Publications by authors named "Rajesh Pandey"

111 Publications

Development of central precocious puberty following cannabinoid use for paediatric epilepsy: causal or coincidence?

BMJ Case Rep 2021 Apr 15;14(4). Epub 2021 Apr 15.

Department of Paediatrics, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, Birmingham, UK.

Research suggests a role for cannabidiol oil in managing certain forms of paediatric onset epilepsy. However, studies on the impact of cannabis on the hypothalamo-pituitary-gonadal (HPG) axis have conflicting results. Delta-9-tetrahydrocannabinol (Δ9-THC) acutely inhibits gonadotropin-releasing hormone in the hypothalamus, reducing testosterone levels by 65% in rhesus monkeys. Additionally, there have been reports of pubertal arrest and delayed puberty in male cannabis users. In contrast, other studies have reported higher testosterone levels following long-term cannabis use.A 2-year-old boy presented with testicular enlargement, increased penile length and growth of coarse pubic hair developing over 6 months. His mother procured cannabidiol oil online, which he started taking 7 months earlier for severe epilepsy refractory to medical management. Subsequent investigations confirmed central precocious puberty. While it is unclear whether the precocious puberty is a direct consequence of HPG axis activation by Δ9-THC, this case demonstrates a temporal association between cannabis use and development of precocious puberty.
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http://dx.doi.org/10.1136/bcr-2020-239678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055150PMC
April 2021

Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India.

Front Med (Lausanne) 2021 9;8:631769. Epub 2021 Mar 9.

International Centre for Genetic Engineering and Biotechnology, New Delhi, India.

SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection. Nasopharyngeal (NP), oropharyngeal (OP) and whole blood (WB) samples were collected from paired samples of four individuals who were suspected of SARS-CoV-2 reinfection based on distinct clinical episodes and RT-PCR tests. Details from their case record files and investigations were documented. RNA was extracted from the NP and OP samples and subjected to WGS, and the nucleotide and amino acid sequences were subjected to genome and protein-based functional annotation analyses. Serial serology was performed for Anti-N IgG, Anti- S1 RBD IgG, and sVNT (surrogate virus neutralizing test). Three patients were more symptomatic with lower Ct values and longer duration of illness. Seroconversion was detected soon after the second episode in three patients. WGS generated a genome coverage ranging from 80.07 to 99.7%. Phylogenetic analysis revealed sequences belonged to G, GR and "Other" clades. A total of 42mutations were identified in all the samples, consisting of 22 non-synonymous, 17 synonymous, two in upstream, and one in downstream regions of the SARS-CoV-2 genome. Comparative genomic and protein-based annotation analyses revealed differences in the presence and absence of specific mutations in the virus sequences from the two episodes in all four paired samples. Based on the criteria of genome variations identified by whole genome sequencing and supported by clinical presentation, molecular and serological tests, we were able to confirm reinfections in two patients, provide weak evidence of reinfection in the third patient and unable to rule out a prolonged infection in the fourth. This study emphasizes the importance of detailed analyses of clinical and serological information as well as the virus's genomic variations while assessing cases of SARS-CoV-2 reinfection.
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http://dx.doi.org/10.3389/fmed.2021.631769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7985553PMC
March 2021

Mapping of the benzoate metabolism by human gut microbiome indicates food-derived metagenome evolution.

Sci Rep 2021 Mar 10;11(1):5561. Epub 2021 Mar 10.

Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.

Sodium benzoate is one of the widely used food preservatives and its metabolism in the human body has been studied only with the host perspective. Despite the human gut microbiome being considered as a virtual human organ, its role in benzoate metabolism is yet to be elucidated. The current study uses a multi-omic approach to rationalize the role of human gut microbes in benzoate metabolism. Microbial diversity analysis with multiple features synchronously indicates the dominance of Bacteroidetes followed by Firmicutes, Actinobacteria, and Proteobacteria. Metagenomic exploration highlights the presence of benzoate catabolic protein features. These features were mapped on to the aerobic and anaerobic pathways of benzoate catabolism. Benzoate catabolism assays identified statistically significant metabolites (P < 0.05) associated with the protocatechuate branch of the beta-ketoadipate pathway of the benzoate metabolism. Analysis of the 201 human gut metagenomic datasets across diverse populations indicates the omnipresence of these features. Enrichment of the benzoate catabolic protein features in human gut microbes rationalizes their role in benzoate catabolism, as well as indicates food-derived microbiome evolution.
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http://dx.doi.org/10.1038/s41598-021-84964-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946887PMC
March 2021

Noncoding RNAs: modulators and modulatable players during infection-induced stress response.

