Papers by Arpita Mukhopadhyay
Scientific Reports, Dec 27, 2021
Venous plasma metabolomics is a potent and highly sensitive tool for identifying and measuring me... more Venous plasma metabolomics is a potent and highly sensitive tool for identifying and measuring metabolites of interest in human health and disease. Accurate and reproducible insights from such metabolomic studies require extreme care in removing preanalytical confounders; one of these is the duration of tourniquet application when drawing the venous blood sample. Using an untargeted plasma metabolomics approach, we evaluated the effect of varying durations of tourniquet application on the variability in plasma metabolite concentrations in five healthy female subjects. Tourniquet application introduced appreciable variation in the metabolite abundances: 73% of the identified metabolites had higher temporal variation compared to interindividual variation [Intra-Class Correlation (ICC) > 0.50]. As such, we recommend tourniquet application for minimal duration and to wait for 5 min with the needle in situ after removing the tourniquet, to reduce hemostasis-induced variability and false flags in interpretation. Metabolomics, or the identification and measurement of metabolites in biological samples, has become an invaluable means for generating new knowledge in terms of markers for prognosis and diagnosis of human pathophysiology as well as of new leads in understanding causal pathways 1-4. Of the various possible sources of samples from human subjects for metabolomic assessments, components of blood (plasma and serum), remain the most relevant and therefore, most studied type of sample 5. However, unlike metabolomics performed with samples generated from in vitro or animal model experiments that are inherently less heterogenous, using plasma or serum metabolomics as a tool in human translational research is subject to the inherent interindividual variability between subjects due to genetic and environmental factors and their interactions. An additional source of variation is pre-analytic factors. Controlling for such variability introducing pre-analytic factors would be key to improving reproducibility of high impact human metabolomic findings such as the use of sarcosine as a biomarker for progression of prostate cancer 6,7. Here, fasting status, type of collection tube, presence of haemolysis, time taken and temperature of sample during processing, temperature and duration of storage of processed samples, and freeze-thaw cycles have been assessed 8-12. Unknown and unaccounted for variation arising due to pre-analytic factors could lead to overestimation of interindividual variation or even intraindividual variation, if the samples have been collected at multiple time points in a longitudinal fashion. However, Agueusop et al. 13 reported remarkable stability of the human serum metabolome over a 4 weeks' time period, when the samples were collected on 3 different days under stringently controlled conditions. An additional, unstudied and potentially significant variation might arise from local tissue hemostasis during venous blood collection due to variable tourniquet application times and associated haemostasis. We could not identify any study that has investigated this effect on metabolomic readouts in the plasma. Therefore, we explored the effect of different durations of tourniquet-induced local hemostasis on fasted venous plasma metabolomic profiles of South Asian Indian women, for a deeper understanding of tourniquet-time related precautions required for reproducible untargeted human metabolomic studies. Our hypothesis was that the number of metabolites differing in abundance from the control, unrestricted blood flow condition would increase in step with the increased time of tourniquet-induced local hemostasis.
PLOS ONE, May 14, 2021
Gut microbiota has been implicated as a modifier of childhood growth. Here, 16S rRNA sequencing-b... more Gut microbiota has been implicated as a modifier of childhood growth. Here, 16S rRNA sequencing-based fecal microbiota profiles of 18-24 month old Indian children were evaluated (n = 41), in relation to their anthropometric parameters, intestinal permeability, body composition and total energy expenditure. Pathway analyses were conducted to assess microbial functions related to stunting, underweight and wasting. The fecal microbiota was enriched in Prevotella 9, Bifidobacterium and Escherichia-Shigella. Weight, weight-forage Z-scores (WAZ) and weight-for-length Z-scores (WLZ), along with age, acted as covariates of microbiota variation specifically in boys (n = 23). Bifidobacterium longum subsp longum abundance was positively associated with WAZ while Bifidobacterium bifidum and Bifidobacterium breve abundances were negatively associated with age. The lipopolysaccharide biosynthesis pathway was upregulated in stunted (n = 16) and wasted (n = 8) children. Findings from this study indicate that child sex may be a critical modifier of the role of gut microbiota on childhood growth.
