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Article ; Online: Association of Human Leukocyte AntigenCw6 in Psoriasis Patients with Disease Severity and Morphological Patterns

Akhilesh Behra / Gobinda Chatterjee / Aditi Chandra / Raghunath Chatterjee

Journal of Clinical and Diagnostic Research, Vol 15, Iss 8, Pp WC01-WC

A Cross-control Study in a Tertiary Care Referral Centre in Eastern India

2021 Volume 03

Abstract: 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 ... ...

Abstract	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 sequencespecific 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 ...
Keywords	morphological patterns ; nail involvement ; polymerase chain reaction ; psoriasis area and severity index ; Medicine ; R
Subject code	616
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Epigenome-wide DNA methylation regulates cardinal pathological features of psoriasis

Aditi Chandra / Swapan Senapati / Sudipta Roy / Gobinda Chatterjee / Raghunath Chatterjee

Clinical Epigenetics, Vol 10, Iss 1, Pp 1-

2018 Volume 16

Abstract: Abstract Background Psoriasis is a chronic inflammatory autoimmune skin disorder. Several studies suggested psoriasis to be a complex multifactorial disease, but the exact triggering factor is yet to be determined. Evidences suggest that in addition to ... ...

Abstract	Abstract Background Psoriasis is a chronic inflammatory autoimmune skin disorder. Several studies suggested psoriasis to be a complex multifactorial disease, but the exact triggering factor is yet to be determined. Evidences suggest that in addition to genetic factors, epigenetic reprogramming is also involved in psoriasis development. Major histopathological features, like increased proliferation and abnormal differentiation of keratinocytes, and immune cell infiltrations are characteristic marks of psoriatic skin lesions. Following therapy, histopathological features as well as aberrant DNA methylation reversed to normal levels. To understand the role of DNA methylation in regulating these crucial histopathologic features, we investigated the genome-wide DNA methylation profile of psoriasis patients with different histopathological features. Results Genome-wide DNA methylation profiling of psoriatic and adjacent normal skin tissues identified several novel differentially methylated regions associated with psoriasis. Differentially methylated CpGs were significantly enriched in several psoriasis susceptibility (PSORS) regions and epigenetically regulated the expression of key pathogenic genes, even with low-CpG promoters. Top differentially methylated genes overlapped with PSORS regions including S100A9, SELENBP1, CARD14, KAZN and PTPN22 showed inverse correlation between methylation and gene expression. We identified differentially methylated genes associated with characteristic histopathological features in psoriasis. Psoriatic skin with Munro’s microabscess, a distinctive feature in psoriasis including parakeratosis and neutrophil accumulation at the stratum corneum, was enriched with differentially methylated genes involved in neutrophil chemotaxis. Rete peg elongation and focal hypergranulosis were also associated with epigenetically regulated genes, supporting the reversible nature of these characteristic features during remission and relapse of the lesions. Conclusion Our study, for the first time, ...
Keywords	Differentially methylated probes ; Methylation-sensitive PCR ; Bisulfite cloning and sequencing ; Gene expression ; Histopathology of psoriasis ; Munro’s microabscess ; Medicine ; R ; Genetics ; QH426-470
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In silico analysis of altered expression of long non-coding RNA in SARS-CoV-2 infected cells and their possible regulation by STAT1, STAT3 and interferon regulatory factors

Sayantan Laha / Chinmay Saha / Susmita Dutta / Madhurima Basu / Raghunath Chatterjee / Sujoy Ghosh / Nitai P. Bhattacharyya

Heliyon, Vol 7, Iss 3, Pp e06395- (2021)

2021

Abstract: 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 ...

Abstract	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.
Keywords	Long non-coding RNA ; NEAT1 ; MALAT1 ; Interferon regulatory factors ; SARS-CoV-2 ; COVID-19 ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	570
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dysbiosis of Oral Microbiota During Oral Squamous Cell Carcinoma Development

Purandar Sarkar / Samaresh Malik / Sayantan Laha / Shantanab Das / Soumya Bunk / Jay Gopal Ray / Raghunath Chatterjee / Abhik Saha

Frontiers in Oncology, Vol

2021 Volume 11

Abstract: Infection with specific pathogens and alterations in tissue commensal microbial composition are intricately associated with the development of many human cancers. Likewise, dysbiosis of oral microbiome was also shown to play critical role in the ... ...

