👤 Divya Pandey

Studies suggest that obesity is linked to both autonomic nervous system dysfunction and cognitive impairment, but the specific quantitative associations are not well explored. This study was proposed to explore the quantification of different neurocognitive signatures and heart rate variability (HRV) parameters with increasing body weight among metabolically healthy obese participants for better analytical predictors. The present research is a cross-sectional study, including a total of 101 ( Significant changes were observed for neurocognitive performances and HRV indices for the metabolically healthy obese group compared with the control group. With the association heatmaps, BMI was found to be significantly negatively associated with the BDNF and high-frequency band (HF band, ms The findings of the present study support that HRV could be a valuable early non-invasive tool for future cognitive decline in a population with metabolically healthy obesity. The study was registered at Clinical Trial Registry of India (CTRI/2022/10/046935). Show less

Diabetic nephropathy (DN) is a chronic renal complication characterized by persistent proteinuria, glomerular hypertrophy, impaired filtration capacity, and progressive renal fibrosis, ultimately leading to a gradual decline in kidney function. DN remains one of the leading causes of end-stage renal disease worldwide, contributing substantially to morbidity and mortality. Although the precise etiology of DN is not fully elucidated, its development is closely linked to prolonged hyperglycemia, renal hyperfiltration, accumulation of advanced glycation end products (AGEs), activation of pro-inflammatory cytokines, and oxidative stress-mediated injury. These pathogenic events involve multiple diabetes-associated pathways, including protein kinase C activation and increased reactive oxygen species (ROS) generation. O-linked β-N-acetylglucosamine (O-GlcNAc) modification is a dynamic post-translational protein modification that is significantly upregulated in DN and plays a critical role in regulating cellular signaling pathways associated with disease initiation and progression. This review summarizes current evidence on the role of O-GlcNAcylation in modulating molecular mechanisms underlying DN. Furthermore, Angiopoietin-like 4 (ANGPTL4) has emerged as a key regulator of lipid metabolism through inhibition of lipoprotein lipase and interactions with integrins, influencing vascular permeability, oxidative stress, and tissue remodeling. Increasing evidence suggests that ANGPTL4 plays a pivotal role in DN onset and progression. Show less

'Small extracellular vesicles (sEVs) are nanosized, membrane-enclosed sacs released by diverse cell types. They play a critical role in cell-cell communication through their cargo, which includes a wide range of proteins, lipids, and nucleic acids. Physiologically, sEVs circulate in various body fluids such as blood, urine, and saliva, making them accessible for diagnostic via non-invasive isolation techniques. Recent advances in high-throughput proteomics have significantly enhanced our ability to characterize the protein content of sEVs. Importantly, multiple studies on human fluids have identified specific protein markers across different cancer types, encompassing molecules involved in inflammation, cellular adhesion, immunity, and lipoprotein regulation. Interestingly, some of these proteins are consistently detected across multiple cancer types and sample sources, suggesting the existence of a shared "oncogenic signature" that may be transferred via sEVs. Among body fluids, urine and saliva are particularly promising for easy, non-invasive diagnostics. However, these sample types remain underexplored as compared to the serum, leaving substantial opportunities for future research. Taken together, these findings position sEVs as a powerful tool with significant potential for advancing precision cancer care. SIGNIFICANCE: Living cells release nanosized membrane-enclosed vesicles called small extracellular vesicles (sEVs) into the extracellular environment. sEVs contain protein cargo molecules that critically take part in cell-cell communications. Quantitative proteomics identified potential sEV associated biomarkers for early cancer diagnosis and therapy. sEV Proteins associated with cell adhesion and inflammation, lipoproteins and immunoglobulins are potential molecules that were majorly identified. Interestingly, some of these proteins such as APOA4, SAA4, ITIH4, SERPINC1 and VWF were consistently identified across multiple cancer types and sample sources, highlighting their potential as future biomarkers. Show less

NSCLC-Squamous cell carcinoma (SCC) is characterized by poor survival largely due no definitive markers for targeted therapy. KRAS (Kirsten rat sarcoma viral oncogene homolog) is a proto-oncogene associated with resistance standard chemotherapy regimens. Discoidin domain receptor 2 (DDR2), fibroblast growth factor receptor-1(FGFR-1) and mesenchymal epithelial transition (MET) are receptor tyrosine kinases that regulate proliferation, apoptosis and invasion. The objectives were to assess frequency of FGFR1, DDR2,c-MET protein over-expression and KRAS mutations in NSCLC-SCC and to co-relate expression of molecular markers with clinico-pathological parameters. The study was a retrospective and prospective case series of 150 cases of NSCLC-SCC. Testing for KRAS, DDR-2, cMET and FGFR1 was done using immunohistochemistry (IHC). KRAS IHC was validated using real time polymerase chain reaction testing. Molecular marker expression was identified in 37.33% (n=56/150) cases, among which 80.35% (n=45/56) cases had a single mutation and 19.64% cases(n=11/56) had multiple mutations. FGFR-1 protein over-expression was identified in 8% cases and cMET protein over-expression in 4.67% cases. DDR-2 over-expression was present in 19.33% cases and KRAS protein over-expression in 14.67% cases. Co-expression of DDR-2 and KRAS was identified in 72.72% cases. DDR2 protein over-expression is identified in smokers and cases with distant metastasis. KRAS protein over-expression was more frequent in cases >40 years of age with advanced disease stage. The targets evaluated have potential drugs currently under trial phase. This may help to define the subgroup for use of targeted therapy in NSCLC-SCC and in designing new treatment protocols. Show less