Current Opinion in Hematology, May 1, 2008
The present review presents a current view of vascular development, with a focus on the factors c... more The present review presents a current view of vascular development, with a focus on the factors contributing to the establishment of arterial-venous identity and the potential of chemical biology for providing new insights into this field. Genetics and gene expression studies have begun to define the complex network of molecular pathways that govern the formation of the embryonic vasculature, but these approaches have limited ability to spatially and temporally manipulate gene expression and function. Recently, the power of chemical biology, combined with model systems like zebrafish, has enabled discovery of additional contributors to vascular development and has provided a means of manipulating gene function with enhanced spatial and temporal control. The molecular pathways directing arterial-venous specification during embryogenesis are relevant for understanding the causes of human arteriovenous malformations, tumor angiogenesis, and diabetic retinopathy. Through the complementary strengths of genetics and chemical biology, it is hoped that novel therapeutic approaches for these conditions will emerge.
The American Journal of Clinical Nutrition, Sep 18, 2018
Background: Maternal macronutrient intake is likely to play a pivotal role in fetoplacental growt... more Background: Maternal macronutrient intake is likely to play a pivotal role in fetoplacental growth. Male fetuses grow faster and their growth is more responsive to maternal size. Objective: We assessed the role of fetal sex in modifying the effect of maternal macronutrient intake on the risk of small-for-gestationalage (SGA) birth. Design: This was a prospective, observational cohort study of 2035 births from an urban South Asian Indian population. Maternal intakes of total energy and macronutrients were recorded by validated food-frequency questionnaires. The interaction of trimester 1 macronutrient intake with fetal sex was tested on the outcome of SGA births. Results: The prevalence of SGA was 28%. Trimester 1 macronutrient composition was high in carbohydrate and low in fat (means ± SDs-carbohydrate: 64.6% ± 5.1%; protein: 11.5% ± 1.1%; and fat: 23.9% ± 4.4% of energy). Higher carbohydrate and lower fat consumption were each associated with an increased risk of SGA [adjusted OR (AOR) per 5% of energy (95% CI): carbohydrate: 1.15 (1.01, 1.32); fat: 0.83 (0.71, 0.97)] specifically among male births (males: n = 1047; females: n = 988). Dietary intake of >70% of energy from carbohydrate was also associated with increased risk (AOR: 1.67; 95% CI: 1.00, 2.78), whereas >25% of energy from fat intake was associated with decreased risk (AOR: 0.61; 95% CI: 0.41, 0.90) of SGA in male births. Conclusions: Higher carbohydrate and lower fat intakes early in pregnancy were associated with increased risk of male SGA births. Therefore, we speculate that fetal sex acts as a modifier of the role of maternal periconceptional nutrition in optimal fetoplacental growth.
Diabetes, Jun 20, 2023
Genetic variants contribute to differential responses to non-insulin antidiabetic drugs (NIADs), ... more Genetic variants contribute to differential responses to non-insulin antidiabetic drugs (NIADs), and consequently to variable plasma glucose control. India’s distinct genetic architecture and its exploding burden of Type 2 Diabetes (T2D) warrants a population-specific survey of NIAD-associated pharmacogenetic (PGx) variants. We mined 1029 Indian whole genomes for PGx variants, drug-drug (DDI) and drug-drug-gene interactions (DDGI) associated with 44 NIADs. Overall, we found 76 known and 52 predicted deleterious common PGx variants associated with response to T2D therapy among Indians. We report remarkable inter-ethnic differences in the relative cumulative counts of decreased and increased response-associated alleles across NIAD classes. Indians and South Asians showed a significant excess of decreased metformin response-associated alleles compared to other global populations. Network analysis of shared PGx genes predicts high DDI risk during co-administration of NIADs with other metabolic disease drugs. We also predict an increased CYP2C19-mediated DDGI risk for CYP3A4/3A5-metabolized NIADs, saxagliptin, linagliptin and glyburide when co-administered with PPIs. Our findings provide an actionable resource for accelerating future diabetes PGx studies in Indians and reconsidering NIAD dosing guidelines to ensure maximum efficacy and safety in the population. Disclosure A.Sivadas: None. A.Mishra: None. A.Mukhopadhyay: None. K.Narayan: None. S.Sivasubbu: None. V.Scaria: None. A.Kurpad: None. S.Sahana: None. B.Jolly: None. R.C.Bhoyar: None. A.Jain: None. D.Sharma: None. M.Imran: None. V.Senthivel: None. M.K.Divakar: None. Funding DBT/Wellcome Trust India Alliance (IA/E/19/1/504945)
