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Article: Temporal variations of country-specific mutational profile of SARS-CoV-2: effect on vaccine efficacy.

Laha, Sayantan / Chatterjee, Raghunath

2021

Abstract: Aim: ...

Abstract	Aim:
Language	English
Publishing date	2021-11-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2254606-6
ISSN	1746-0808 ; 1746-0794
ISSN (online)	1746-0808
ISSN	1746-0794
DOI	10.2217/fvl-2021-0062
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Serum miRNA profiling identified miRNAs associated with disease severity in psoriasis.

Ganguly, Torsa / Laha, Sayantan / Senapati, Swapan / Chatterjee, Gobinda / Chatterjee, Raghunath

Experimental dermatology

2023 Volume 33, Issue 1, Page(s) e14973

Abstract: Psoriasis vulgaris is a chronic, autoimmune skin disease involving a complex interplay of epidermal keratinocytes, dermal fibroblast and infiltrating immune cells. Differential expressions of miRNAs are observed in psoriasis and the deregulated miRNAs ... ...

Abstract	Psoriasis vulgaris is a chronic, autoimmune skin disease involving a complex interplay of epidermal keratinocytes, dermal fibroblast and infiltrating immune cells. Differential expressions of miRNAs are observed in psoriasis and the deregulated miRNAs are sometimes associated with disease severity. This study aims to identify miRNAs altered in the serum of psoriasis patients that are associated with the Psoriasis Area and Severity Index (PASI). In order to assess miRNA levels in the serum of psoriasis patients, we selected 24 differentially expressed miRNAs in the psoriatic skin are possibly derived from the skin and immune cells, as well as five miRNAs that are enriched in other tissues. We identified 16 miRNAs that exhibited significantly (p < 0.05) altered levels in the serum of psoriasis patients compared to healthy individuals. Among these, 13 miRNAs showed similar expression pattern in the serum of psoriasis patients as also observed in the psoriatic skin tissues. Ten miRNAs showed an accuracy of greater than 75% in classifying the psoriasis patients from healthy individuals. Further analysis of differential miRNA levels between the low PASI group and the high PASI group identified three miRNAs (miR-147b, miR-3614-5p, and miR-125a-5p) with significantly altered levels between the low severity and the high severity psoriasis patients. Our systematic investigation of skin and immune cell-derived miRNAs in the serum of psoriasis patients revealed alteration in miRNA levels to be associated with disease severity, which may help in monitoring the disease progression and therapeutic response.
MeSH term(s)	Humans ; MicroRNAs/metabolism ; Psoriasis/metabolism ; Skin/metabolism ; Keratinocytes/metabolism ; Patient Acuity ; Chronic Disease
Chemical Substances	MicroRNAs
Language	English
Publishing date	2023-11-05
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	1130936-2
ISSN	1600-0625 ; 0906-6705
ISSN (online)	1600-0625
ISSN	0906-6705
DOI	10.1111/exd.14973
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Article ; Online: Country specific mutational profile of SARS-CoV-2 in pre- and post-international travel ban: Effect on vaccine efficacy

Laha, Sayantan / Chatterjee, Raghunath

medRxiv

Abstract: 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 ... ...

Abstract	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.
Keywords	covid19
Language	English
Publishing date	2021-02-11
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.02.08.21251359
Database	COVID19

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Article ; Online: Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis.

Saha, Chinmay / Laha, Sayantan / Chatterjee, Raghunath / Bhattacharyya, Nitai P

Non-coding RNA

2021 Volume 7, Issue 4

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2021-11-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna7040074
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Article: Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission

Laha, Sayantan / Chakraborty, Joyeeta / Das, Shantanab / Manna, Soumen Kanti / Biswas, Sampa / Chatterjee, Raghunath

Infection, genetics, and evolution. 2020 Nov., v. 85

2020

Abstract: The recent pandemic of SARS-CoV-2 infection has affected more than 3.0 million people worldwide with more than 200 thousand reported deaths. The SARS-CoV-2 genome has the capability of gaining rapid mutations as the virus spreads. Whole-genome sequencing ...

