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Article ; Online: Spontaneous preterm birth: the underpinnings in the maternal and fetal genomes.

Bhattacharjee, Esha / Maitra, Arindam

2021 Volume 6, Issue 1, Page(s) 43

Abstract: Preterm birth (PTB) is a major cause of neonatal mortality and health complications in infants. Elucidation of its genetic underpinnings can lead to improved understanding of the biological mechanisms and boost the development of methods to predict PTB. ... ...

Abstract	Preterm birth (PTB) is a major cause of neonatal mortality and health complications in infants. Elucidation of its genetic underpinnings can lead to improved understanding of the biological mechanisms and boost the development of methods to predict PTB. Although recent genome-based studies of both mother and fetus have identified several genetic loci which might be implicated in PTB, these results suffer from a lack of consistency across multiple studies and populations. Moreover, results of functional validation of most of these findings are unavailable. Since medically indicated preterm deliveries have well-known heterogeneous causes, we have reviewed only those studies which investigated spontaneous preterm birth (sPTB) and have attempted to suggest probable biological mechanisms by which the implicated genetic factors might result in sPTB. We expect our review to provide a panoramic view of the genetics of sPTB.
Language	English
Publishing date	2021-06-08
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2813848-X
ISSN	2056-7944 ; 2056-7944
ISSN (online)	2056-7944
ISSN	2056-7944
DOI	10.1038/s41525-021-00209-5
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Article ; Online: Maternal DNA Methylation During Pregnancy: a Review.

Das, Jagyashila / Maitra, Arindam

Reproductive sciences (Thousand Oaks, Calif.)

2021 Volume 28, Issue 10, Page(s) 2758–2769

Abstract: Multiple environmental, behavioral, and hereditary factors affect pregnancy. Recent studies suggest that epigenetic modifications, such as DNA methylation (DNAm), affect both maternal and fetal health during the period of gestation. Some of the pregnancy- ...

Abstract	Multiple environmental, behavioral, and hereditary factors affect pregnancy. Recent studies suggest that epigenetic modifications, such as DNA methylation (DNAm), affect both maternal and fetal health during the period of gestation. Some of the pregnancy-related risk factors can influence maternal DNAm, thus predisposing both the mother and the neonate to clinical adversities with long-lasting consequences. DNAm alterations in the promoter and enhancer regions modulate gene expression changes which play vital physiological role. In this review, we have discussed the recent advances in our understanding of maternal DNA methylation changes during pregnancy and its associated complications such as gestational diabetes and anemia, adverse pregnancy outcomes like preterm birth, and preeclampsia. We have also highlighted some major gaps and limitations in the area which if addressed might improve our understanding of pregnancy and its associated adverse clinical conditions, ultimately leading to healthy pregnancies and reduction of public health burden.
MeSH term(s)	DNA Methylation/genetics ; Epigenesis, Genetic/genetics ; Female ; Humans ; Maternal Health/trends ; Pregnancy ; Pregnancy Complications/diagnosis ; Pregnancy Complications/epidemiology ; Pregnancy Complications/genetics ; Pregnancy Outcome/epidemiology
Language	English
Publishing date	2021-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2276411-2
ISSN	1933-7205 ; 1933-7191
ISSN (online)	1933-7205
ISSN	1933-7191
DOI	10.1007/s43032-020-00456-4
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Article ; Online: Spontaneous preterm birth

Esha Bhattacharjee / Arindam Maitra

npj Genomic Medicine, Vol 6, Iss 1, Pp 1-

the underpinnings in the maternal and fetal genomes

2021 Volume 6

Abstract: Abstract Preterm birth (PTB) is a major cause of neonatal mortality and health complications in infants. Elucidation of its genetic underpinnings can lead to improved understanding of the biological mechanisms and boost the development of methods to ... ...