European Journal of Clinical Nutrition, Oct 5, 2021
Dysregulation of microRNAs (miRNAs) and their target genes in placental tissue is associated with... more Dysregulation of microRNAs (miRNAs) and their target genes in placental tissue is associated with foetal growth restriction. We aimed to evaluate associations of placental miR-21-5p, miR-141-3p and miR-210-3p expression with maternal, placental and newborn parameters and with placental expression of their potential target genes PTEN, VEGF, FLT and ENG in a set of well-characterized small- (SGA) and appropriate- (AGA) for gestational age full-term singleton pregnancies. Placental samples (n = 80) from 26 SGA and 54 AGA were collected from full-term singleton pregnancies. Placental transcript abundances of miR-21-5p, miR-141-3p and miR-210-3p were assessed after normalization to a reference miRNA, mir-16-5p by real-time quantitative PCR. Placental transcript abundances of PTEN, VEGF, FLT and ENG were assessed after normalizing to a panel of reference genes. Placental miR-21-5p transcript abundance was negatively associated with placental weight (n = 80, r = −0.222, P = 0.047) and this association was specific to the AGA births (n = 54, r = −0.292, P = 0.032). Placental transcript abundances of miR-210-3p and miR-141-3p were not associated with placental weight or birth weight in all 80 births. However, placental miR-210-3p transcript abundance was positively associated with birth weight specifically in the SGA births (n = 26, r = 0.449, P = 0.021). Placental transcript abundance of miR-21-5p was negatively associated with PTEN transcript abundance (Spearman’s ρ = −0.245, P = 0.028) while that of miR-141-3p was positively associated with FLT (Spearman’s ρ = 0.261, P = 0.019) and ENG (Spearman’s ρ = 0.259, P = 0.020) transcript abundances in all 80 births. We conclude that placental miR-21-5p and miR-210-3p may be involved in fetoplacental growth. However, this regulation is unlikely to be mediated through placental expression of PTEN, VEGF, FLT or ENG.
Clinical nutrition ESPEN, Jun 1, 2018
Background: A striking number of low birth weight (LBW) Indian babies are born annually. Previous... more Background: A striking number of low birth weight (LBW) Indian babies are born annually. Previous studies have confirmed the positive association between milk intake and birth weight. However, the relations between protein and vitamin B 12 from milk and birth weight have not been systematically explored. Aims: We examined the relations between birth weight and maternal intake of milk, protein from milk and vitamin B 12 from milk. Methods: This prospective, observational cohort study was conducted in an urban South Indian hospital. The dietary intakes of milk and milk products were assessed using validated food frequency questionnaire and at delivery birth outcomes were measured. The relations between milk products, milk protein, and vitamin B 12 from milk with birth weight and gestational weight gain were assessed in 2036 births with first trimester dietary and delivery data. Results: Median consumption of milk products in the first trimester was 310 g$day À1 and average birth weight was 2876 g. Birth weight was positively associated with intake of milk products and of % protein from milk products (%milk protein) in the first trimester [b ¼ 86.8, 95% confidence interval (CI): 29.1, 144.6; b ¼ 63.1, 95% CI: 10.8, 115.5; P < 0.001 for both]. Intake of milk products and of %milk protein in the third trimester was positively associated with gestational weight gain (GWG) between the second and third trimester (One-way ANOVA, P < 0.001 and ¼ 0.001, respectively). Neither birth weight nor GWG were associated with %vitamin B 12 from milk products. Conclusions: These findings indicate that intake of milk products in the first trimester and especially, protein from milk products is positively associated with birth weight in this South Asian Indian population.