We previously used a myoblast model of fusion-positive rhabdomyosarcoma (FP-RMS) to show that FGF8, a PAX3-FOXO1 (P3F) transcriptional target, is required for P3F-driven tumorigenicity and, when aberrantly expressed, can maintain tumorigenicity in P3F-independent recurrent tumors. We report in this study that FGF8, FGFR1, and FGFR4 are often highly expressed in FP-RMS tumors. High FGF8 expression in FP-RMS cells is associated with high sensitivity to an FGFR4 inhibitor and a pan-FGFR inhibitor. Although downregulating FGF8 resulted in loss of sensitivity to these inhibitors, FGF8 upregulation in myoblasts decreased FGFR4 expression and sensitized the cells to an FGFR1 inhibitor and a pan-FGFR inhibitor. FGF8 downregulation of FGFR4 expression was reverted by inhibitors of FGFR1, MEK, or ERK, thus defining a signaling pathway by which FGF8 mediates this regulatory effect. Finally, high FGF8 expression in P3F-independent recurrent tumors was attributable to a rearrangement of viral long terminal repeat (LTR) sequences into the FGF8 3' untranslated region, resulting in increased FGF8 mRNA stability. These findings indicate that FGF8 exerts oncogenic effects in FP-RMS via FGFR4 and may exert oncogenic effects in P3F-independent relapses via FGFR1. Our study reveals the functional significance of FGF8 in FP-RMS and provides a rationale for preclinical studies of FGFR inhibitors in FP-RMS. Show less

Fluoroquinolones (FQs) are key components of World Health Organization (WHO)-recommended regimens for multidrug-resistant tuberculosis (MDR-TB). Accurate detection of FQ resistance is essential for optimizing treatment. This study evaluated the concordance between the Second-Line Line Probe Assay (SL-LPA) and Liquid Culture Drug Susceptibility Testing (LC-DST) for detecting FQ resistance in Mycobacterium tuberculosis isolates. In this retrospective study, 1402 non-duplicate clinical isolates of MDR TB were tested using SL-LPA and LC-DST at a reference laboratory. Genotypic resistance was identified through mutations in the gyrA and gyrB genes identified by SL-LPA, while phenotypic resistance was determined using MGIT-based LC-DST at critical concentrations for fluoroquinolones. Targeted nanopore sequencing was performed on a subset of isolates with discordant molecular and phenotypic results to investigate resistance-associated mutations. SL-LPA detected FQ resistance in 907 (64.7%) isolates, whereas LC-DST identified resistance in 852 (60.8%) isolates. Using LC-DST as the reference standard, SL-LPA showed a sensitivity of 93.2%, specificity of 98.6%, positive predictive value of 99.2%, and negative predictive value of 88.7%. Overall concordance between the two methods was observed in 1292 (92.2%) isolates. Discordant results occurred in 110 (7.8%) isolates, mainly involving low-level resistance mutations or inferred resistance due to missing wild-type bands on SL-LPA. Nanopore sequencing of 15 discordant isolates identified high-confidence mutations (Asp94Tyr, Asp94Gly, Asp94Asn) and interim or low-confidence mutations (Ala90Val, Ser91Pro, Asp94Ala, gyrB Asn499Asp, Asp461Asn). SL-LPA demonstrates excellent specificity and positive predictive value for detecting FQ resistance; however, discordance associated with low-confidence mutations and heteroresistance highlights the importance of integrating molecular assays with phenotypic DST and sequencing to improve MDR-TB resistance detection and guide treatment decisions. Show less