Abstract	Abstract Preterm birth (PTB) is a major cause of neonatal mortality and health complications in infants. Elucidation of its genetic underpinnings can lead to improved understanding of the biological mechanisms and boost the development of methods to predict PTB. Although recent genome-based studies of both mother and fetus have identified several genetic loci which might be implicated in PTB, these results suffer from a lack of consistency across multiple studies and populations. Moreover, results of functional validation of most of these findings are unavailable. Since medically indicated preterm deliveries have well-known heterogeneous causes, we have reviewed only those studies which investigated spontaneous preterm birth (sPTB) and have attempted to suggest probable biological mechanisms by which the implicated genetic factors might result in sPTB. We expect our review to provide a panoramic view of the genetics of sPTB.
Keywords	Medicine ; R ; Genetics ; QH426-470
Subject code	610
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: MAL expression downregulation through suppressive H3K27me3 marks at the promoter in HPV16-related cervical cancers is prognostically relevant and manifested by the interplay of novel MAL antisense long noncoding RNA AC103563.8, E7 oncoprotein and EZH2.

Sinha, Abarna / Ghosh, Abhisikta / Ghosh, Arnab / Mathai, Sonia / Bhaumik, Jaydip / Mukhopadhyay, Asima / Maitra, Arindam / Biswas, Nidhan K / Sengupta, Sharmila

Clinical epigenetics

2024 Volume 16, Issue 1, Page(s) 40

Abstract: Background: MAL (T-lymphocyte maturation-associated protein) is highly downregulated in most cancers, including cervical cancer (CaCx), attributable to promoter hypermethylation. Long noncoding RNA genes (lncGs) play pivotal roles in CaCx pathogenesis, ... ...

Abstract	Background: MAL (T-lymphocyte maturation-associated protein) is highly downregulated in most cancers, including cervical cancer (CaCx), attributable to promoter hypermethylation. Long noncoding RNA genes (lncGs) play pivotal roles in CaCx pathogenesis, by interacting with human papillomavirus (HPV)-encoded oncoproteins, and epigenetically regulating coding gene expression. Hence, we attempted to decipher the impact and underlying mechanisms of MAL downregulation in HPV16-related CaCx pathogenesis, by interrogating the interactive roles of MAL antisense lncRNA AC103563.8, E7 oncoprotein and PRC2 complex protein, EZH2. Results: Employing strand-specific RNA-sequencing, we confirmed the downregulated expression of MAL in association with poor overall survival of CaCx patients bearing HPV16, along with its antisense long noncoding RNA (lncRNA) AC103563.8. The strength of positive correlation between MAL and AC103563.8 was significantly high among patients compared to normal individuals. While downregulated expression of MAL was significantly associated with poor overall survival of CaCx patients bearing HPV16, AC103563.8 did not reveal any such association. We confirmed the enrichment of chromatin suppressive mark, H3K27me3 at MAL promoter, using ChIP-qPCR in HPV16-positive SiHa cells. Subsequent E7 knockdown in such cells significantly increased MAL expression, concomitant with decreased EZH2 expression and H3K27me3 marks at MAL promoter. In silico analysis revealed that both E7 and EZH2 bear the potential of interacting with AC103563.8, at the same binding domain. RNA immunoprecipitation with anti-EZH2 and anti-E7 antibodies, respectively, and subsequent quantitative PCR analysis in E7-silenced and unperturbed SiHa cells confirmed the interaction of AC103563.8 with EZH2 and E7, respectively. Apparently, AC103563.8 seems to preclude EZH2 and bind with E7, failing to block EZH2 function in patients. Thereby, enhanced EZH2 expression in the presence of E7 could potentially inactivate the MAL promoter through H3K27me3 marks, corroborating our previous results of MAL expression downregulation in patients. Conclusion: AC103563.8-E7-EZH2 axis, therefore, appears to crucially regulate the expression of MAL, through chromatin inactivation in HPV16-CaCx pathogenesis, warranting therapeutic strategy development.
MeSH term(s)	Female ; Humans ; Chromatin/metabolism ; DNA Methylation ; Down-Regulation ; Enhancer of Zeste Homolog 2 Protein/genetics ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Histones/metabolism ; Human papillomavirus 16/genetics ; Oncogene Proteins, Viral/genetics ; Oncogene Proteins, Viral/metabolism ; Papillomavirus E7 Proteins/genetics ; Papillomavirus E7 Proteins/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Uterine Cervical Neoplasms/pathology ; Myelin and Lymphocyte-Associated Proteolipid Proteins/genetics ; Myelin and Lymphocyte-Associated Proteolipid Proteins/metabolism
Chemical Substances	Chromatin ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; EZH2 protein, human (EC 2.1.1.43) ; Histones ; Oncogene Proteins, Viral ; Papillomavirus E7 Proteins ; RNA, Long Noncoding ; MAL protein, human ; Myelin and Lymphocyte-Associated Proteolipid Proteins
Language	English
Publishing date	2024-03-10
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553921-8
ISSN	1868-7083 ; 1868-7075
ISSN (online)	1868-7083
ISSN	1868-7075
DOI	10.1186/s13148-024-01651-9
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Article ; Online: Genome-wide temporal landscaping of DNA methylation in pregnant women delivering at term: a GARBH-InI study.

