein have been reported in the cerebrospinal fluid of sporadic PD patients. Several case-control association studies have identified DJ-1 g.168_185del (rs200968609) variants conferring susceptibility towards PD pathogenesis. Similarly, among the PD patients in eastern India, the deletion allele (g.168_185) of this DJ-1 promoter polymorphism was found to be associated with PD. Hence, we aimed to find out the functional contribution of this promoter variant of DJ-1 in PD pathogenesis. The expression of DJ-1 was observed to be significantly reduced in the presence of both deletion and duplication sequences as identified from the luciferase promoter activity assay. The transcription factor binding prediction tool identified DJ-1 promoter 18 bp insertion polymorphism as the only binding partner of REST (RE1 Silencing Transcription Factor). Transient Chromatin Immuno-precipitation (ChIP) assay further confirmed this prediction. Previous reports have highlighted the role of REST in regulating the expression of stress-responsive genes. Our study has identified the functional involvement of DJ-1 promoter variants and REST-mediated regulation of DJ-1 expression in PD pathogenesis.

Bacterial virulence factors are often located in their genomic islands (GIs). Helicobacter pylori, a highly diverse organism is reported to be associated with several gastrointestinal diseases like, gastritis, gastric cancer (GC), peptic ulcer, duodenal ulcer (DU) etc. A novel similarity score (Sm)-based comparative analysis with GIs of 50 H. pylori strains revealed clear idea of the various factors which promote disease progression. Two putative pathogenic GIs in some of the H. pylori strains were identified. One GI, having a putative labile enterotoxin and other dynamin-like proteins (DLPs), is predicted to increase the release of toxin by membrane vesicular formation. Another island contains a virulence-associated protein D (vapD) which is a component of a type-II toxin–antitoxin system (TAs), leads to enhance the severity of the H. pylori infection. Besides the well-known virulence factors like Cytotoxin-associated gene A (CagA) and vacA, several GIs have been identified which showed to have direct or indirect impact on H. pylori clinical outcomes. One such GI, containing lipopolysaccharide (LPS) biosynthesis genes was revealed to be directly connected with disease development by inhibiting the immune response. Another collagenase-containing GI worsens ulcers by slowing down the healing process. GI consisted of fliD operon was found to be connected to flagellar assembly and biofilm production. By residing in biofilms, bacteria can avoid antibiotic therapy, resulting in chronic infection. Along with well-studied CagA and vacuolating toxin A (vacA) virulent genes, it is equally important to study these identified virulence factors for better understanding H. pylori-induced disease prognosis.

Imbalance in lipid metabolism induces steatosis in liver during Chronic hepatitis C (CHC). Contribution of microRNAs in regulating lipid homoeostasis and liver disease progression is well established using small RNA-transcriptome data. Owing to the complexity in the development of liver diseases, the existence and functional importance of yet undiscovered regulatory miRNAs in disease pathogenesis was explored in this study using the unmapped sequences of the transcriptome data of HCV-HCC liver tissues following miRDeep2.pl pipeline. MicroRNA-c12 derived from the first intron of LGR5 of chromosome 12 was identified as one of the miRNA like sequences retrieved in this analysis that showed human specific origin. Northern blot hybridization has proved its existence in the hepatic cell line. Enrichment of premiR-c12 in dicer-deficient cells and miR-c12 in Ago2-RISC complex clearly suggested that it followed canonical miRNA biogenesis pathway and accomplished its regulatory function. Expression of this miRNA was quite low in CHC tissues than normal liver implying HCV-proteins might be regulating its biogenesis. Promoter scanning and ChIP analysis further revealed that under expression of p53 and hyper-methylation of STAT3 binding site upon HCV infection restricted its expression in CHC tissues. Centrosomal protein 350 (CEP350), which sequestered PPARα, was identified as one of the targets of miR-c12 using Miranda and validated by luciferase assay/western blot analysis. Furthermore, reduced triglyceride accumulation and enhanced PPARα mediated transcription of β-oxidation genes upon restoration of miR-c12 in liver cells suggested its role in lipid catabolism. Thus this study is reporting miR-c12 for the first time and showed its' protective role during chronic HCV infection.