Abstract	Infection with specific pathogens and alterations in tissue commensal microbial composition are intricately associated with the development of many human cancers. Likewise, dysbiosis of oral microbiome was also shown to play critical role in the initiation as well as progression of oral cancer. However, there are no reports portraying changes in oral microbial community in the patients of Indian subcontinent, which has the highest incidence of oral cancer per year, globally. To establish the association of bacterial dysbiosis and oral squamous cell carcinoma (OSCC) among the Indian population, malignant lesions and anatomically matched adjacent normal tissues were obtained from fifty well-differentiated OSCC patients and analyzed using 16S rRNA V3-V4 amplicon based sequencing on the MiSeq platform. Interestingly, in contrast to the previous studies, a significantly lower bacterial diversity was observed in the malignant samples as compared to the normal counterpart. Overall our study identified Prevotella, Corynebacterium, Pseudomonas, Deinococcus and Noviherbaspirillum as significantly enriched genera, whereas genera including Actinomyces, Sutterella, Stenotrophomonas, Anoxybacillus, and Serratia were notably decreased in the OSCC lesions. Moreover, we demonstrated HPV-16 but not HPV-18 was significantly associated with the OSCC development. In future, with additional validation, this panel could directly be applied into clinical diagnostic and prognostic workflows for OSCC in Indian scenario.
Keywords	oral squamous cell carcinoma ; 16S rRNA sequence analysis ; oral microbiology ecology ; dysbiosis ; human papillomavirus-16 ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Subject code	610
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genetic and epigenetic basis of psoriasis pathogenesis

Chandra, Aditi / Aditi Ray / Raghunath Chatterjee / Swapan Senapati

Molecular Immunology. 2015 Apr., v. 64

2015

Abstract: Psoriasis is a chronic inflammatory skin disease whose prevalence varies among different populations worldwide. It is a complex multi-factorial disease and the exact etiology is largely unknown. Family based studies have indicated a genetic ... ...

Abstract	Psoriasis is a chronic inflammatory skin disease whose prevalence varies among different populations worldwide. It is a complex multi-factorial disease and the exact etiology is largely unknown. Family based studies have indicated a genetic predisposition; however they cannot fully explain the disease pathogenesis. In addition to genetic susceptibility, environmental as well as gender and age related factors were also been found to be associated. Recently, imbalances in epigenetic networks are indicated to be causative elements in psoriasis. The present knowledge of epigenetic involvement, mainly the DNA methylation, chromatin modifications and miRNA deregulation is surveyed here. An integrated approach considering genetic and epigenetic anomalies in the light of immunological network may explore the pathogenesis of psoriasis.
Keywords	chromatin ; DNA methylation ; epigenetics ; etiology ; gender ; microRNA ; pathogenesis ; psoriasis
Language	English
Dates of publication	2015-04
Size	p. 313-323.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	424427-8
ISSN	1872-9142 ; 0161-5890
ISSN (online)	1872-9142
ISSN	0161-5890
DOI	10.1016/j.molimm.2014.12.014
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A combination of circulating microRNA-375-3p and chemokines CCL11, CXCL12, and G-CSF differentiate Crohn’s disease and intestinal tuberculosis

Susree Roy / Suchandrima Ghosh / Mallica Banerjee / Sayantan Laha / Dipanjan Bhattacharjee / Rajib Sarkar / Sujay Ray / Arko Banerjee / Ranajoy Ghosh / Aniket Halder / Alakendu Ghosh / Raghunath Chatterjee / Simanti Datta / Gopal Krishna Dhali / Soma Banerjee

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 10

Abstract: Abstract 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 ... ...

Abstract	Abstract 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.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Julian M. Rozenberg / Paramita Bhattacharya / Raghunath Chatterjee / Kimberly Glass / Charles Vinson

PLoS ONE, Vol 8, Iss

Combinatorial Recruitment of CREB, C/EBPβ and c-Jun Determines Activation of Promoters upon Keratinocyte Differentiation

2013 Volume 12

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Julian M. Rozenberg / Paramita Bhattacharya / Raghunath Chatterjee / Kimberly Glass / Charles Vinson

PLoS ONE, Vol 8, Iss

Combinatorial Recruitment of CREB, C/EBPβ and c-Jun Determines Activation of Promoters upon Keratinocyte Differentiation.