Lipoprotein(a) [Lp(a)] is a genetically determined and independent risk factor for atherosclerotic cardiovascular disease, including acute coronary syndrome, peripheral arterial disease, and stroke, as well as calcific aortic stenosis. Despite its high prevalence, affecting an estimated 20% of Canadians, Lp(a) remains under-recognized and undermeasured in clinical practice. This report provides guidance on the assessment and management of Lp(a) in primary and secondary prevention in the Canadian context. It outlines when and how to measure Lp(a), with a recommendation for universal, one-time testing in adulthood. The report summarizes the pathophysiologic role of Lp(a) in promoting atherosclerosis, thrombosis, and aortic stenosis, and highlights significant ethnic variability in Lp(a) levels and associated risk. It also addresses the limitations of existing cardiovascular risk calculators that omit Lp(a) and discusses the potential role of emerging imaging and treatment strategies, including novel Lp(a)-lowering therapies. Special attention is given to clinical interpretation of Lp(a) values, the role of cascade screening in families, and recommendations for preventive interventions, with an emphasis on current approaches for managing patients with elevated Lp(a) level while awaiting the availability of targeted therapies. The goal of this report is to support clinicians in identifying at-risk individuals earlier and guiding appropriate risk reduction strategies in primary and secondary prevention settings. Show less

Globally, colorectal cancer (CRC) is the third most common type of cancer, and its treatment frequently includes the utilization of drugs based on antibodies and small molecules. The development of CRC has been linked to various signaling pathways, with the Wnt/β-catenin pathway identified as a key target for intervention. We have explored the impact of imidazopyridine-tethered chalcone-C (CHL-C) in CRC models. To determine the influence of CHL-C on apoptosis and autophagy, Western blot analysis, annexin V assay, cell cycle analysis, acridine orange staining, and immunocytochemistry were performed. Next, the activation of the Wnt/β-catenin signaling pathway and the anti-cancer effects of CHL-C in vivo were examined in an orthotopic HCT-116 mouse model. We describe the synthesis and biological assessment of the CHL series as inhibitors of the viability of HCT-116, SW480, HT-29, HCT-15, and SNU-C2A CRC cell lines. Further biological evaluations showed that CHL-C induced apoptosis and autophagy in down-regulated β-catenin, Wnt3a, FZD-1, Axin-1, and p-GSK-3β (Ser9), and up-regulated p-GSK3β (Tyr216) and β-TrCP. In-depth analysis using structure-based bioinformatics showed that CHL-C strongly binds to β-catenin, with a binding affinity comparable to that of ICG-001, a well-known β-catenin inhibitor. Additionally, our in vivo research showed that CHL-C markedly inhibited tumor growth and triggered the activation of both apoptosis and autophagy in tumor tissues. CHL-C is capable of inducing apoptosis and autophagy by influencing the Wnt/β-catenin signaling pathway. Show less

This study aims to evaluate cognitive impairment utilizing the Montreal Cognitive Assessment (MoCA) scale, while also exploring the correlation between cognitive impairment and various serum biomarkers, including Brain-derived neurotrophic factor (BDNF), Beta Secretase-1 (BACE1), Vascular Endothelial Growth Factors (VEGF), Glial fibrillary acidic protein (GFAP), and Interleukin-1 (IL-1β) in adults living with epilepsy. In this study, 74 participants aged between 18 and 50 years, who were visiting neurology outpatient consultations, were included. The cognitive assessment was executed using the MoCA test. Serum levels of BDNF, BACE1, VEGF, GFAP, and IL-1β were evaluated through ELISA in patients with and without cognitive impairments. To determine the association between MoCA scores and the biomarkers, both Spearman and Pearson correlation analyses, as well as linear regression, were conducted. Among the 74 PWE, 61 exhibited cognitive impairment as determined by the MoCA assessment. Noteworthy alterations were detected across various MoCA subscales, encompassing visuospatial and executive functions, attention, language, abstraction, and delayed recall, with statistical significance established ( We conclude that adult PWE in India demonstrate a significant cognitive impairment. Further, our findings indicate that BDNF may serve as a potential biomarker for evaluating cognitive impairment in adult PWE. Further longitudinal, prospective and multi-center studies are required to confirm the same. Show less

Proinflammatory cytokines, especially interleukin-17 A (IL-17 A) have been found to be significantly associated with AD patients. IL-17 A amplifies neuroinflammation during AD pathology. This study highlighted the ability of IL-17 A to exacerbate amyloid-beta-induced pathology in animals. The AD pathology was induced with repeated intranasal administration of Aβ along with recombinant mouse IL-17 A (rmIL-17) at 1, 2 and 4 µg/kg for seven alternate days. Although, the combination of rmIL-17 and Aβ did not have severe effects on memory of the animals, but it drastically increased the IL-17 A mediated signaling, level of proinflammatory cytokines, oxidative stress and reduced antioxidants in the hippocampus and cortex regions of the animal brains. Interestingly, combining rmIL-17 with Aβ also triggered the expression of AD structural markers like pTau, amyloid-beta and BACE1 in the brain regions. Furthermore, rmIL-17 with Aβ exposure stimulated astrocytes and microglia leading to activation of proinflammatory signaling in the brain of the animals. These results showed the propensity of IL-17 A to promote severity of AD pathology and suggest IL-17 A as potent therapeutic target to control AD progression. Show less