BackgroundThe serological evaluations of IgG, IgM, and IgA to the SARS-CoV-2 proteins are widely used for the epidemiological assessment of COVID-19. The Health Care Workers (HCWs) are presumably exposed to a higher risk of acquiring the disease owing to their regular contact with the patients.MethodsCOVID-19 prevalence was investigated by classifying 313 HCWs into four groups based on their degree of exposure and estimating the IgG and total antibody. The serological assessment of the anti-SARS-CoV-2 antibody was conducted 21 days post-vaccination of first or both doses of the ChAdOx1 nCoV-19 vaccine among 174 HCWs. The vaccinated HCWs were followed up for 3 months for SARS-CoV-2 infection.FindingsThe levels of anti-SARS-CoV-2 IgG were comparable among different groups, but the seroprevalence gradually decreased from the most exposed to the less exposed group. The neutralizing antibody was positively correlated with IgG as well as total antibody. IgG was marginally decreased after 2 months followed by a significant drop after 4-6 months post-infection. However, 80% of the HCWs developed a detectable amount of IgG after the first dose of vaccination, the median titer of which was comparable to the seropositive HCWs after natural infection. Almost 100% of the HCWs developed antibodies after the second dose of vaccine with boosting effect among the seropositive HCWs. Although ∼11.5% of the vaccinated HCWs were infected with the SARS-CoV-2, ∼94% of them showed mild symptoms and recovered in home isolation without any O2 support.InterpretationsThe varying level of seroprevalence among the four groups suggested stratified spread of the disease. One dose of SARS-CoV-2 vaccination was found to be effective in terms of the antibody titer, while the second dose was required to cover the larger population. The effectiveness of the ChAdOx1 nCoV-19 vaccine was noticeable due to the low rate of post-vaccination infection with moderate or severe symptoms.

To decipher the genetic architecture of human disease, various types of omics data are generated. Two common omics data are genotypes and gene expression. Often genotype data for a large number of individuals and gene expression data for a few individuals are generated due to biological and technical reasons, leading to unequal sample sizes for different omics data. Unavailability of standard statistical procedure for integrating such datasets motivates us to propose a two-step multi-locus association method using latent variables. Our method is powerful than single/separate omics data analysis and it unravels comprehensively deep-seated signals through a single statistical model. Extensive simulation confirms that it is robust to various genetic models as its power increases with sample size and number of associated loci. It provides p-values very fast. Application to real dataset on psoriasis identifies 17 novel SNPs, functionally related to psoriasis-associated genes, at much smaller sample size than standard GWAS.

Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients. The functional role and mechanism (s) of transcriptional regulation of deregulated genes in COVID-19 remain largely unknown. In the present communication, reanalyzing publicly available gene expression data, we observed that 66 lncRNA and 5491 PCG were deregulated in more than one experimental condition. Combining our earlier published results and using different publicly available resources, it was observed that 72 deregulated lncRNA interacted with 3228 genes/proteins. Many targets of deregulated lncRNA could also interact with SARS-CoV-2 coded proteins, modulated by IFN treatment and identified in CRISPR screening to modulate SARS-CoV-2 infection. The majority of the deregulated lncRNA and PCG were targets of at least one of the transcription factors (TFs), interferon responsive factors (IRFs), signal transducer, and activator of transcription (STATs), NFκB, MYC, and RELA/p65. Deregulated 1069 PCG was joint targets of lncRNA and TF. These joint targets are significantly enriched with pathways relevant for SARS-CoV-2 infection indicating that joint regulation of PCG could be one of the mechanisms for deregulation. Over all this manuscript showed possible involvement of lncRNA and mechanisms of deregulation of PCG in the pathogenesis of COVID-19.