2013 Volume 12

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Combinatorial recruitment of CREB, C/EBPβ and c-Jun determines activation of promoters upon keratinocyte differentiation.

Julian M Rozenberg / Paramita Bhattacharya / Raghunath Chatterjee / Kimberly Glass / Charles Vinson

PLoS ONE, Vol 8, Iss 11, p e

2013 Volume 78179

Abstract: Transcription factors CREB, C/EBPβ and Jun regulate genes involved in keratinocyte proliferation and differentiation. We questioned if specific combinations of CREB, C/EBPβ and c-Jun bound to promoters correlate with RNA polymerase II binding, mRNA ... ...

Abstract	Transcription factors CREB, C/EBPβ and Jun regulate genes involved in keratinocyte proliferation and differentiation. We questioned if specific combinations of CREB, C/EBPβ and c-Jun bound to promoters correlate with RNA polymerase II binding, mRNA transcript levels and methylation of promoters in proliferating and differentiating keratinocytes.Induction of mRNA and RNA polymerase II by differentiation is highest when promoters are bound by C/EBP β alone, C/EBPβ together with c-Jun, or by CREB, C/EBPβ and c-Jun, although in this case CREB binds with low affinity. In contrast, RNA polymerase II binding and mRNA levels change the least upon differentiation when promoters are bound by CREB either alone or in combination with C/EBPβ or c-Jun. Notably, promoters bound by CREB have relatively high levels of RNA polymerase II binding irrespective of differentiation. Inhibition of C/EBPβ or c-Jun preferentially represses mRNA when gene promoters are bound by corresponding transcription factors and not CREB. Methylated promoters have relatively low CREB binding and, accordingly, those which are bound by C/EBPβ are induced by differentiation irrespective of CREB. Composite "Half and Half" consensus motifs and co localizing consensus DNA binding motifs are overrepresented in promoters bound by the combination of corresponding transcription factors.Correlational and functional data describes combinatorial mechanisms regulating the activation of promoters. Colocalization of C/EBPβ and c-Jun on promoters without strong CREB binding determines high probability of activation upon keratinocyte differentiation.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: PCB congener specific oxidative stress response by microarray analysis using human liver cell line

Supriyo De / Somiranjan Ghosh / Raghunath Chatterjee / Y-Q Chen / Linda Moses / Akanchha Kesari / Eric P. Hoffman / Sisir K. Dutta

Environment International, Vol 36, Iss 8, Pp 907-

2010 Volume 917

Abstract: In this study we have examined the effect of exposure to different congeners of PCBs and their role in oxidative stress response. A metabolically competent human liver cell line (HepG2) was exposed with two prototype congeners of PCBs: coplanar PCB-77 ... ...

Abstract	In this study we have examined the effect of exposure to different congeners of PCBs and their role in oxidative stress response. A metabolically competent human liver cell line (HepG2) was exposed with two prototype congeners of PCBs: coplanar PCB-77 and non-coplanar PCB-153. After the predetermined times of exposure (0–24 h) at 70 μM concentration, the HepG2 cells showed significant apoptotic changes by fluorescent microscopy after 12 h of exposure. Gene set enrichment analysis (GSEA) identified oxidative stress as the predominant enrichment. Further, paraquat assay showed that PCB congeners lead to oxidative stress to different extents, PCB-77 being more toxic. This study, with emphasis on all recommended microarray quality control steps, showed that apoptosis was one of the most significant cellular processes as a result of oxidative stress, but each of these congeners had a unique signature gene expression, which was further validated by Taqman real time PCR and immunoblotting. The pathways involved leading to the common apoptotic effect were completely different. Further in-silico analysis showed that PCB-153 most likely acted through the TNF receptor, leading to oxidative stress involving metallothionein gene families, and causing apoptosis mainly by the Fas receptor signaling pathway. In contrast, PCB-77 acted through the aryl hydrocarbon receptor. It induced oxidative stress through the involvement of cytochrome P450 (CYP1A1) leading to apoptosis through AHR/ARNT pathway. Keywords: Apoptosis, Aryl hydrocarbon receptor, Cytochrome P450, PCB 77, PCB 153, Oxidative stress
Keywords	Environmental sciences ; GE1-350
Language	English
Publishing date	2010-11-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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