Seven compounds, comprising three anthraquinones and four stilbenoids, were isolated from the roots of Rheum palmatum L. These compounds include chrysophanol (1), aloe-emodin (2), aloe-emodin 8-O-β-D-glucopyranoside (3), desoxyrhapontigenin (4), rhapontigenin (5), desoxyrhaponticin (6), and piceatannol 3'-O-β-D-glucopyranoside (7). Among these, compound 5 showed potent β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitory activity with an IC Show less

Circulating tumor cells (CTCs) have emerged as a key biomarker in cancer detection and prognosis, and their molecular profiling is gaining importance in precision oncology. Liquid biopsies, which allow the extraction of CTCs, circulating tumor DNA (ctDNA) or cell-free DNA (cfDNA), have measurable advantages over traditional tissue biopsies, especially when molecular material is difficult to obtain. However, this method is not without limitations. Difficulties in differentiating between primary and metastatic lesions, uncertain predictive values and the complexity of the biomarkers used can prove challenging. Recently, high cell heterogeneity has been identified as the main obstacle to achieving high diagnostic accuracy. Because not all cells undergo epithelial-mesenchymal transition (EMT) at the same time, there is a large population of hybrid CTCs that express both epithelial and mesenchymal markers. Since traditional diagnostic tools primarily detect epithelial markers, they are often unable to detect cells with a hybrid phenotype; therefore, additional markers may be required to avoid false negatives. In this review, we summarize recent reports on emerging CTCs markers, with particular emphasis on their use in cancer diagnosis. Most of them, including vimentin, TWIST1, SNAI1, ZEB1, cadherins, CD44, TGM2, PD-L1 and GATA, hold promise for the detection of CTCs, but are also implicated in cancer progression, metastasis, and therapeutic resistance. Therefore, understanding the nature and drivers of epithelial-mesenchymal plasticity (EMP) is critical to advancing our knowledge in this field. Show less

Steroidal alkaloids are secondary metabolites that are often found in plants, fungi and sponges. These compounds are considered as a source of bioactive compounds for the treatment of chronic diseases, such as neurological disorder like Alzheimer's disease (AD). Some examples of alkaloid derivatives currently used to treat AD symptoms include galantamine, huperzine A, and other alkaloids. AD is a multifactorial disease caused by multiple factors such as inflammation, oxidative stress, and protein aggregation. Based on the various important neuroprotective activities and different pharmacological effects of steroidal alkaloids with polypharmacological modulatory effects, they can lead to the development of new drugs for the treatment of AD. There are limited studies on the involvement of steroidal alkaloids in AD. Therefore, the mechanisms and neuroprotective abilities of these compounds are still poorly understood. The purpose of this review article is to provide an overview of the mechanism, toxicity and neuroprotective benefits of steroidal alkaloids and to discuss future possibilities to improve the application of steroidal alkaloids as anti-AD agents. The therapeutic value and limitations of the steroidal alkaloid are investigated to provide new perspectives for future clinical development studies. Show less

Iron is one of the essential metals that functions as a cofactor in various biological cascades in the brain. However, excessive iron accumulation in the brain may lead to neurodegeneration and may show toxic effects. Quercetin, a pigment flavonoid compound, has been proven to be a potent antioxidant and anti-inflammatory that can inhibit lipid peroxidation during metal-induced neurotoxicity. Although iron-induced neuroinflammation and neurodegeneration have been reported in many studies, but the proof for its exact mechanisms needs to be explored. The key target of the study was to explore the neuroprotective effect of quercetin after oral exposure of iron in rats and explore its underlying molecular mechanisms. The outcomes of the study have shown that oral exposure to ferrous sulfate may modulate behavioral paradigms such as locomotor activity, neuromuscular coordination, and increased anxiety level. The pro-inflammatory cytokines (TNF-α, IL-1β and IL-6), apoptotic protein (caspase 3), beta-amyloid and phosphorylated tau were found to be increased on iron exposure. Also, the expressions of ferritin heavy and light chain, BACE-1 and GFAP expressions were altered. These behavioral, structural, and biochemical alterations in the brain were significantly and dose-dependently reversed by treatment with quercetin. The current study provides a fundamental understanding of molecular signaling pathways, and structural proteins implicated in iron-induced neurotoxicity along with the ameliorative effects of quercetin. Show less