Das, Jagyashila / Wadhwa, Nitya / Natchu, Uma Cm / Thiruvengadam, Ramachandran / Kshetrapal, Pallavi / Bhatnagar, Shinjini / Majumder, Partha P / Maitra, Arindam

Epigenomics

2023 Volume 15, Issue 9, Page(s) 543–556

Abstract: Background: ...

Abstract	Background:
MeSH term(s)	Humans ; Female ; Pregnancy ; DNA Methylation ; Epigenesis, Genetic ; Pregnant Women ; Epigenome ; Longitudinal Studies
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2537199-X
ISSN	1750-192X ; 1750-1911
ISSN (online)	1750-192X
ISSN	1750-1911
DOI	10.2217/epi-2023-0145
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Article ; Online: Association of exosomal miR-96-5p and miR-146a-5p with the disease severity in dengue virus infection.

Pradhan, Aunji / Aneja, Ashish / Ghosh, Sahana / Devvanshi, Himadri / C, Deepika / Sahu, Risabh / Ross, Celil / Kshetrapal, Pallavi / Maitra, Arindam / Das, Saumitra

Journal of medical virology

2023 Volume 95, Issue 3, Page(s) e28614

Abstract: Exosomes are small extracellular vesicles secreted by cells and have a major role in cell-to-cell signaling. As dengue infection progresses from a mild to a severe form of infection, the exosome's microRNA (miRNA) composition might change, which may ... ...

Abstract	Exosomes are small extracellular vesicles secreted by cells and have a major role in cell-to-cell signaling. As dengue infection progresses from a mild to a severe form of infection, the exosome's microRNA (miRNA) composition might change, which may contribute to pathogenesis. In this study, a comprehensive analysis of serum exosomal miRNAs was performed and their involvement in dengue virus-induced disease progression in an Indian cohort was assessed. Small RNA-seq showed 50 differentially expressed exosomal miRNAs that were significantly dysregulated during dengue infection. After extensive validation, miR-96-5p was found to be significantly upregulated, whereas miR-146a-5p was significantly downregulated with the progression of disease to severe form. Interestingly, a strong positive correlation was found between the expression levels of miR-96-5p and miR-146a-5p and the platelet levels of the patients. Further, study of miR-146a-5p showed that it regulates the expression of the proteins which are involved in the immune responses. These results suggest that miR-96-5p and miR-146a-5p could be used as diagnostic and prognostic markers for dengue disease progression, in addition to the already available biochemical and pathological parameters.
MeSH term(s)	Humans ; Dengue/genetics ; Disease Progression ; MicroRNAs/metabolism ; Patient Acuity ; Virus Diseases ; Exosomes/genetics
Chemical Substances	MicroRNAs ; MIRN96 microRNA, human ; MIRN146 microRNA, human
Language	English
Publishing date	2023-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28614
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Article ; Online: Ocular conjunctival microbiome profiling in dry eye disease: A case control pilot study.

Gupta, Noopur / Chhibber-Goel, Jyoti / Gupta, Yogita / Mukherjee, Souvik / Maitra, Arindam / Sharma, Amit / Tandon, Radhika

Indian journal of ophthalmology

2023 Volume 71, Issue 4, Page(s) 1574–1581

Abstract: Purpose: Keratoconjunctivitis sicca (KCS) or dry eye disease (DED) is a multifactorial disease that results in discomfort, visual disturbance, and tear film instability with potential damage to the ocular surface. A pilot study was undertaken to ... ...