Brief Funct Genomics 2021 03;20(1):28-41

The human genome has an almost equal distribution of unique and transposable genetic elements. Although at the transcriptome level, a relatively higher contribution from transposable elements derived RNA has been reported. This is further highlighted with evidence from pervasive transcription. Of the total RNA, noncoding RNAs (ncRNAs) are significant contributors to the transcriptome pool with sizeable fraction from repetitive elements of the human genome, inclusive of Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs). ncRNAs are increasingly being implicated in diverse functional roles especially during conditions of stress. These stress responses are driven through diverse mediators, inclusive of long and short ncRNAs. ncRNAs such as MALAT1, GAS5, miR-204 and miR-199a-5p have been functionally involved during oxidative stress, endoplasmic reticulum (ER) stress and unfolded protein response (UPR). Also, within SINEs, Alu RNAs derived from primate-specific Alu repeats with ~11% human genome contribution, playing a significant role. Pathogenic diseases, including the recent COVID-19, leads to differential regulation of ncRNAs. Although, limited evidence suggests the need for an inquest into the role of ncRNAs in determining the host response towards pathogen challenge.
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http://dx.doi.org/10.1093/bfgp/elaa026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7929421PMC
March 2021

Multiple Alu Exonization in 3'UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge.

Genome Biol Evol 2021 Jan;13(1)

Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.

Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Our study highlights how exonized Alus could nucleate large-scale mRNA-miRNA interactions. Using a functional genomics approach, we characterize a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) that has exonization of 23 Alus in its 3'UTR. CYP20A1_Alu-LT, confirmed by 3'RACE, is an outlier in length (9 kb 3'UTR) and widely expressed. Using publically available data sets, we demonstrate its expression in higher primates and presence in single nucleus RNA-seq of 15,928 human cortical neurons. miRanda predicts ∼4,700 miRNA recognition elements (MREs) for ∼1,000 miRNAs, primarily originated within these 3'UTR-Alus. CYP20A1_Alu-LT could be a potential multi-miRNA sponge as it harbors ≥10 MREs for 140 miRNAs and has cytosolic localization. We further tested whether expression of CYP20A1_Alu-LT correlates with mRNAs harboring similar MRE targets. RNA-seq with conjoint miRNA-seq analysis was done in primary human neurons where we observed CYP20A1_Alu-LT to be downregulated during heat shock response and upregulated in HIV1-Tat treatment. In total, 380 genes were positively correlated with its expression (significantly downregulated in heat shock and upregulated in Tat) and they harbored MREs for nine expressed miRNAs which were also enriched in CYP20A1_Alu-LT. MREs were significantly enriched in these 380 genes compared with random sets of differentially expressed genes (P = 8.134e-12). Gene ontology suggested involvement of these genes in neuronal development and hemostasis pathways thus proposing a novel component of Alu-miRNA-mediated transcriptional modulation that could govern specific physiological outcomes in higher primates.
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http://dx.doi.org/10.1093/gbe/evaa233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7802813PMC
January 2021

Nature and dimensions of the systemic hyper-inflammation and its attenuation by convalescent plasma in severe COVID-19.

J Infect Dis 2021 Jan 12. Epub 2021 Jan 12.

IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India.

Novel coronavirus SARS-CoV2, causing coronavirus disease 2019 or COVID-19, led to significant morbidity and mortality. While most suffer from mild symptoms, some patients progress to a severe disease with acute respiratory distress syndrome (ARDS) and an associated systemic hyper-inflammation. First to characterize key cytokines and their dynamics in this hyper-inflammatory condition, we assessed abundance and correlative expression of a panel of forty eight cytokines in patients progressing to ARDS, as compared to patients with mild disease. Then in an ongoing randomized control trial of convalescent plasma therapy (CPT), we analyzed rapid effects of CPT on the systemic cytokine dynamics, as a correlate for the level of hypoxia experienced by the patients. We identified an anti-inflammatory role of CPT independent of its neutralizing antibody content. Neutralizing antibodies as well as reductions in circulating interleukin-6 and interferon gamma induced protein 10, contributed to marked rapid reductions in hypoxia in response to CPT.
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http://dx.doi.org/10.1093/infdis/jiab010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7928875PMC
January 2021

Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature.