Placenta, Nov 1, 2015
Imprinted genes play an important role in mammalian fetoplacental growth and development. We have... more Imprinted genes play an important role in mammalian fetoplacental growth and development. We have evaluated whether the placental expression of two imprinted genes, growth factor receptor-binding protein 10 (GRB10) and pleckstrin homology-like domain, family A, member 2 (PHLDA2) correlate with human fetoplacental growth parameters. Placentae (n = 77) were collected from small- (SGA) and appropriate- (AGA) for gestational age full-term singleton pregnancies (n = 36 SGA and 41 AGA). Placentae and neonates were weighed at birth. Realtime quantitative PCR was performed to assess placental transcript abundance of GRB10 and PHLDA2 normalized to a panel of reference genes. Placental GRB10 transcript abundance associated positively with placental weight (r = 0.307, P = 0.007), birth weight (r = 0.267, P = 0.019) and neonatal head circumference (r = 0.280, P = 0.014). Placental GRB10 transcript levels were significantly lower in male SGA placentae compared to the male AGA placentae. Placental PHLDA2 transcript abundance did not show any associations with maternal, placental or neonatal parameters. Placental GRB10 expression was found to be associated positively with placental weight, birth weight, and neonatal head circumference, especially in males. Hence, we speculate that placental GRB10 plays a role in regulating fetoplacental growth and thereby in the pathophysiology of fetal growth restriction in the context of fetal gender.
Current Opinion in Chemical Biology, Aug 1, 2006
The discovery of antibiotics and other antimicrobial agents in the 1930s is arguably the most sig... more The discovery of antibiotics and other antimicrobial agents in the 1930s is arguably the most significant therapeutic advance in medical history. Penicillin and the sulfa drugs touched off the search for and discovery of countless derivative compounds and several new antibiotic classes. However, the pace of discovery has slowed down, and there is growing appreciation that much of the low-lying fruit accessible to traditional methods of antimicrobial discovery has been harvested. Combating emerging drug-resistant strains of infectious agents may require the adoption of fresh approaches to drug target validation, small-molecule discovery and safety assessment. The recent development of several infectious disease models in zebrafish raises the possibility of a new paradigm in antimicrobial discovery.
European Journal of Clinical Nutrition, Nov 5, 2021
Placental-origin microRNA (miRNA) profiles can be useful toward early diagnosis and management of... more Placental-origin microRNA (miRNA) profiles can be useful toward early diagnosis and management of fetal growth restriction (FGR) and associated complications. We conducted a systematic review to identify case–control studies that have examined miRNA signatures associated with human FGR. We systematically searched PubMed and ScienceDirect databases for relevant articles and manually searched reference lists of the relevant articles till May 18th, 2021. Of the 2133 studies identified, 21 were included. FGR-associated upregulation of miR-210 and miR-424 and downregulation of a placenta-specific miRNA cluster miRNA located on C19MC (miR-518b, miR-519d) and miR-221-3p was reported by >1 included studies. Analysis of the target genes of these miRNA as well as pathway analysis pointed to the involvement of angiogenesis and growth signaling pathways, such as the phosphatidylinositol 3-kinase- protein kinase B (PI3K-Akt) pathway. Only 3 out of the 21 included studies reported FGR-associated miRNAs in matched placental and maternal blood samples. We conclude that FGR-associated placental miRNAs could be utilized to inform clinical practice towards early diagnosis of FGR, provided enough evidence from studies on matched placental and maternal blood samples become available. Prospective Register of Systematic Reviews (PROSPERO) registration number: CRD42019136762.
Developmental Dynamics, Jul 24, 2003
We have identified a novel gene expressed in murine embryonic stem (ES) cells and in a restricted... more We have identified a novel gene expressed in murine embryonic stem (ES) cells and in a restricted, tissue-specific pattern during mouse development. The gene is also expressed in blood vessels; hence, we have named it asrij (Sanskrit; asRˆij ؍ blood). The gene encodes a novel conserved, predicted transmembrane protein of 247 amino acids, which is localized to lysosomes and endosomes. During ES cell-derived blood vessel formation in vitro, Asrij expression precedes and partially overlaps with the vascular markers Flk-1 and PECAM. During development, Asrij is expressed predominantly in mouse embryonic blood vessels. The asrij transcript is alternatively spliced, and its expression is regulated in a tissue-specific manner. An asrij splice variant that is enriched in the adult mouse brain encodes a protein of 196 amino acids. Asrij can serve as an early stem cell marker that is down-regulated in nonvascular tissues. Our data indicate that Asrij belongs to a novel class of conserved proteins with a complex developmental profile and suggests multiple functions for the gene.