In this study, we developed an economical treatment process for highly acidic effluents from steel rolling mills containing toxic heavy metals. Our method involves a pH-dependent approach using mining waste and hydrated lime. The treatment occurs in two steps: First, metal oxides precipitate at pH 3-3.5 using mining waste, followed by lime precipitation at pH 9-9.5. The process, completed in less than 6 h without heavy machinery, reduces sludge formation by extracting high-purity gypsum, a valuable industrial product. Water quality posttreatment matches local groundwater standards. Compared to conventional methods like common effluent treatment plant (CETP) in Jodhpur, India, our approach reduces operational costs by over 58%. In this study, we also characterized the by-product formed, that is, gypsum using various characterization tools and performed a detailed cost analysis. PRACTITIONER POINTS: A quick, efficient, and economical treatment process for extremely acidic (pH ~ 1) wastewater from steel industries. Stepwise treatment strategy without involving heavy machinery or high manpower. Processed water quality closely resembles groundwater with all the major heavy metals been removed. Sludge quantity reduced by regeneration of pure gypsum (96% purity). Reduced the overall operation cost of effluent treatment by 58%. Show less

Earlier investigations on biological methods of wastewater treatment have revealed that algal based wastewater treatment could be a green, cost effective and efficient approach for the removal of heavy metals. So, this study aimed to assess the potential of microalga Chlorella pyrenoidosa for remediation of heavy metals (Cr, Cu, Pb, Zn, Cd, Mn, and Ni) from varying concentration (25%, 50%, 75 and 100%) of wastewater collected from Common Effluent Treatment Plant. Heavy metals such as Cr, Cu, Pb, Zn, Cd, Mn, and Ni have been removed significantly from the wastewater, with percentage removal ranging from 73%, 60%, 75%, 66%, 87%, 83%, and 74% with 50% test solution, 57%, 59%, 70%, 56%, 72%, 66%, and 62% with 75% test solution, and 47%, 55%, 56%, 71%, 61%, 77%, and 72% with 100% test solution respectively. Studies on biochemical assay (protein, carbohydrate, and pigment) of Chlorella pyrenoidosa were also an important part of the present investigation to understand the interaction of heavy metals with algal biochemical compounds using Pearson correlation co-efficient. Biomass grown in CETP wastewater can be used for synthesis of various fruitful value-added end products like bio-diesel, pharmaceutical products, cosmetic products, bio-adsorbent etc. Show less

Despite recent success in vaccinating populations against SARS-CoV-2, concerns about immunity duration, continued efficacy against emerging variants, protection from infection and transmission, and worldwide vaccine availability, remain. Although mRNA, pDNA, and viral-vector based vaccines are being administered, no protein subunit-based SARS-CoV-2 vaccine is approved. Molecular adjuvants targeting pathogen-recognition receptors (PRRs) on antigen-presenting cells (APCs) could improve and broaden the efficacy and durability of vaccine responses. Native SARS-CoV-2 infection stimulate various PRRs, including toll-like receptors (TLRs) and retinoic-acid-inducible gene I-like receptors (RIG-I). We hypothesized that targeting the same PRRs using adjuvants on nanoparticles along with a stabilized spike (S) protein antigen could provide broad and efficient immune responses. Formulations targeting TLR4 (MPLA), TLR7/8 (R848), TLR9 (CpG), and RIG-I (PUUC) delivered on degradable polymer-nanoparticles (NPs) were combined with the S1 subunit of S protein and assessed in vitro with isogeneic mixed lymphocyte reactions (iso-MLRs). For in vivo studies, the adjuvanted nanoparticles were combined with stabilized S protein and assessed using intranasal and intramuscular prime-boost vaccination models in mice. Combination NP-adjuvants targeting both TLR and RIG-I (MPLA+PUUC, CpG+PUUC, or R848+PUUC) differentially increased proinflammatory cytokine secretion (IL-1β, IL-12p70, IL-27, IFN-β) by APCs cultured in vitro, and induced differential T cell proliferation. When delivered intranasally, MPLA+PUUC NPs enhanced local CD4+CD44+ activated memory T cell responses while MPLA NPs increased anti-S-protein-specific IgG and IgA in the lung. Following intramuscular delivery, PUUC-carrying NPs induced strong humoral immune responses, characterized by increases in anti-S-protein IgG and neutralizing antibody titers and germinal center B cell populations (GL7+ and BCL6+ B cells). MPLA+PUUC NPs further boosted S-protein-neutralizing antibody titers and T follicular helper cell populations in draining lymph nodes. These results suggest that SARS-CoV-2-mimicking adjuvants and subunit vaccines could lead to robust and unique route-specific adaptive immune responses and may provide additional tools against the pandemic. Show less