Front Microbiol 2020 16;11:588545. Epub 2020 Oct 16.

Department of Biochemistry, Maharshi Dayanand University, Rohtak, India.

Vanillin is a phenolic food additive commonly used for flavor, antimicrobial, and antioxidant properties. Though it is one of the widely used food additives, strategies of the human gut microbes to evade its antimicrobial activity await extensive elucidation. The current study explores the human gut microbiome with a multi-omics approach to elucidate its composition and metabolic machinery to counter vanillin bioactivity. A combination of SSU rRNA gene diversity, metagenomic RNA features diversity, phylogenetic affiliation of metagenome encoded proteins, uniformly ( = 0.99) indicates the abundance of Bacteroidetes followed by Firmicutes and Proteobacteria. Manual curation of metagenomic dataset identified gene clusters specific for the vanillin metabolism (, and ) and intermediary metabolic pathways ( and operon). Metagenomic dataset comparison identified the omnipresence of vanillin catabolic features across diverse populations. The metabolomic analysis brings forth the functionality of the vanillin catabolic pathway through the Protocatechuate branch of the beta-ketoadipate pathway. These results highlight the human gut microbial features and metabolic bioprocess involved in vanillin catabolism to overcome its antimicrobial activity. The current study advances our understanding of the human gut microbiome adaption toward changing dietary habits.
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http://dx.doi.org/10.3389/fmicb.2020.588545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605359PMC
October 2020

Threading the Pieces Together: Integrative Perspective on SARS-CoV-2.

Pathogens 2020 Nov 4;9(11). Epub 2020 Nov 4.

INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has challenged the research community globally to innovate, interact, and integrate findings across hierarchies. Research on SARS-CoV-2 has produced an abundance of data spanning multiple parallels, including clinical data, SARS-CoV-2 genome architecture, host response captured through transcriptome and genetic variants, microbial co-infections (metagenome), and comorbidities. Disease phenotypes in the case of COVID-19 present an intriguing complexity that includes a broad range of symptomatic to asymptomatic individuals, further compounded by a vast heterogeneity within the spectrum of clinical symptoms displayed by the symptomatic individuals. The clinical outcome is further modulated by the presence of comorbid conditions at the point of infection. The COVID-19 pandemic has produced an expansive wealth of literature touching many aspects of SARS-CoV-2 ranging from causal to outcome, predisposition to protective (possible), co-infection to comorbidity, and differential mortality globally. As challenges provide opportunities, the current pandemic's challenge has underscored the need and opportunity to work for an integrative approach that may be able to thread together the multiple variables. Through this review, we have made an effort towards bringing together information spanning across different domains to facilitate researchers globally in pursuit of their response to SARS-CoV-2.
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http://dx.doi.org/10.3390/pathogens9110912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7694192PMC
November 2020

Integrated genomic view of SARS-CoV-2 in India.

Wellcome Open Res 2020 3;5:184. Epub 2020 Aug 3.

Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India.

India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
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http://dx.doi.org/10.12688/wellcomeopenres.16119.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7506191PMC
August 2020

Lactose-free infant formula does not change outcomes of neonatal abstinence syndrome (NAS): a randomized clinical trial.

J Perinatol 2021 Mar 31;41(3):598-605. Epub 2020 Aug 31.

Department of Pediatrics, MetroHealth Medical Center, Case Western Reserve University, Cleveland, OH, USA.

Objective: To determine if lactose-free formula, compared to lactose-containing formula, decreases the cumulative morphine dose required to treat neonatal abstinence syndrome (NAS).

Study Design: In a double-blind clinical trial, we randomized 74 infants (36-42 weeks gestation) at risk for developing NAS due to in-utero exposure to opioids to receive either lactose-free (Similac Sensitive®) or lactose-containing (Similac Advance®) infant formula. The primary outcome measure was the cumulative dose of morphine used for the treatment of NAS during the first 14 days of life.

Results: Data on 69 (4 withdrew consent and 1 ineligible)/74 randomized infants were analyzed. Patient characteristics between the infant groups fed lactose-free (n = 34) vs. lactose-containing (n = 35) infant formula were similar except more common maternal heroin abuse in the latter group (p = 0.013). Cumulative morphine dose (20.7 ± 19.8 vs. 23 ± 23.5 mg, p = 0.61) between the two groups were similar.