Munro's Microabscess (MM) is the diagnostic hallmark of psoriasis. Neutrophil detection in the Stratum Corneum (SC) of the skin epidermis is an integral part of MM detection in skin biopsy. The microscopic inspection of skin biopsy is a tedious task and staining variations in skin histopathology often hinder human performance to differentiate neutrophils from skin keratinocytes. Motivated from this, we propose a computational framework that can assist human experts and reduce potential errors in diagnosis. The framework first segments the SC layer, and multiple patches are sampled from the segmented regions which are classified to detect neutrophils. Both UNet and CapsNet are used for segmentation and classification. Experiments show that of the two choices, CapsNet, owing to its robustness towards better hierarchical object representation and localisation ability, appears as a better candidate for both segmentation and classification tasks and hence, we termed our framework as MICaps. The training algorithm explores both minimisation of Dice Loss and Focal Loss and makes a comparative study between the two. The proposed framework is validated with our in-house dataset consisting of 290 skin biopsy images. Two different experiments are considered. Under the first protocol, only 3-fold cross-validation is done to directly compare the current results with the state-of-the-art ones. Next, the performance of the system on a held-out data set is reported. The experimental results show that MICaps improves the state-of-the-art diagnosis performance by 3.27% (maximum) and reduces the number of model parameters by 50%.

Glioblastoma Multiforme (GBM) is an aggressive form of glioma, exhibiting very poor survival. Genomic input, in the form of RNA sequencing data (RNA-seq), is expected to provide vital information about the characteristics of the genes that affect the Overall Survival (OS) of patients. This could have a significant impact on treatment planning. We present a new Autoencoder (AE)-based strategy for the prediction of survival (low or high) of GBM patients, using the RNA-seq data of 129 GBM samples from The Cancer Genome Atlas (TCGA). This is a novel interdisciplinary approach to integrating genomics with deep learning towards survival prediction. First, the Differentially Expressed Genes (DEGs) were selected using EdgeR. These were further reduced using correlation-based analysis. This was followed by the application of ranking with different feature subset selection and feature extraction algorithms, including the AE. In each case, fifty features were selected/extracted, for subsequent prediction with different classifiers. An exhaustive study for survival group prediction, using eight different classifiers with the accuracy and Area Under the Curve (AUC), established the superiority of the AE-based feature extraction method, called DeepSGP. It produced a very high accuracy (0.83) and AUC (0.90). Of the eight classifiers, using the extracted features by DeepSGP, the MLP was the best at Overall Survival (OS) prediction with an accuracy of 0.89 and an AUC of 0.97. The biological significance of the genes extracted by the AE were also analyzed to establish their importance. Finally, the statistical significance of the predicted output of the DeepSGP algorithm was established using the concordance index.

Oral submucous fibrosis is a potentially malignant disorder of the oral cavity, with a high rate of malignant transformation. It is very common among habitual areca nut chewers. The pathogenesis of oral submucous fibrosis is not well established, but it is believed to be a disease of multifactorial origin, including areca nut chewing, ingestion of chilies, genetic factors, immunologic processes and nutritional deficiencies. Genetically susceptible individuals when exposed to areca nut chewing develop this disease over a variable period of time. Oral submucous fibrosis is considered to be a disease of collagen metabolism. Several genetic factors are reported but there is no consensus about the exact mechanism of disease initiation. Variations in histopathological presentation are noted among oral submucous fibrosis patients with habitual areca nut chewing in different forms and other additive agents, eg betel quid, pan masala and gutkha, together with a variety of tobacco habits. The role of epigenetic modifications, such as miRNA regulation, and DNA methylation is also being reported as part of the pathogenesis of oral submucous fibrosis. A combined approach, including analysis of genetic and epigenetic regulations with different habits, might be helpful to better understand the contributory factors and pathogenesis of this serious disorder.

Oral cancer is one of the leading cancers in South-Asian countries. Despite the easy access of the oral cavity, the detection and five year survival rates of OSCC patients are dismal. Identification of non-invasive biomarkers to determine the progression and recurrence of OSCC could be of immense help to patients. Recent studies on oral cancer suggest the importance of non-invasive biomarker development. Micro-RNAs (miRNAs) are one of the important components of the cell-free nucleic acids available in different body fluids. Here, we have reviewed the current understanding of circulating miRNAs as non-invasive biomarkers in different body fluids of oral cancer patients. A number of circulating miRNAs are found to be common in the body fluids of OSCC patients, while many of these are study specific, the possible sources of this variability could be due to differences in sample processing, assay procedure, clinical stage of the disease, oral habit and environmental factors. The prognostic and therapeutic significance of these circulating miRNAs are suggested by several studies. Mir-371, mir-150, mir-21 and mir-7d were found to be potential prognostic markers, while mir-134, mir-146a, mir-338 and mir-371 were associated with metastases. The prognostic markers, mir-21 and mir-7d were also found to be significantly correlated with resistance to chemotherapy, while mir-375, mir-196 and mir-125b were significantly correlated with sensitivity to radiotherapy. Despite the promising roles of circulating miRNAs, challenges still remain in unravelling the exact regulation of these miRNAs before using them for targeted therapy.