Abstract	Purpose: Keratoconjunctivitis sicca (KCS) or dry eye disease (DED) is a multifactorial disease that results in discomfort, visual disturbance, and tear film instability with potential damage to the ocular surface. A pilot study was undertaken to determine if there were any major substantial differences in the ocular microbiome in DED patients versus healthy controls. Methods: The bacterial communities residing in the conjunctiva of patients with DED (n = 4) and healthy controls (n = 4) were assessed by 16S ribosomal RNA (rRNA) gene sequencing of the V4-V5 region. Results: The phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were most dominant and accounted for 97% and 94.5% of all bacterial sequences in patients and controls, respectively. At the genus level, 27 bacterial genera were found with more than two-fold difference between patients and controls. Four of these - Acinetobacter, Corynebacterium, Lactobacillus, and Pseudomonas spp. - dominated the ocular microbiome of all subjects, but were proportionately lower in DED (16.5%) compared to controls (37.7%). Several bacterial genera were found to be unique in DED (34) and controls (24). Conclusion: This pilot study is an attempt to profile the ocular microbiome in patients with DED that demonstrated a higher concentration of microbial DNA compared to controls, with Firmicutes phyla dominating the bacterial population in patients with DED.
MeSH term(s)	Humans ; Pilot Projects ; Conjunctiva/microbiology ; Dry Eye Syndromes/diagnosis ; Microbiota ; Bacteria/genetics ; Tears ; Case-Control Studies
Language	English
Publishing date	2023-03-09
Publishing country	India
Document type	Journal Article
ZDB-ID	187392-1
ISSN	1998-3689 ; 0301-4738
ISSN (online)	1998-3689
ISSN	0301-4738
DOI	10.4103/ijo.IJO_1756_22
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Article ; Online: Unfurling the functional association between long intergenic noncoding RNAs (lincRNAs) and HPV16-related cervical cancer pathogenesis through weighted gene co-expression network analysis of differentially expressed lincRNAs and coding genes.

Sinha, Abarna / Ghosh, Sahana / Ghosh, Abhisikta / Ghosh, Arnab / Mathai, Sonia / Bhaumik, Jaydip / Mukhopadhyay, Asima / Maitra, Arindam / Biswas, Nidhan K / Sengupta, Sharmila

Carcinogenesis

2024

Abstract: Long intergenic noncoding RNAs (lincRNAs) do not overlap annotated coding genes and are located in intergenic regions, as opposed to antisense and sense-intronic lncRNAs, located in genic regions. LincRNAs influence gene expression profiles and are ... ...

Abstract	Long intergenic noncoding RNAs (lincRNAs) do not overlap annotated coding genes and are located in intergenic regions, as opposed to antisense and sense-intronic lncRNAs, located in genic regions. LincRNAs influence gene expression profiles and are thereby key to disease pathogenesis. In this study, we assessed the association between lincRNAs and HPV16-positive cervical cancer (CaCx) pathogenesis using weighted gene co-expression network analysis (WGCNA) with coding genes, comparing differentially expressed lincRNA and coding genes (DElincGs and DEcGs, respectively) in HPV16-positive patients with CaCx (n = 44) with those in HPV-negative healthy individuals (n = 34). Our analysis revealed five DElincG modules, co-expressing and correlating with DEcGs. We validated a substantial number of such module-specific correlations in the HPV16-positive cancer TCGA-CESC dataset. Four such modules, displayed significant correlations with patient traits, such as HPV16 physical status, lymph node involvement, and overall survival (OS), highlighting a collaborative effect of all genes within specific modules on traits. Using the DAVID bioinformatics knowledgebase, we identified the underlying biological processes associated with these modules as cancer development and progression-associated pathways. Next, we identified the top 10 DElincGs with the highest connectivity within each functional module. Focusing on the prognostic module hub genes, downregulated CTD-2619J13.13 expression was associated with poor patient OS. This lincRNA gene interacted with 25 coding genes of its module and was associated with such biological processes as keratinization loss and keratinocyte differentiation, reflecting severe disease phenotypes. This study has translational relevance in fighting various cancers with high mortality rates in underdeveloped countries.
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Journal Article
ZDB-ID	603134-1
ISSN	1460-2180 ; 0143-3334
ISSN (online)	1460-2180
ISSN	0143-3334
DOI	10.1093/carcin/bgae019
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Article ; Online: A nonsense variant in the Hexokinase 1 gene (HK1) causing severe non-spherocytic haemolytic anaemia: genetic analysis exemplifies ambiguity due to multiple Isoforms.