Conclusion: Lactose-free vs. lactose-containing infant formula did not change the outcomes of infants with NAS.
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http://dx.doi.org/10.1038/s41372-020-00797-7DOI Listing
March 2021

Spontaneous parieto-occipital haematoma: lessons for the primary care clinician.

Authors:
Rajesh Pandey

BJGP Open 2020 Aug 25;4(3). Epub 2020 Aug 25.

Priory Road Surgery, Hastings, UK

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http://dx.doi.org/10.3399/bjgpopen20X101104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465588PMC
August 2020

Hypoxia Inducible Factor-1α: The Curator of Gut Homeostasis.

Front Cell Infect Microbiol 2020 15;10:227. Epub 2020 May 15.

Department of Biochemistry, Maharshi Dayanand University, Rohtak, India.

The human gut microbiome is a stratified and resilient ecosystem co-inhabited by a diverse and dynamic pool of microorganisms. Microbial selection, establishment, and colonization are modulated through a complex molecular network of host-microbial interactions. These molecular bioprocesses ensure the taxonomic composition of the mature human gut microbiome. The human gut microbiome plays a vital role in host health; otherwise, any microbial dysbiosis could predispose to the onset of physiological and metabolic disorder/s. Focussed research are being carried out to identify key molecular agents defining gut homeostasis. These molecules hold the potential to develop effective therapeutic solutions for microbial dysbiosis-associated human disorders. Of these, Hypoxia-inducible factor-1α (HIF-1α) is a central player in host-microbial crosstalk to maintain gut homeostasis. Human gut microbial metabolites regulate its cellular stability, which in turn regulates various cellular processes required for the stable gut microbiome. In the present review, an effort has been made to summarize the key role of HIF-1α to maintain gut homeostasis.

Highlights: - Explain the molecular process of host microbial molecular interactions.- Establish the explicit role of HIF-1α in intestinal epithelial integrity and gut health.- Regulation of HIF-1α by human gut commensals and vice a versa.- Regulation of the host immune response for survival and colonization of human gut commensal.
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http://dx.doi.org/10.3389/fcimb.2020.00227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242652PMC
May 2020

Lower versus traditional treatment threshold for neonatal hypoglycaemia: No difference between the groups at 18 months of age, awaiting long-term outcomes.

Acta Paediatr 2020 10 12;109(10):2164-2165. Epub 2020 May 12.

McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1111/apa.15314DOI Listing
October 2020

Characterization and evaluation of mycosterol secreted from endophytic strain of Gymnema sylvestre for inhibition of α-glucosidase activity.

Sci Rep 2019 11 21;9(1):17302. Epub 2019 Nov 21.

Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.

Endophytic fungi produce various types of chemicals for establishment of niche within the host plant. Due to symbiotic association, they secrete pharmaceutically important bioactive compounds and enzyme inhibitors. In this research article, we have explored the potent α-glucosidse inhibitor (AGI) produced from Fusarium equiseti recovered from the leaf of Gymnema sylvestre through bioassay-guided fraction. This study investigated the biodiversity, phylogeny, antioxidant activity and α-glucosidse inhibition of endophytic fungi isolated from Gymnema sylvestre. A total of 32 isolates obtained were grouped into 16 genera, according to their morphology of colony and spores. A high biodiversity of endophytic fungi were observed in G. sylvestre with diversity indices. Endophytic fungal strain Fusarium equiseti was identified through DNA sequencing and the sequence was deposited in GenBank database (https://ncbi.nim.nih.gov) with acession number: MF403109. The characterization of potent compound was done by FTIR, LC-ESI-MS and NMR spectroscopic analysis with IUPAC name 17-(5-ethyl-6-methylheptan-2-yl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a] phenanthren-3-ol. The isolated bioactive compound showed significant α-amylase and α-glucosidase inhibition activity with IC values, 4.22 ± 0.0005 µg/mL and 69.72 ± 0.001 µg/mL while IC values of acarbose was 5.75 ± 0.007 and 55.29 ± 0.0005 µg/mL respectively. This result is higher in comparison to other previous study. The enzyme kinetics study revealed that bioactive compound was competitive inhibitor for α-amylase and α-glucosidase. In-silico study showed that bioactive compound binds to the binding site of α-amylase, similar to that of acarbose but with higher affinity. The study highlights the importance of endophytic fungi as an alternative source of AGI (α-glucosidase inhibition) to control the diabetic condition in vitro.
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http://dx.doi.org/10.1038/s41598-019-53227-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872796PMC
November 2019

The development of a high throughput drug-responsive model of white adipose tissue comprising adipogenic 3T3-L1 cells in a 3D matrix.