Genomic Islands (GIs) play an important role in the evolution and adaptation of prokaryotes. The origin and extent of ecological diversity of prokaryotes can be analyzed by comparing GIs across closely or distantly related prokaryotes. Understanding the importance of GI and to study the bacterial evolution, several GI prediction tools have been generated. An unsupervised method, Design-Island, was developed to identify GIs using Monte-Carlo statistical test on randomly selected segments of a chromosome. Here, in the present study Design-Island was modified with the incorporation of majority voting, multiple hypothesis testing correction. The performance of the modified version, Design-Island-II was tested and compared with the existing GI prediction tools. The performance assessment and benchmarking of the GI prediction tools require experimentally validated dataset, which is lacking. So, different datasets, generated or taken from literature were utilized to compare the sensitivity (SN), specificity (SP), precision (PPV) and accuracy (AC) of Design-Island-II. It showed substantial enhancement in term of SN, SP, PPV and AC, and significantly reduced the computation time of the algorithm. The performance of Design-Island-II has also been compared with several GI prediction tools using curated dataset of putative horizontally transferred genes. Design-Island-II showed the highest sensitivity and F1 score, comparable specificity, precision and accuracy in comparison to the other available methods. IslandViewer4 and Islander outperformed all the available methods in terms of AC and PPV respectively. Our study suggested Design-Island-II, IslandViewer4 and GIHunter among the top performing GI prediction tools considering both sensitivity and specificity of the methods.

Aim: In order to curb the transmission of SARS-CoV-2, nation-wide travel restrictions at different levels were implemented in different countries. Country-specific mutational profile may exist and have an impact on vaccine efficacy. Materials & methods: We identified nonsynonymous mutations in approximately 215,000 SARS-CoV-2 sequences during the first year of the pandemic in 35 countries. Mutational profiles on a bimonthly basis were traced over time. We also examined the mutations that overlapped with the spike protein vaccine epitopes. Results: Several new mutations emerged over time and were dominating in specific countries. Many nonsynonymous mutations were within multiple spike protein epitopes that might impact the vaccine efficacy. Conclusion: Our study advocates requirement of active monitoring of country-specific mutations and vaccine efficacies in respective countries.

Altered expression of long noncoding RNA (lncRNA), longer than 200 nucleotides without potential for coding protein, has been observed in diverse human diseases including viral diseases. It is largely unknown whether lncRNA would deregulate in SARS-CoV-2 infection, causing ongoing pandemic COVID-19. To identify, if lncRNA was deregulated in SARS-CoV-2 infected cells, we analyzed in silico the data in GSE147507. It was revealed that expression of 20 lncRNA like MALAT1, NEAT1 was increased and 4 lncRNA like PART1, TP53TG1 was decreased in at least two independent cell lines infected with SARS-CoV-2. Expression of NEAT1 was also increased in lungs tissue of COVID-19 patients. The deregulated lncRNA could interact with more than 2800 genes/proteins and 422 microRNAs as revealed from the database that catalogs experimentally determined interactions. Analysis with the interacting gene/protein partners of deregulated lncRNAs revealed that these genes/proteins were associated with many pathways related to viral infection, inflammation and immune functions. To find out whether these lncRNAs could be regulated by STATs and interferon regulatory factors (IRFs), we used ChIPBase v2.0 that catalogs experimentally determined binding from ChIP-seq data. It was revealed that any one of the transcription factors IRF1, IRF4, STAT1, STAT3 and STAT5A had experimentally determined binding at regions within -5kb to +1kb of the deregulated lncRNAs in at least 2 independent cell lines/conditions. Our analysis revealed that several lncRNAs could be regulated by IRF1, IRF4 STAT1 and STAT3 in response to SARS-CoV-2 infection and lncRNAs might be involved in antiviral response. However, these in silico observations are necessary to be validated experimentally., Long non-coding RNA; NEAT1; MALAT1; Interferon regulatory factors; SARS-CoV-2; COVID-19