The National Medical Journal of India, 2018
Background. Medical professionals in India need to understand the concepts of molecular genetics ... more Background. Medical professionals in India need to understand the concepts of molecular genetics to stay up-to-date with clinical care as well as to strengthen basic research in the biomedical sciences. Methods. We introduced a modular course on ‘Fundamentals in molecular and cellular biology’ for first-year medical undergraduate students in the second semester of the first MBBS year in 2015, as part of ‘Innovations in teaching physiology’ at St John’s Medical College. This was a voluntary, add-on course with didactic lectures, hands-on practical classes and a research paper presentation. Evaluation of students’ performance in the course took into account their performance in the research paper presentation-based group activity and their attendance for the hands-on practical sessions. Feedback on the content, delivery, evaluation and future improvements of the course was sought from the students. Results. About 65% of students regularly attended the 10-hour long course. Of the students evaluated for the course, 43% achieved the highest, and 11% achieved the lowest grade assigned. Nearly 72% of the students provided feedback on the course. Conclusion. This first outing of the modular course on ‘Fundamentals in molecular and cellular biology’ generated excitement among the students and achieved some learning for them. It also brought to light hidden challenges in conducting such a voluntary course for medical students in India. Our experience with the course will help in designing a better-integrated course for exposure of first-year medical students to advances in molecular biology and its applied aspects as they progress through the MBBS course.
Journal of the Indian Institute of Science, Jul 5, 2013
Circulation, Oct 28, 2008
Background : Arterial morphogenesis is an important and poorly understood process. We have previo... more Background : Arterial morphogenesis is an important and poorly understood process. We have previously demonstrated that disruption of synectin gene expression in mice and zebrafish results in impaired arterial development and branching morphogenesis. Synectin null endothelial cells demonstrate reduced VEGF responsiveness in terms of migration, proliferation and differentiation and ERK-1/2 activation (Chittenden et al, Dev Cell 2006). Since ERK has been established as major participants in the regulation of cell growth and differentiation and Erk activation has been previously linked to arterial morphogenesis, we evaluated whether activation of Erk signaling in synectin disrupted mice and zebrafish as well as synectin KO arterial endothelial cells (ECs) would restore defective migration, arterial differentiation, angiogenesis and arteriogenesis. To stimulate ERK signaling we used partial inhibition of PI3-K activity to reduce Akt-dependent suppression of Raf1 activation or introduction of constitutively active ERK construct. Methods : In vitro studies were conducted with primary arterial ECs isolated from synectin wild type (WT) and knock out (KO) mice. In vivo studies were carried out in WT and synectin deficient mice and synectin knockdown zebrafish embryos. Results: Exposure of synectin −/− arterial EC to two selective PI3K inhibitors GS4898 or LY294002 in vitro restored ERK activation in a dose-dependent manner and returned cell migration and in vitro branching morphogenesis to wild type levels. Transduction of a constitutively active ERK construct in vitro or in a Matrigel model in vivo had similar effect. Systemic treatment of synectin −/− mice with GS4898 fully restored impaired angiogenesis and arterial morphogenesis in adult animals in the setting of hindlimb ischemia. Similar treatment nearly completely restored arterial development defects in zebrafish treated with a synectin morpholino. Conclusions: ERK activation plays a key role in arteriogenesis both in adult tissues and during embryonic development. Activation of compromised ERK-1/2 signaling may be a novel therapeutic intervention to stimulate arteriogenesis.