Biofabrication 2019 12 11;12(1):015018. Epub 2019 Dec 11.

OxSyBio Ltd, Building R27, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, United Kingdom.

Adipose models have been applied to mechanistic studies of metabolic diseases (such as diabetes) and the subsequent discovery of new therapeutics. However, typical models are either insufficiently complex (2D cell cultures) or expensive and labor intensive (mice/in vivo). To bridge the gap between these models and in order to better inform pre-clinical studies we have developed a drug-responsive 3D model of white adipose tissue (WAT). Here, spheroids (680 ± 60 μm) comprising adipogenic 3T3-L1 cells encapsulated in 3D matrix were fabricated manually on a 96 well scale. Spheroids were highly characterised for lipid morphology, selected metabolite and adipokine secretion, and gene expression; displaying significant upregulation of certain adipogenic-specific genes compared with a 2D model. Furthermore, induction of lipolysis and promotion of lipogenesis in spheroids could be triggered by exposure to 8-br-cAMP and oleic-acid respectively. Metabolic and high content imaging data of spheroids exposed to an adipose-targeting drug, rosiglitazone, resulted in dose-responsive behavior. Thus, our 3D WAT model has potential as a powerful scalable tool for compound screening and for investigating adipose biology.
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http://dx.doi.org/10.1088/1758-5090/ab56feDOI Listing
December 2019

A Patient of Severe Ankylosing Spondylitis with Severe Dilated Cardiomyopathy: What is the Treatment Option?

J Assoc Physicians India 2018 Jun;66(6):110

Professor, Dept. of Medicine, Medical College, Kolkata, West Bengal.

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June 2018

Multiple Cerebral Venous Sinus Thrombosis as Fist Manifestation of Primary Anti-Phospholipid Antibody Syndrome.

J Assoc Physicians India 2018 Oct;66(10):11-12

Resident, Dept. of Medicine, Medical College, Kolkata, West Bengal.

Antiphospholipid antibody syndrome (APS) is an autoimmune disorder, mainly found in young females, presenting with vascular thrombosis and/or obstetric complications. Thrombosis at anatomically significant sites may lead to considerable morbidity and/or mortality. We here present a case of primary APS presenting with sudden onset bilateral multiple cerebral venous sinus thrombosis. The patient, a 17 year old female with no prior rheumatological history, presented with sudden onset bilateral painful blindness and massive proptosis. MRI venography was instrumental in diagnosis. She also had significant thrombocytopenia. Except for the visual dimness, the other symptoms responded to therapy. Such massive cerebral venous thrombosis is extremely rare in primary APS.
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October 2018

Array-based DNA methylation profiling reveals peripheral blood differential methylation in male infertility.

Fertil Steril 2019 07 15;112(1):61-72.e1. Epub 2019 May 15.

Division of Endocrinology, Central Drug Research Institute, Lucknow, India. Electronic address:

Objective: To study peripheral blood DNA differential methylation in oligozoospermic infertile men in comparison with normozoospermic fertile controls.

Design: Case-control study.

Setting: Reproductive biology laboratory.

Patients(s): Azoospermic and oligozoospermic infertile patients (n = 6) and normozoospermic fertile controls (n = 6) in the discovery phase, and oligo/asthenozoospermic infertile men (n = 11) and normozoospermic fertile controls (n = 10) in the validation phase.

Intervention(s): Blood samples drawn from all participants, DNA isolation and methylation analysis.

Main Outcome Measure(s): DNA methylation values analyzed using genomewide methylation 450K BeadChip array, followed by deep sequencing of selected regions for methylation analysis in the neighborhood regions of differentially methylated CpGs.

Result(s): We found 329 differentially methylated CpG spots, out of which 245 referred to the genes, representing 170 genes. Deep-sequencing analysis confirmed the methylation pattern suggested by 450K array. A thorough literature search suggested that 38 genes play roles in spermatogenesis (PDHA2, PARP12, FHIT, RPTOR, GSTM1, GSTM5, MAGI2, BCAN, DDB2, KDM4C, AGPAT3, CAMTA1, CCR6, CUX1, DNAH17, ELMO1, FNDC3B, GNRHR, HDAC4, IRS2, LIF, SMAD3, SOD3, TALDO1, TRIM27, GAA, PAX8, RNF39, HLA-C, HLA-DRB6), are testis enriched (NFATC1, NMNAT3, PIAS2, SRPK2, WDR36, WWP2), or show methylation differences between infertile cases and controls (PTPRN2, RPH3AL).