Abstract	The recent pandemic of SARS-CoV-2 infection has affected more than 3.0 million people worldwide with more than 200 thousand reported deaths. The SARS-CoV-2 genome has the capability of gaining rapid mutations as the virus spreads. Whole-genome sequencing data offers a wide range of opportunities to study mutation dynamics. The advantage of an increasing amount of whole-genome sequence data of SARS-CoV-2 intrigued us to explore the mutation profile across the genome, to check the genome diversity, and to investigate the implications of those mutations in protein stability and viral transmission. We have identified frequently mutated residues by aligning ~660 SARS-CoV-2 genomes and validated in 10,000 datasets available in GISAID Nextstrain. We further evaluated the potential of these frequently mutated residues in protein structure stability of spike glycoprotein and their possible functional consequences in other proteins. Among the 11 genes, surface glycoprotein, nucleocapsid, ORF1ab, and ORF8 showed frequent mutations, while envelop, membrane, ORF6, ORF7a and ORF7b showed conservation in terms of amino acid substitutions. Combined analysis with the frequently mutated residues identified 20 viral variants, among which 12 specific combinations comprised more than 97% of the isolates considered for the analysis. Some of the mutations across different proteins showed co-occurrences, suggesting their structural and/or functional interaction among different SARS-COV-2 proteins, and their involvement in adaptability and viral transmission. Analysis of protein structure stability of surface glycoprotein mutants indicated the viability of specific variants and are more prone to be temporally and spatially distributed across the globe. A similar empirical analysis of other proteins indicated the existence of important functional implications of several variants. Identification of frequently mutated variants among COVID-19 patients might be useful for better clinical management, contact tracing, and containment of the disease.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; data collection ; empirical research ; evolution ; glycoproteins ; infection ; nucleocapsid ; pandemic ; people ; protein structure ; viability ; virus transmission ; viruses
Language	English
Dates of publication	2020-11
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104445
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 5645: Show issues

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Article: Dysbiosis of Oral Microbiota During Oral Squamous Cell Carcinoma Development.

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

Frontiers in oncology

2021 Volume 11, Page(s) 614448

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
Language	English
Publishing date	2021-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2021.614448
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Article ; Online: Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission.

Laha, Sayantan / Chakraborty, Joyeeta / Das, Shantanab / Manna, Soumen Kanti / Biswas, Sampa / Chatterjee, Raghunath

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2020 Volume 85, Page(s) 104445

Abstract	The recent pandemic of SARS-CoV-2 infection has affected more than 3.0 million people worldwide with more than 200 thousand reported deaths. The SARS-CoV-2 genome has the capability of gaining rapid mutations as the virus spreads. Whole-genome sequencing data offers a wide range of opportunities to study mutation dynamics. The advantage of an increasing amount of whole-genome sequence data of SARS-CoV-2 intrigued us to explore the mutation profile across the genome, to check the genome diversity, and to investigate the implications of those mutations in protein stability and viral transmission. We have identified frequently mutated residues by aligning ~660 SARS-CoV-2 genomes and validated in 10,000 datasets available in GISAID Nextstrain. We further evaluated the potential of these frequently mutated residues in protein structure stability of spike glycoprotein and their possible functional consequences in other proteins. Among the 11 genes, surface glycoprotein, nucleocapsid, ORF1ab, and ORF8 showed frequent mutations, while envelop, membrane, ORF6, ORF7a and ORF7b showed conservation in terms of amino acid substitutions. Combined analysis with the frequently mutated residues identified 20 viral variants, among which 12 specific combinations comprised more than 97% of the isolates considered for the analysis. Some of the mutations across different proteins showed co-occurrences, suggesting their structural and/or functional interaction among different SARS-COV-2 proteins, and their involvement in adaptability and viral transmission. Analysis of protein structure stability of surface glycoprotein mutants indicated the viability of specific variants and are more prone to be temporally and spatially distributed across the globe. A similar empirical analysis of other proteins indicated the existence of important functional implications of several variants. Identification of frequently mutated variants among COVID-19 patients might be useful for better clinical management, contact tracing, and containment of the disease.
MeSH term(s)	Humans ; Models, Molecular ; Mutation ; Phylogeny ; Protein Conformation ; Protein Domains ; SARS-CoV-2/genetics ; Sequence Alignment ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Whole Genome Sequencing
Chemical Substances	Spike Glycoprotein, Coronavirus
Keywords	covid19
Language	English
Publishing date	2020-06-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104445
Database	MEDical Literature Analysis and Retrieval System OnLINE

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ab Jg. 2022: Lesesaal (EG)

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Article: In silico

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

Heliyon

2021 Volume 7, Issue 3, Page(s) e06395

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.
Language	English
Publishing date	2021-02-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e06395
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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 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 ; 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 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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