In order to curb the rapid transmission of SARS-CoV-2, nation-wide lockdowns were implemented as a preliminary measure. Since most countries enforced travel-bans during end of March 2020, the country-specific patterns should be discernible in the subsequent months. We identified frequently mutated non-synonymous mutations in ∼2,15,000 SARS-CoV-2 sequences during pre- and post-travel-ban periods in 35 countries. We further investigated the mutational profile on a bi-monthly basis and traced the progress over the time. Several new mutations have emerged post-travel-ban and on the rise in specific countries, chief among them being A222V and S477N in Spike, and A220V in Nucleocapsid protein. Consequently, we examined the Spike protein epitopes to inspect whether any of these country-specific mutations overlapped with these epitopes. Several mutations were found to be contained within one or more epitopes, including the highly mutated residues of Spike protein, advocating the requirement of active monitoring of vaccine efficacies in respective countries.

Introduction: Psoriasis is a multifactorial disorder in which genetic and environmental factors play an essential role in disease pathogenesis. The Human Leukocyte Antigen-Cw6 (HLA-Cw6) allele has shown the strongest genetic association with this condition across several populations studied. Aim: To estimate the risk of HLA-Cw6 association with psoriasis compared to the control group and its association with the severity of psoriasis expressed as Psoriasis Area and Severity Index (PASI) score and morphological patterns. Materials and Methods: A cross-control study was conducted from March 2014 to February 2015 in a tertiary care centre in the eastern part of India. All patients who were diagnosed clinically as psoriasis and gave written informed consent were included in the study. Healthy controls were taken to compare the HLA-Cw6 after duly signing the informed consent for detailed history, clinical examination, PASI score, and digital photographs of lesions were taken. A blood sample was taken from patients and the control for HLA-Cw6 typing by sequence- specific Polymerase Chain Reaction (PCR) method. Data was analysed by appropriate statistical test (Chi-square test) using R statistical software. Results: A total of 100 patients with psoriasis and 100 controls were recruited, of which 61 were positive for HLA-Cw6 among the psoriasis group and nine in the control group. Positivity of the HLA-Cw6 allele was significantly higher in psoriasis cases (n=61) compared to normal individuals (n=9) (p-value: 1.79×10-15, OR: 15.8148, 95% CI: 7.15-34.99). It was also observed that HLA-Cw6 positive individuals had a more severe form of the disease, determined by a PASI score >6 (p-value: 0.0494, OR: 2.22, 95% CI: 0.96-5.15), and significant involvement of scalp psoriasis (p-value: 0.0054, OR: 13.125, 95% CI: 1.55-111.42). However, no significant association of HLA-Cw6 was seen with positive family history, nail involvement, and joint pain (arthralgia). Conclusion: The HLA-Cw6 positivity was associated with a more severe form of disease and scalp psoriasis.

Functional studies to delineate the molecular mechanisms of causal genetic variants are the main focus in the post-GWAS era. Previous GWASs have identified >50 susceptibility loci associated with psoriasis. Functional understanding of the biology underlying the disease risk of most of these associated loci is unclear. In this study, we identified a regulatory SNP at the putative enhancer of the LCE3A gene within the epidermal differentiation complex that showed epistatic interaction with HLA-Cw6. The variant allele disrupted signal transducer and activator of transcription 3 binding to the region, thereby regulating the expression of the downstream LCE3A gene. Electrophoretic mobility shift and pulldown assay confirmed the preferential binding of signal transducer and activator of transcription 3 to the DNA with a wild-type allele compared with the DNA with a variant allele. The reporter assay further validated the IL-6‒stimulated phosphorylated signal transducer and activator of transcription 3‒mediated LCE3A activation in the presence of the wild-type allele. Interestingly, the presence of the HLA-Cw6 allele leads to IL-6‒mediated phosphorylation of signal transducer and activator of transcription 3, followed by its nuclear localization in the epidermal keratinocytes of psoriatic skin, suggesting indirect interaction of the HLA-Cw6 allele and a regulatory SNP upstream of the LCE3A gene. This study reflects an interesting approach to dissecting the molecular mechanism underlying the genetic interaction observed between HLA-Cw6 and LCE3A in psoriasis pathogenesis.