Conclusion(s): We found a statistically significant correlation between peripheral blood DNA methylation and male infertility, raising the hope that epigenome-based blood markers can be used for screening male infertility risk. The study also identified new candidates for spermatogenesis and fertility.
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http://dx.doi.org/10.1016/j.fertnstert.2019.03.020DOI Listing
July 2019

Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing.

Nucleic Acids Res 2019 06;47(11):5852-5866

CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.

Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3'-5' RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3'-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.
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http://dx.doi.org/10.1093/nar/gkz371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582341PMC
June 2019

Cerebral venous sinus thrombosis as a warning signal for double positive crescentic glomerulonephritis in a young male with complete renal recovery.

Saudi J Kidney Dis Transpl 2018 Nov-Dec;29(6):1488-1493

Department of Renal Pathology, Lal Path Lab, New Delhi, India.

Double positive crescentic glomerulonephritis is relatively rare in young population and has variable outcomes. Although increased incidence of deep venous thrombosis in antineutrophil cytoplasmic antibody-associated vasculitis has been reported, cerebral venous sinus thrombosis (CVT) is very rare. We present a young male who presented with CVT followed by rapidly progressive crescentic glomerulonephritis and with appropriate therapeutic modalities he had complete renal and partial neurological recovery.
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http://dx.doi.org/10.4103/1319-2442.248291DOI Listing
October 2019

Genome-wide differential methylation analyses identifies methylation signatures of male infertility.

Hum Reprod 2018 12;33(12):2256-2267

Division of Endocrinology, Central Drug Research Institute, Lucknow, India.

Study Question: Do methylation changes in sperm DNA correlate with infertility?

Study Answer: Loss of spermatogenesis and fertility was correlated with 1680 differentially-methylated CpGs (DMCs) across 1052 genes.

What Is Known Already: Methylation changes in a number of genes have been correlated with reduced sperm count and motility.

Study Design, Size, Duration: This case-control study used spermatozoal DNA from 38 oligo-/oligoastheno-zoospermic infertile patients and 26 normozoospermic fertile men.

Participants/materials, Settings, Methods: Genome-wide methylation analysis was undertaken using 450 K BeadChip on spermatozoal DNA from six infertile and six fertile men to identify DMCs. This was followed by deep sequencing of spermatozoal DNA from 32 infertile patients and 20 fertile controls.

Main Results And The Role Of Chance: A total of 1680 DMCs were identified, out of which 1436 were hypermethylated and 244 were hypomethylated. Classification of DMCs according to the genes identified BCAN, CTNNA3, DLGAP2, GATA3, MAGI2 and TP73 among imprinted genes, SPATA5, SPATA7, SPATA16 and SPATA22 among spermatogenesis-associated genes, KDM4C and JMJD1C, EZH2 and HDAC4 among genes which regulate methylation and gene expression, HLA-C, HLA-DRB6 and HLA-DQA1 among complementation and immune response genes, and CRISPLD1, LPHN3 and CPEB2 among other genes. Genes showing significant differential methylation in deep sequencing, i.e. HOXB1, GATA3, EBF3, BCAN and TCERG1L, are strong candidates for further investigations. The role of chance was ruled out by deep sequencing of select genes.

Large-scale Data: N/A.

Limitations, Reason For Caution: Genome-wide analyses are fairly accurate, but may not be exactly validated in replication studies across all DMCs. We used the 't' test in the genome-wide methylation analysis, whereas other tests could provide a more robust and powerful analysis.

Wider Implications Of The Findings: DMCs can serve as markers for inclusion in infertility screening panels, particularly those in the genes showing differential methylation consistent with previous studies. The genes validated by deep sequencing are strong candidates for investigations of their roles in spermatogenesis.

Study Funding/competing Interest(s): The study was funded by the Council of Scientific and Industrial Research (CSIR), Govt. of India with grant number BSC0101 awarded to Rajender Singh. None of the authors has any competing interest to declare.
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http://dx.doi.org/10.1093/humrep/dey319DOI Listing
December 2018

miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin

J Endocrinol 2018 10 1;239(1):1–17. Epub 2018 Oct 1.