Atrial fibrillation (AF), known as the most common arrhythmia in the developed world, affects 1.5-2.0% of the population. Numerous basic studies have been carried out to identify the roles of electric and structural remodeling in the pathophysiological changes of AF, but more explorations are required to further understand the mechanisms of AF development. Proteomics enables researchers to identify protein alterations responsible for the pathological developing progresses of diseases. Compared to the genome, the proteome is closely related to the disease phenotype and can better manifest the progression of diseases. In this study, AF patients proteomically analyzed to identify possible mechanisms. Totally 20 patients undergoing cardiac surgery (10 with paroxysmal AF and 10 with persistent AF) and 10 healthy subjects were recruited. The differentially expressed proteins identified here included AKR1A1, LYZ, H2AFY, DDAH1, FGA, FGB, LAMB1, LAMC1, MYL2, MYBPC3, MYL5, MYH10, HNRNPU, DKK3, COPS7A, YWHAQ, and PAICS. These proteins were mainly involved in the development of structural remodeling. The differently expressed proteins may provide a new perspective for the pathological process of AF, and may enable useful targets for drug interference. Nevertheless, more research in terms of multi-omics is required to investigate possible implicated molecular pathways of AF development. Show less

To study peripheral blood DNA differential methylation in oligozoospermic infertile men in comparison with normozoospermic fertile controls. Case-control study. Reproductive biology laboratory. 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. Blood samples drawn from all participants, DNA isolation and methylation analysis. 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. 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). 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. Show less

Incretin therapy is one of the most potential approaches in the treatment of diabetes. In contrast to markedly available drugs, the herbal incretin modulators have lesser side effects with low economic cost. The main aim of this work was to analyze the potential of previously reported DPPIV inhibitor, aqueous extract of Pueraria tuberosa tubers (PTY-2) as incretin hormones receptor agonist against streptozotocin (STZ)-induced diabetes. Chronic diabetes was induced with STZ (65mg/kg bw) in rats for 60days and grouped into diabetic control and PTY-2. Expression of genes was assessed by PCR, IHC, and ELISA. Morphological analysis of tissue was observed using H & E stain. In silico molecular docking approach has been used to see the interaction of active phytochemicals of PTY-2 on the basis of their binding energy [kcal/mol] and dissociation constant [pM] using YASARA software. Interactive visualization was done using Discovery studio 3.0. In comparison to diabetic control, the size and number of islet cells along with the plasma level of GLP-1, GIP, and pancreatic expressions of GLP-1R, GIP-R, Bcl2, and insulin were enhanced significantly after PTY-2 treatment. Through in silico molecular docking, tuberostan showed the best interaction for GLP-1R with binding energy at 8.15kcal/mol and dissociation constant at 1061624.125 pM. Puererone showed the best interaction for GIP-R with binding energy at 8.31kcal/mol and dissociation constant at 810381 pM. In addition to previously studied DPPIV inhibitor, PTY-2 also acts as incretin receptors agonist and protects against STZ-induced diabetes by down regulating β cells apoptosis. Show less

Do methylation changes in sperm DNA correlate with infertility? Loss of spermatogenesis and fertility was correlated with 1680 differentially-methylated CpGs (DMCs) across 1052 genes. Methylation changes in a number of genes have been correlated with reduced sperm count and motility. This case-control study used spermatozoal DNA from 38 oligo-/oligoastheno-zoospermic infertile patients and 26 normozoospermic fertile men. 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. 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. N/A. 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. 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. 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. Show less

Genetic differences in the target proteins, metabolizing enzymes and transporters that contribute to inter-individual differences in drug response are not integrated in contemporary drug development programs. Ayurveda, that has propelled many drug discovery programs albeit for the search of new chemical entities incorporates inter-individual variability "Prakriti" in development and administration of drug in an individualized manner. Prakriti of an individual largely determines responsiveness to external environment including drugs as well as susceptibility to diseases. Prakriti has also been shown to have molecular and genomic correlates. We highlight how integration of Prakriti concepts can augment the efficiency of drug discovery and development programs through a unique initiative of Ayurgenomics TRISUTRA consortium. Five aspects that have been carried out are (1) analysis of variability in FDA approved pharmacogenomics genes/SNPs in exomes of 72 healthy individuals including predominant Prakriti types and matched controls from a North Indian Indo-European cohort (2) establishment of a consortium network and development of five genetically homogeneous cohorts from diverse ethnic and geo-climatic background (3) identification of parameters and development of uniform standard protocols for objective assessment of Prakriti types (4) development of protocols for Prakriti evaluation and its application in more than 7500 individuals in the five cohorts (5) Development of data and sample repository and integrative omics pipelines for identification of genomic correlates. Highlight of the study are (1) Exome sequencing revealed significant differences between Prakriti types in 28 SNPs of 11 FDA approved genes of pharmacogenomics relevance viz. CYP2C19, CYP2B6, ESR1, F2, PGR, HLA-B, HLA-DQA1, HLA-DRB1, LDLR, CFTR, CPS1. These variations are polymorphic in diverse Indian and world populations included in 1000 genomes project. (2) Based on the phenotypic attributes of Prakriti we identified anthropometry for anatomical features, biophysical parameters for skin types, HRV for autonomic function tests, spirometry for vital capacity and gustometry for taste thresholds as objective parameters. (3) Comparison of Prakriti phenotypes across different ethnic, age and gender groups led to identification of invariant features as well as some that require weighted considerations across the cohorts. Considering the molecular and genomics differences underlying Prakriti and relevance in disease pharmacogenomics studies, this novel integrative platform would help in identification of differently susceptible and drug responsive population. Additionally, integrated analysis of phenomic and genomic variations would not only allow identification of clinical and genomic markers of Prakriti for application in personalized medicine but also its integration in drug discovery and development programs. Show less