Thalassemia is the commonest inherited hemoglobinopathy worldwide. Variation of clinical symptoms entail differences in disease-onset and transfusion requirements. Our objective was to investigate the role of alpha gene deletions in modulating the clinical heterogeneity of thalassemia syndromes. A total of 214 individuals with diagnosed beta-thalassemia major/intermedia were included in the study. Beta globin mutations were determined and categorized as β+ and β0. Eight common alpha globin gene deletions were detected by multiplex GAP-PCR. Out of the 17 individuals with β+/β+, 16 did not harbour alpha deletions (αα/αα), and most of them were non-severe. On the other hand, out of 46 individuals with β0/β0, 30 did not reveal alpha deletions, whereas 16 possessed one or more alpha deletion(s). Accordingly, most of them presented as clinically severe. Out of the 151 β0/β+ individuals, 119 were negative for alpha deletion, whereas 32 possessed alpha deletions. It was observed that, only in this last category, alpha deletions made a significant contribution (P< 0.0001) in modulation of clinical non severity in this genotype. In conclusion, alpha globin gene deletions play a role to help in ameliorating the phenotype in the β+/β0 genotype. However, they may have only minor/no role in patients with β+/β+ or β0/β0 genotype.

Altered expression levels of protein-coding genes and microRNAs have been implicated in the pathogenesis of Huntington’s disease (HD). The involvement of other ncRNAs, especially long ncRNAs (lncRNA), is being realized recently and the related knowledge is still rudimentary. Using small RNA sequencing and PCR arrays we observed perturbations in the levels of 12 ncRNAs in HD mouse brain, eight of which had human homologs. Of these, Meg3, Neat1, and Xist showed a consistent and significant increase in HD cell and animal models. Transient knock-down of Meg3 and Neat1 in cell models of HD led to a significant decrease of aggregates formed by mutant huntingtin and downregulation of the endogenous Tp53 expression. Understanding Meg3 and Neat1 functions in the context of HD pathogenesis is likely to open up new strategies to control the disease.

Diagnosis of hepatocellular carcinoma (HCC) remains challenging to clinicians, particularly in a patient with low alpha-fetoprotein. Here, in silico, ex vivo and in vitro data were combined to identify liver-specific exosomal miRNAs as an early diagnostic marker for HCC. Transcriptome profiling for mRNA and small RNA in same HCV-HCC and normal liver tissues followed by cross-validation of 41 deregulated miRNAs (log2 FoldChange > 1.5, Padj

Interferon-γ-induced aminopeptidase ERAP1 trims peptides within the endoplasmic reticulum so that they can be loaded onto MHC class I and presented to the CD8+ T-cells. ERAP1 association and its interaction with HLA-C∗06 is controversial across different populations. We have investigated the association and possible functional role of non-synonymous SNPs at different exons of ERAP1 (rs26653: Arg127Pro, rs30187: Lys528Arg and rs27044: Gln730Glu) and their interactions with HLA-C∗06 in psoriasis. Significant associations of HLA-C∗06 (OR=5.47, P

Altered expressions of protein-coding genes and microRNAs have been implicated in the pathogenesis of Alzheimer's disease (AD). The disrupted miRNA landscape (degradome) has been studied in AD mainly from the Aβ perspective. That Amyloid Precursor Protein C- terminal Domain (AICD) is involved in altering the cellular transcriptome has been reported, but its role in the degradome is still unexplored. The involvement of other long non-coding RNAs (lncRNA) is being realized recently. Using small RNA sequencing from an AD cell model, we observed perturbations in the levels of 47 miRNAs deregulated between the control and Aβ groups, and 26 deregulated miRNAs between the control and AICD + Aβ (AD) groups. Additionally, using a novel bioinformatics pipeline, we obtained a total of 263 differentially expressed lncRNAs in Aβ versus control group, and 41 deregulated lncRNAs in the AD versus control group. Effect of Aβ and AICD, individually and in combination, were validated with top regulated miRNA hits. Several of these miRNAs were found to target key Receptor Tyrosine Kinase (RTK) - many of which are implicated in AD. Understanding the total cellular non-coding transcriptome in the context of AD is likely to open up new putative targets for the disease intervention.