Division of Pharmacology, CSIR-Central Drug Research Institute, Lucknow, India

miRNA has been known to regulate diverse cellular and molecular functions. In the earlier study, we have reported that adipocytes differentiated from human mesenchymal stem cells (hMSC) on 72-h chronic insulin (CI) treatment exhibit insulin resistance (IR). Present study has further explored above model to investigate the role of early expressed miRNAs within human adipocytes to modulate differential adipokine expression as observed during IR. Our results highlight that miR-876-3p regulate glucose homeostasis and its dysregulation leads to IR. We found that miR-876-3p level is a critical determinant of adiponectin expression by virtue of its target within adiponectin 3′UTR. Regulatory effect of miR-876-3p impacts crosstalk between adiponectin and insulin signaling. Rosiglitazone treatment in CI-induced IR adipocytes drastically reduced miR-876-3p expression and increased adiponectin level. In line with this, lentiviral-mediated inhibition of miR-876-3p expression ameliorated CI and high-fat diet (HFD)-induced IR in adipocytes differentiated from hMSC and C57BL/6 mice, respectively. Our findings thus suggest that modulating miR-876-3p expression could provide novel opportunities for therapeutic intervention of obesity-associated metabolic syndrome.
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http://dx.doi.org/10.1530/JOE-17-0387DOI Listing
October 2018

First Degree Relatives of Patients with Celiac Disease Harbour an Intestinal Transcriptomic Signature that Might Protect them from Enterocyte Damage.

Clin Transl Gastroenterol 2018 10 8;9(10):195. Epub 2018 Oct 8.

Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, 110029, India.

Introduction: Celiac disease (CeD) is an autoimmune enteropathy which affects approximately 0.7% of the global population. While first-degree relatives (FDR) of patients with CeD have a 7.5% risk of developing enteropathy, many remain protected. Therefore, intestinal mucosa of FDR might have protective compensatory mechanisms against immunological injury. We have explored the protective mechanisms that may be active in intestinal mucosa of FDR.

Methods: Intestinal mucosal biopsies (4-5 pieces) from treatment naïve patients with CeD (n = 12), FDR (n = 12) (anti-tTG negative) and controls (n = 12) (anti-tTG negative) were obtained from each individual and subjected to microarray analysis using HT-12-v4 Human Expression BeadChips (Illumina). Differential gene expression analysis was carried out among CeD, FDR and controls; and resulting gene lists were analyzed using gene ontology and pathway enrichment tools.

Results: Patients with CeD, FDR and control groups displayed significant differential gene expression. Thirty seven genes were upregulated and 372 were downregulated in the intestinal mucosa of FDR in comparison to CeD and controls. Pseudogenes constituted about 18% (315/1751) of FDR differentially expressed genes, and formed "clusters" that associated uniquely with individual study groups. The three study groups segregated into distinct clusters in unsupervised (PCA) and supervised (random forests) modelling approaches. Pathways analysis revealed an emphasis on crypt-villous maintenance and immune regulation in the intestinal mucosa of FDR.

Conclusions: Our analysis suggests that the intestinal mucosa of celiac FDR consist of a unique molecular phenotype that is distinct from CeD and controls. The transcriptomic landscape of FDR promotes maintenance of crypt-villous axis and modulation of immune mechanisms. These differences clearly demonstrate the existence of compensatory protective mechanisms in the FDR intestinal mucosa.
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http://dx.doi.org/10.1038/s41424-018-0059-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174158PMC
October 2018

Does inhaled budesonide for bronchopulmonary dysplasia affect the neurodevelopmental outcomes?

J Perinatol 2018 12 5;38(12):1607-1609. Epub 2018 Oct 5.

McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41372-018-0239-zDOI Listing
December 2018

Large scale changes in the transcriptome of Eisenia fetida during regeneration.

PLoS One 2018 27;13(9):e0204234. Epub 2018 Sep 27.

CSIR - Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.

Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum Annelida, in which the genomes of the marine oligochaete Capitella telata and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the transcriptomic changes in Eisenia fetida (Indian isolate) during regeneration. Following injury, E. fetida regenerates the posterior segments in a time spanning several weeks. We analyzed gene expression changes both in the newly regenerating cells and in the adjacent tissue, at early (15days post amputation), intermediate (20days post amputation) and late (30 days post amputation) by RNAseq based de novo assembly and comparison of transcriptomes. We also generated a draft genome sequence of this terrestrial red worm using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm showed that many miRNA gene families have undergone extensive duplications. Sox4, a master regulator of TGF-beta mediated epithelial-mesenchymal transition was induced in the newly regenerated tissue. Genes for several proteins such as sialidases and neurotrophins were identified amongst the differentially expressed transcripts. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. We identified 315 novel differentially expressed transcripts in the transcriptome, that have no homolog in any other species. Surprisingly, 82% of these novel differentially expressed transcripts showed poor potential for coding proteins, suggesting that novel ncRNAs may play a critical role in regeneration of earthworm.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204234PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160089PMC
March 2019

S9A Serine Protease Engender Antigenic Gluten Catabolic Competence to the Human Gut Microbe.