Jamwal, Manu / Aggarwal, Anu / Palodi, Arindam / Sharma, Prashant / Bansal, Deepak / Maitra, Arindam / Das, Reena

British journal of haematology

2019 Volume 186, Issue 5, Page(s) e142–e145

MeSH term(s)	Anemia, Hemolytic/genetics ; Codon, Nonsense ; Genetic Testing/methods ; Hexokinase/adverse effects ; Hexokinase/deficiency ; Humans ; Infant ; Male ; Protein Isoforms/genetics
Chemical Substances	Codon, Nonsense ; Protein Isoforms ; Hexokinase (EC 2.7.1.1)
Language	English
Publishing date	2019-05-23
Publishing country	England
Document type	Case Reports ; Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.15981
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Article ; Online: Overexpression of CD73 is associated with recurrence and poor prognosis of gingivobuccal oral cancer as revealed by transcriptome and deep immune profiling of paired tumor and margin tissues.

Chatterjee, Ankita / Chaudhary, Amrita / Ghosh, Arnab / Arun, Pattatheyil / Mukherjee, Geetashree / Arun, Indu / Maitra, Arindam / Biswas, Nidhan / Majumder, Partha P

Cancer medicine

2023 Volume 12, Issue 16, Page(s) 16774–16787

Abstract: Background: For various cancers, differences in response to treatment and subsequent survival period have been reported to be associated with variation in immune contextures.: Aim: We sought to identify whether such association exists in respect of ... ...

Abstract	Background: For various cancers, differences in response to treatment and subsequent survival period have been reported to be associated with variation in immune contextures. Aim: We sought to identify whether such association exists in respect of gingivobuccal oral cancer. Materials and methods: We performed deep immune profiling of tumor and margin tissues collected from 46 treatment naïve, Human Papillomavirus (HPV) negative, patients. Each patient was followed for 24 months and prognosis (recurrence/death) noted. Key findings were validated by comparing with TCGA-HNSC cohort data. Results: About 28% of patients showed poor post-treatment prognosis. These patients exhibited a high probability of recurrence even within 1 year and death within 2 years. There was restricted immune cell infiltration in tumor, but not in margin, among these patients. Reduced expression of eight immune-related genes (IRGs) (NT5E, THRA, RBP1, TLR4, ITGA6, BMPR1B, ITGAV, SSTR1) in tumor strongly predicted better quality of prognosis, both in our patient cohort and in TCGA-HNSC cohort. Tumors of patients with better prognosis were associated with (a) lower CD73+ cells with concomitant lower expression level of NT5E/CD73, (b) higher proportions of CD4+ and CD8+ T cells, B cells, NK cells, M1 macrophages, (c) higher %Granzyme+ cells, (d) higher TCR and BCR repertoire diversities. CD73 expression in tumor was associated with low CD8+ and CD4+ T cells, low immune repertoire diversity, and advanced cancer stage. Discussion and conclusion: High infiltration of anti-tumor immune cells in both tumors and margins results in good prognosis, while in patients with minimal infiltration in tumors in spite of high infiltration in margins results in poor prognosis. Targeted CD73 immune-checkpoint inhibition may improve clinical outcome.
MeSH term(s)	Humans ; Transcriptome ; Lymphocytes, Tumor-Infiltrating ; Prognosis ; Neoplasm Staging ; Mouth Neoplasms/pathology ; Tumor Microenvironment ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2023-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2659751-2
ISSN	2045-7634 ; 2045-7634
ISSN (online)	2045-7634
ISSN	2045-7634
DOI	10.1002/cam4.6299
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