Mutations in the TP53 gene are one of the most frequent events in cancers. Certain missense mutant p53 proteins gain oncogenic functions (gain-of-functions) and drive tumorigenesis. Apart from the coding genes, a few non-coding microRNAs (miRNAs) are implicated in mediating mutant p53-driven cancer phenotypes. Here, we identified miRNAs in mutant p53R273H bearing non-small cell lung carcinoma (NSCLC) cells while using small RNA deep sequencing. Differentially regulated miRNAs were validated in the TCGA lung adenocarcinoma patients with p53 mutations and, subsequently, we identified specific miRNA signatures that are associated with lymph node metastasis and poor survival of the patients. Pathway analyses with integrated miRNA-mRNA expressions further revealed potential regulatory molecular networks in mutant p53 cancer cells. A possible contribution of putative mutant p53-regulated miRNAs in epithelial-to-mesenchymal transition (EMT) is also predicted. Most importantly, we identified a novel miRNA from the unmapped sequencing reads through a systematic computational approach. The newly identified miRNA promotes proliferation, colony-forming ability, and migration of NSCLC cells. Overall, the present study provides an altered miRNA expression profile that might be useful in biomarker discovery for non-small cell lung cancers with TP53 mutations and discovers a hitherto unknown miRNA with oncogenic potential.

Chronic pressure overload-induced left ventricular hypertrophy in heart is preceded by a metabolic perturbation that prefers glucose over lipid as substrate for energy requirement. Here, we establish C/EBPβ (CCAAT/enhancer-binding protein β) as an early marker of the metabolic derangement that triggers the imbalance in fatty acid (FA) oxidation and glucose uptake with increased lipid accumulation in cardiomyocytes during pathological hypertrophy, leading to contractile dysfunction and endoplasmic reticulum (ER) stress. This is the first study that shows that myocardium-targeted C/EBPβ knockdown prevents the impaired cardiac function during cardiac hypertrophy led by maladaptive metabolic response with persistent hypertrophic stimuli, whereas its targeted overexpression in control increases lipid accumulation significantly compared to control hearts. A new observation from this study was the dual and opposite transcriptional regulation of the alpha and gamma isoforms of Peroxisomal proliferator activated receptors (PPARα and PPARγ) by C/EBPβ in hypertrophied cardiomyocytes. Before the functional and structural remodeling sets in the diseased myocardium, C/EBPβ aggravates lipid accumulation with the aid of the increased FA uptake involving induced PPARγ expression and decreased fatty acid oxidation (FAO) by suppressing PPARα expression. Glucose uptake into cardiomyocytes was greatly increased by C/EBPβ via PPARα suppression. The activation of mammalian target of rapamycin complex-1 (mTORC1) during increased workload in presence of glucose as the only substrate was prevented by C/EBPβ knockdown, thereby abating contractile dysfunction in cardiomyocytes. Our study thus suggests that C/EBPβ may be considered as a novel cellular marker for deranged metabolic milieu before the heart pathologically remodels itself during hypertrophy.