Indian J Microbiol 2018 Sep 27;58(3):294-300. Epub 2018 Apr 27.

1Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana 124001 India.

The human gut microbiome has a significant role in host physiology; however its role in gluten catabolism is debatable. Present study explores the role of human gut microbes in gluten catabolism and a native human gut microbe sp. HM71 was identified. SSU rDNA analysis has described human gut microbiome structure and also confirmed the permanent residentship of sp. HM71. Catabolic potential of sp. HM71 to cleave antigenic gluten peptides indicates presence of candidate gene encoding biocatalytic machinery. Genome analysis has identified the presence of gene encoding S9A serine protease family-prolyl endopeptidase, with Ser591, Asp664 and His685 signature residues. sp. HM71 prolyl endopeptidase activity was found optimal at pH 7.0 and 37 °C with a of 35.53 μmol and specifically cleaves at proline residue. Current study describes the gluten catabolism potential of sp. HM71 depicting possible role of human gut microbes in gluten catabolism to confer resistance mechanisms for the onset of celiac diseases in populations with gluten diet.
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http://dx.doi.org/10.1007/s12088-018-0732-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6023808PMC
September 2018

Differential strengths of molecular determinants guide environment specific mutational fates.

PLoS Genet 2018 05 29;14(5):e1007419. Epub 2018 May 29.

CSIR- Institute of Genomics and Integrative Biology, New Delhi, India.

Organisms maintain competitive fitness in the face of environmental challenges through molecular evolution. However, it remains largely unknown how different biophysical factors constrain molecular evolution in a given environment. Here, using deep mutational scanning, we quantified empirical fitness of >2000 single site mutants of the Gentamicin-resistant gene (GmR) in Escherichia coli, in a representative set of physical (non-native temperatures) and chemical (small molecule supplements) environments. From this, we could infer how different biophysical parameters of the mutations constrain molecular function in different environments. We find ligand binding, and protein stability to be the best predictors of mutants' fitness, but their relative predictive power differs across environments. While protein folding emerges as the strongest predictor at minimal antibiotic concentration, ligand binding becomes a stronger predictor of mutant fitness at higher concentration. Remarkably, strengths of environment-specific selection pressures were largely predictable from the degree of mutational perturbation of protein folding and ligand binding. By identifying structural constraints that act as determinants of fitness, our study thus provides coarse mechanistic insights into the environment specific accessibility of mutational fates.
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http://dx.doi.org/10.1371/journal.pgen.1007419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993328PMC
May 2018

A-C Estrogens as Potent and Selective Estrogen Receptor-Beta Agonists (SERBAs) to Enhance Memory Consolidation under Low-Estrogen Conditions.

J Med Chem 2018 06 4;61(11):4720-4738. Epub 2018 Jun 4.

Department of Pharmaceutical Sciences, Center for Structure-Based Drug Design and Development , Concordia University Wisconsin , Mequon , Wisconsin 53097 , United States.

Estrogen receptor-beta (ERβ) is a drug target for memory consolidation in postmenopausal women. Herein is reported a series of potent and selective ERβ agonists (SERBAs) with in vivo efficacy that are A-C estrogens, lacking the B and D estrogen rings. The most potent and selective A-C estrogen is selective for activating ER relative to seven other nuclear hormone receptors, with a surprising 750-fold selectivity for the β over α isoform and with ECs of 20-30 nM in cell-based and direct binding assays. Comparison of potency in different assays suggests that the ER isoform selectivity is related to the compound's ability to drive the productive conformational change needed to activate transcription. The compound also shows in vivo efficacy after microinfusion into the dorsal hippocampus and after intraperitoneal injection (0.5 mg/kg) or oral gavage (0.5 mg/kg). This simple yet novel A-C estrogen is selective, brain penetrant, and facilitates memory consolidation.
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http://dx.doi.org/10.1021/acs.jmedchem.7b01601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217030PMC
June 2018