Placenta, 2016
Aims: Placental physiology and morphology is critically regulated by DNA methylation. As such, pl... more Aims: Placental physiology and morphology is critically regulated by DNA methylation. As such, placental global DNA methylation and transcript abundance of placental DNA methyltransferases (DNMT1 and DNMT3A) may relate to placental and fetal growth in human pregnancies. We aimed to test correlations of human fetoplacental parameters and birth weight with the placental expression of DNA methyltransferases (DNMT1 and DNMT3A) and placental global methylation. Subjects and methods: Placentae (n ¼ 109) were collected from small-(SGA) and appropriate-(AGA) for gestational age full-term singleton pregnancies (n ¼ 56 SGA and 53 AGA). Placentae and neonates were weighed at birth. Realtime quantitative PCR was performed to assess placental transcript abundance of DNMT1, DNMT3A and DNTMT3B normalized to a panel of reference genes. LINE-1 methylation was measured using a quantitative MethyLight assay in a subset of samples (n ¼ 68). Associations of placental transcript abundances of DNMT1, DNMT3A and DNMT3B and of LINE-1 methylation levels with maternal, placental and neonatal parameters were tested. Results: Placental DNMT1 transcript abundance associated positively with placental weight (b ¼ 10.21, P ¼ 0.013). This association was specific to the AGA births (b ¼ 12.77, P ¼ 0.022) and was absent in the SGA births. Association of DNMT1 expression with placental weight and birth weight within the AGA births was specific to the female gender (Birth weight: b ¼ 83.61, P ¼ 0.043; Placental weight: b ¼ 23.92, P ¼ 0.025). Placental DNMT1 transcript levels were not different according to SGA status or gender. Placental DNMT3A transcript levels and LINE-1 methylation levels did not show any associations with maternal, placental and neonatal parameters. Conclusions: Placental DNMT1 expression was found to be associated positively with placental weight and birth weight, specifically in the female AGA births. Thus, we hypothesize that placental DNMT1 participates in fetoplacental growth in a fetal gender-specific manner.
European Journal of Clinical Nutrition, 2021
The current study aimed to identify suitable reference miRNA for placental miRNA expression analy... more The current study aimed to identify suitable reference miRNA for placental miRNA expression analysis in a set of well-characterized and fetal-sex balanced small- (SGA) and appropriate- (AGA) for gestational age full-term singleton pregnancies. In this retrospective study, placental samples (n = 106) from 35 SGA (19 male and 16 female) and 71 AGA (30 male and 41 female) full-term singleton pregnancies were utilized. Placental transcript abundance of three widely used reference miRNAs [miR-16-5p and Small nucleolar RNAs (snoRNAs) RNU44 and RNU48] were assessed by real-time quantitative PCR. Raw cycle threshold (Ct) analysis and RefFinder tool analysis were conducted for evaluating stability of expression of these miRNAs. Raw Ct values of miR-16-5p were similar between SGA and AGA births (P = 0.140) and between male and female births within SGA (P = 0.159) and AGA (P = 0.060) births while that of RNU44 and RNU48 were higher in SGA births (P = 0.008 and 0.006 respectively) and in male births within the SGA group (P = 0.005) for RNU44 and in female births within the AGA group (P = 0.048) for RNU48. Across all 106 samples tested using the RefFinder tool, miR-16-5p and RNU44 were equally stable reference miRNAs. We recommend miR-16-5p and RNU44 as suitable reference miRNAs for placental samples from settings similar to our study.
Current Developments in Nutrition
Clinical and Translational Gastroenterology
INTRODUCTION: The gene-environment interaction of the REarranged during Transfection (RET) gene w... more INTRODUCTION: The gene-environment interaction of the REarranged during Transfection (RET) gene with vitamin A in the etiopathogenesis of Hirschsprung disease (HSCR) has been suggested in rodents. The aim of this study was to evaluate vitamin A status in mothers of children with HSCR and to assess its association with pathogenic variants of the RET gene in affected children. METHODS: This was a case-control study of stable isotope–based vitamin A measurement stores of mothers of children diagnosed with HSCR (within 8 months from birth, n = 7) and age-matched mothers of normal children (n = 6). Next-generation sequencing of RET exons, along with their upstream promoter region, was performed in the 7 HSCR proband-parent triads to evaluate pathogenic variants. RESULTS: Maternal vitamin A stores in the HSCR group was almost 50% that of those in controls, tending toward significance (0.50 ± 0.17 vs 0.89 ± 0.51 μmol/g respectively, P = 0.079). Two novel pathogenic de novo mutations were i...
Current Developments in Nutrition
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Papers by Arpita Mukhopadhyay