Background: The underlying complex molecular mechanism of Hepatitis C virus (HCV) mediated liver disease progression is still unresolved. Next generation sequencing of small RNAs provides genome-wide data about regulatory microRNAs. Here, we have identified undiscovered low abundant regulatory miRNAs and investigated the role of a novel human liver specific miRNAs in HCV mediated liver disease development. Methods: To discover unannotated miRNAs, unmapped sequences from small RNA transcriptome profiling of HCV infected and un-infected liver tissues were subjected to miRDeep2.pl pipeline. Targets predicted using MiRanda and Ingenuity pathway analysis (IPA). Northern-blot, Dicer knock down (K/D), Ago2-RNA immunoprecipitation (RIP), Stem-loop Real-time PCR (SLRTPCR), immunoblot (IB) analysis, luciferase assay, Chromatin immunoprecipitation (ChIP) etc. were used as required. Findings: Among seven predicted novel miRNAs, miR-c12 was found human liver specific miRNA. Dicer K/D and RIP assays showed that miR-c12 followed canonical miRNA biogenesis pathways. Its low expression in chronic HCV infected (CHC) tissues than normal liver indicated its protective role against HCV infection. Furthermore, upon HCV infection downregulation of p53 expression and hypermethylation of STAT3 binding site in the promoter of miR-c12 restricted its expression in CHC. IPA analysis revealed miR-c12 controlled mostly the fatty acid metabolism pathway. Reduced triglyceride accumulation and enhanced PPARα mediated fatty-acid catabolism upon miR-c12 retention in cells by targeting CAP350, a suppressor of PPARα, confirmed its role in lipid metabolism pathways. Interpretations: We discovered a previously unidentified low abundant human-liver specific miRNA having role in lipid homeostasis maintenance. Hence, miR-c12 together with anti-virals might be more effective therapeutic in restricting HCV infection. Funding Statement: Department of Biotechnology (DBT), Government of India [BT/PR11971/MED/29/890/2014]. Declaration of Interests: The authors declare no conflict of interest. Ethics Approval Statement: Ethics committee of the Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India and Indraprastha Apollo Hospital, New Delhi had approved the study. Blood and tissues were collected from patients who were willing to participate in the study with prior written consent.

Aberrant DNA methylation, consequent activation of oncogenes, and silencing of tumor suppressor genes are general phenomena observed in different carcinomas including oral squamous cell carcinoma. Despite the general accessibility of the oral cavity during physical examination, many malignancies are not diagnosed until late stages of the disease. The recent advancement of massively parallel next-generation sequencing and microarray technologies enabled researchers to generate epigenome-wide DNA methylation data for several cell types of diseased and healthy individuals. The urgent need to handle these data led to development of several computational and statistical tools. Here, we have deliberated the recent advancement in computational and statistical tools for genome-wide DNA methylation data analysis and up-to-date progress of DNA methylomics in oral cancer. Identification of epigenetically regulated genes in early stages of oral cancer may be used as potential biomarker for early detection and better clinical management of oral cancer.

Psoriasis is a chronic inflammatory skin disorder. Several studies suggested psoriasis to be a complex multifactorial genetic disease, but the exact triggering factor is yet to be determined. Many psoriasis susceptibility loci are located near genes that belong to immunologic pathways, indicating that defective immune system might play a major role in psoriasis pathogenesis. Human leukocyte antigen (HLA)-Cw6 allele within the major histocompatibility complex (MHC) Class I region was found to be the most significantly associated allele. Several other genetic loci have been reported, but the risk assessed by these factors is variable across populations. Epistatic interactions between HLA-Cw6 and other susceptibility loci have also been demonstrated in some populations. Furthermore, recent studies have suggested the association of several genetic markers with the drug response. Genetic studies are thus important not only to identify markers for disease predisposition and pathogenesis but also to predict drug response and develop personalised medications. Key Concepts Psoriasis is a common chronic inflammatory disease characterised by hyper-proliferating keratinocytes, with varying prevalence among different populations worldwide. Population-, family- and twin-based studies have indicated a genetic predisposition in psoriasis; however, they cannot fully explain the disease pathogenesis. Many of the strongly associated loci with psoriasis are also associated with the immune system. HLA-Cw6 allele is the most important risk allele within the MHC Class I region. Several genetic susceptibility loci show differential associations between ethnic populations, suggesting potential genetic heterogeneity of psoriasis across diverse ancestries. Population-specific genetic association studies are essential to elucidate the actual causal variants and develop more targeted therapeutics. The impact of genetic polymorphisms on the response to drugs has been demonstrated in psoriasis. Development of such targeted treatment based on patients' genetic background (pharmacogenetics) is a prospective area for disease management in psoriasis. Keywords: psoriasis vulgaris; genetic markers; single-nucleotide polymorphism; genome-wide association studies; major histocompatibility complex; HLA-Cw6; immunogenetics; pharmacogenetics; cyclosporine A; ustekinumab