Multicomponent molecular modifications such as DNA methylation may offer sensitive and specific cervical intraepithelial neoplasia and cervical cancer biomarkers. In this study, we tested cervical tissues at various stages of tumor progression for 5-methylcytosine and 5-hydroxymethylcytosine levels and also DNA promoter methylation profile of a panel of genes for its diagnostic potential. In total, 5-methylcytosine, 5-hydroxymethylcytosine, and promoter methylation of 33 genes were evaluated by reversed-phase high-performance liquid chromatography, enzyme-linked immunosorbent assay based technique, and bisulfate-based next generation sequencing. The 5-methylcytosine and 5-hydroxymethylcytosine contents were significantly reduced in squamous cell carcinoma and receiver operating characteristic curve analysis showed a significant difference in (1) 5-methylcytosine between normal and squamous cell carcinoma tissues (area under the curve = 0.946) and (2) 5-hydroxymethylcytosine levels among normal, squamous intraepithelial lesions and squamous cell carcinoma. Analyses of our next generation sequencing results and data from five independent published studies consisting of 191 normal, 10 low-grade squamous intraepithelial lesions, 21 high-grade squamous intraepithelial lesions, and 335 malignant tissues identified a panel of nine genes ( ARHGAP6, DAPK1, HAND2, NKX2-2, NNAT, PCDH10, PROX1, PITX2, and RAB6C) which could effectively discriminate among the various groups with sensitivity and specificity of 80%-100% (p < 0.05). Furthermore, 12 gene promoters (ARHGAP6, HAND2, LHX9, HEY2, NKX2-2, PCDH10, PITX2, PROX1, TBX3, IKBKG, RAB6C, and DAPK1) were also methylated in one or more of the cervical cancer cell lines tested. The global and gene-specific methylation of the panel of genes identified in our study may serve as useful biomarkers for the early detection and clinical management of cervical cancer. Show less

Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10 Show less

Mechanosensory hair cells (HCs) residing in the inner ear are critical for hearing and balance. Precise coordination of proliferation, sensory specification, and differentiation during development is essential to ensure the correct patterning of HCs in the cochlear and vestibular epithelium. Recent studies have revealed that FGF20 signaling is vital for proper HC differentiation. However, the mechanisms by which FGF20 signaling promotes HC differentiation remain unknown. Here, we show that mitogen-activated protein 3 kinase 4 (MEKK4) expression is highly regulated during inner ear development and is critical to normal cytoarchitecture and function. Mice homozygous for a kinase-inactive MEKK4 mutation exhibit significant hearing loss. Lack of MEKK4 activity in vivo also leads to a significant reduction in the number of cochlear and vestibular HCs, suggesting that MEKK4 activity is essential for overall development of HCs within the inner ear. Furthermore, we show that loss of FGF20 signaling in vivo inhibits MEKK4 activity, whereas gain of Fgf20 function stimulates MEKK4 expression, suggesting that Fgf20 modulates MEKK4 activity to regulate cellular differentiation. Finally, we demonstrate, for the first time, that MEKK4 acts as a critical node to integrate FGF20-FGFR1 signaling responses to specifically influence HC development and that FGFR1 signaling through activation of MEKK4 is necessary for outer hair cell differentiation. Collectively, this study provides compelling evidence of an essential role for MEKK4 in inner ear morphogenesis and identifies the requirement of MEKK4 expression in regulating the specific response of FGFR1 during HC development and FGF20/FGFR1 signaling activated MEKK4 for normal sensory cell differentiation. Sensory hair cells (HCs) are the mechanoreceptors within the inner ear responsible for our sense of hearing. HCs are formed before birth, and mammals lack the ability to restore the sensory deficits associated with their loss. In this study, we show, for the first time, that MEKK4 signaling is essential for the development of normal cytoarchitecture and hearing function as MEKK4 signaling-deficient mice exhibit a significant reduction of HCs and a hearing loss. We also identify MEKK4 as a critical hub kinase for FGF20-FGFR1 signaling to induce HC differentiation in the mammalian cochlea. These results reveal a new paradigm in the regulation of HC differentiation and provide significant new insights into the mechanism of Fgf signaling governing HC formation. Show less

Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its progression to more severe disease states. Show less

Androgens are essential for sexual development and reproduction. However, androgen regulation in health and disease is poorly understood. We showed that human adrenocortical H295R cells grown under starvation conditions acquire a hyperandrogenic steroid profile with changes in steroid metabolizing enzymes HSD3B2 and CYP17A1 essential for androgen production. Here we studied the regulatory mechanisms underlying androgen production in starved H295R cells. Microarray expression profiling of normal versus starved H295R cells revealed fourteen differentially expressed genes; HSD3B2, HSD3B1, CYP21A2, RARB, ASS1, CFI, ASCL1 and ENC1 play a role in steroid and energy metabolism and ANGPTL1, PLK2, DUSP6, DUSP10 and FREM2 are involved in signal transduction. We discovered two new gene networks around RARB and ANGPTL1, and show how they regulate androgen biosynthesis. Transcription factor RARB stimulated the promoters of genes involved in androgen production (StAR, CYP17A1 and HSD3B2) and enhanced androstenedione production. For HSD3B2 regulation RARB worked in cooperation with Nur77. Secretory protein ANGPTL1 modulated CYP17A1 and DUSP6 expression by inducing ERK1/2 phosphorylation. By contrast, our studies revealed no evidence for hormones or cell cycle involvement in regulating androgen biosynthesis. In summary, these studies establish a firm role for RARB and ANGPTL1 in the regulation of androgen production in H295R cells. Show less

Diabetes impacts approximately 200 million people worldwide, of whom approximately 10% are affected by type 1 diabetes (T1D). The application of genome-wide association studies (GWAS) has robustly revealed dozens of genetic contributors to the pathogenesis of T1D, with the most recent meta-analysis identifying in excess of 40 loci. To identify additional genetic loci for T1D susceptibility, we examined associations in the largest meta-analysis to date between the disease and ∼2.54 million SNPs in a combined cohort of 9,934 cases and 16,956 controls. Targeted follow-up of 53 SNPs in 1,120 affected trios uncovered three new loci associated with T1D that reached genome-wide significance. The most significantly associated SNP (rs539514, P = 5.66×10⁻¹¹) resides in an intronic region of the LMO7 (LIM domain only 7) gene on 13q22. The second most significantly associated SNP (rs478222, P = 3.50×10⁻⁹ resides in an intronic region of the EFR3B (protein EFR3 homolog B) gene on 2p23; however, the region of linkage disequilibrium is approximately 800 kb and harbors additional multiple genes, including NCOA1, C2orf79, CENPO, ADCY3, DNAJC27, POMC, and DNMT3A. The third most significantly associated SNP (rs924043, P = 8.06×10⁻⁹ lies in an intergenic region on 6q27, where the region of association is approximately 900 kb and harbors multiple genes including WDR27, C6orf120, PHF10, TCTE3, C6orf208, LOC154449, DLL1, FAM120B, PSMB1, TBP, and PCD2. These latest associated regions add to the growing repertoire of gene networks predisposing to T1D. Show less

Extracellular signal-regulated kinase 5 (ERK5), the newest member of the mitogen-activated protein (MAP) kinase family, is regulated differently than the other MAP kinases. Emerging evidence suggest the role of ERK5 signaling in promoting cell proliferation, differentiation, neuronal survival, and neuroprotection. The present study investigates whether suicide brain is associated with alterations in components of the ERK5 signaling cascade. In the prefrontal cortex (PFC) and hippocampus of suicide subjects (n=28) and nonpsychiatric control subjects (n=21), we examined the catalytic activities and protein levels of ERK5 and upstream MAP kinase kinase MEK5 in various subcellular fractions; mRNA levels of ERK5 in total RNA; and DNA-binding activity of myocyte enhancer factor (MEF)2C, a substrate of ERK5. In the hippocampus of suicide subjects, we observed that catalytic activity of ERK5 was decreased in cytosolic and nuclear fractions, whereas catalytic activity of MEK5 was decreased in the total fraction. Further, decreased mRNA and protein levels of ERK5, but no change in protein level of MEK5 were noted. A decrease in MEF2C-DNA-binding activity in the nuclear fraction was also observed. No significant alterations were noted in the PFC of suicide subjects. The observed changes were not related to a specific psychiatric diagnosis. Our findings of reduced activation and/or expression of ERK5 and MEK5, and reduced MEF2C-DNA-binding activity demonstrate abnormalities in ERK5 signaling in hippocampus of suicide subjects and suggest possible involvement of this aberrant signaling in pathogenic mechanisms of suicide. Show less