👤 Shivani Mishra

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder driven by complex genetic and molecular interactions. Despite major advances in genomics, current discoveries explain less than 40% of AD heritability, underscoring the need for integrative approaches that capture cross-omic regulation. Here, we propose a multiomics integration framework combining genomic, epigenomic, and transcriptomic data sets to identify convergent molecular signatures underlying AD pathogenesis. An integrated epigenome-wide association study-genome wide association study (EWAS-GWAS) analysis using GeneCards and VarElect identified 42 candidate genes, showing overlap between genetic susceptibility and epigenetic dysregulation. These include canonical AD loci (APOE, CLU, BIN1, PICALM, and TREM2) and novel regulatory genes such as AKT1, DOT1L, SREBF1, and PVT1. Network analysis revealed 32 nodes and 30 edges with an average node degree of 1.88 and a protein-protein interaction (PPI) enrichment p-value of 6.45 × 10 Show less

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by memory loss, cognitive decline, and neuronal dysfunction. Despite thorough research efforts, effective disease-modifying treatments have yet to be discovered. MicroRNAs (miRNAs), small noncoding RNAs that control gene expression after transcription, have become key factors in AD development. Changes in miRNA levels influence critical molecular pathways such as amyloid precursor protein (APP) processing, tau phosphorylation, oxidative stress, neuroinflammation, and synaptic plasticity, all of which contribute to neuronal damage. By increasing β-secretase (BACE1) activity, downregulation of miR-29a/b and miR-107 encourages the buildup of amyloid-β (Aβ) and the development of plaques. Through the deregulation of the CDK5 and MAPK pathways, overexpression of miR-125b and decreased levels of miR-132/212 lead to tau hyperphosphorylation. While oxidative stress-associated miRNAs like miR-34a and miR- 21 worsen mitochondrial malfunction and neuronal death, pro-inflammatory miRNAs like miR-146a and miR-155 cause NF-κB-mediated signalling and glial activation. Circulating miRNAs found in blood and cerebral fluid are potential, minimally invasive indicators for tracking the course of a disease and making early diagnoses. Additionally, therapeutic manipulation with antagomiRs or miRNA mimics has the potential to prevent neurodegeneration and restore normal gene regulation. This review deciphers the molecular mechanisms underlying miRNA dysregulation in AD and explores their translational potential as biomarkers and therapeutic targets. A comprehensive understanding of miRNA-protein interaction networks could facilitate the development of targeted, precision- based interventions for Alzheimer's disease. Show less

Glyphosate, one of the most widely used herbicides worldwide, has raised significant concerns regarding its potential involvement in hepatotoxicity and molecular changes associated with liver cancer biology. These concerns highlight the need to better understand its underlying molecular mechanisms in hepatoma cells. Emerging evidence suggests that glyphosate exposure may increase the risk of liver cancer and chronic liver disease. However, the precise molecular alterations and promising biomarkers associated with glyphosate-induced hepatic toxicity and disease remain largely unexplored. In this study, an RNA-Seq-based in silico systems biology approach was employed to elucidate glyphosate-induced differential transcriptional profiling in hepatoma cells. This analysis revealed significant transcriptional profiling characterized by the upregulated hub genes Show less

This study investigates how sorafenib induces toxicity in glomerular cells and examines the protective role of 8,9-epoxyeicosatrienoic acid (8,9-EET) analogs in reducing this kidney damage. Human renal mesangial cells (HRMCs) and podocytes were treated with no treatment, sorafenib alone, or sorafenib combined with 8,9-EET analogs. Cell viability and apoptosis were measured in both cell types. Sorafenib (1-10 µM) lowered cell viability and increased caspase 3/7 activity in a dose-dependent way in HRMCs and podocytes. Five of twenty 8,9-EET analogs significantly enhanced cell survival and decreased apoptosis. RNA sequencing showed that sorafenib altered 1244 genes, including those involved in cell cycle and the Raf/MEK/ERK pathway. The 8,9-EET analog MDB-52a raised ANGPTL4 levels, linked to metabolism and vascular health, and reduced ACTA2, which could activate protective pathways. Nephroseq data correlated these gene changes with glomerulosclerosis. MDB-52 appears to counteract gene disruptions and protect against sorafenib-induced kidney damage. Overall, 8,9-EET analogs targeting glomerular cells could be potential therapeutic agents to lessen sorafenib-related nephrotoxicity. Show less

Gene-environment (GxE) interactions crucially contribute to complex phenotypes. The statistical power of a GxE interaction study is limited mainly due to weak GxE interaction effect sizes. Joint tests of the main genetic and GxE effects for a univariate phenotype were proposed to utilize the individually weak GxE effects to improve the discovery of associated genetic loci. We develop a testing procedure to evaluate combined genetic and GxE effects on multiple related phenotypes to enhance the power by merging pleiotropy in the main genetic and GxE effects. We base the approach on a general linear hypothesis testing framework for multivariate regression of continuous phenotypes. We implement the generalized estimating equations (GEE) technique under the seemingly unrelated regressions (SUR) setup for binary or mixed phenotypes. We use extensive simulations to show that the test for joint multi-phenotype genetic and GxE effects outperforms the univariate joint test of genetic and GxE effects and the test for multi-phenotype GxE effect concerning power when there is pleiotropy. The test produces a higher power than the test for the multi-phenotype marginal genetic effect for a weak genetic and substantial GxE effect. For more prominent genetic effects, the latter performs better with a limited increase in power. Overall, the multi-phenotype joint approach offers robust, high power across diverse simulation scenarios. We apply the methods to lipid phenotypes with sleep duration as an environmental factor in the UK Biobank. The proposed approach identified ten independent associated genetic loci missed by other competing methods. In a multi-phenotype analysis of apolipoproteins, ApoA1, and ApoB, our approach discovered two distinct loci considering sleep duration as the environmental factor. Show less

The Sahiwal are among the most prominent international transboundary dairy cattle distributed in large numbers between India and Pakistan. With the elapse of more than seven decades after the independence and limited cross-border exchange of Sahiwal germplasm, one thought-provoking question arises as to whether natural and artificial selection could alter the genomic signature patterns in the Sahiwal, reared for different purposes in these two countries. Deciphering the genetic mechanisms that underlie economic traits is essential for advancement and long-term breeding plans that are reflected in the distinct selection signatures they carry. To identify these genomic signatures, three medium-density SNP datasets of Sahiwal from three geographical locations of India and Pakistan were analyzed, using De-Correlated Composite of Multiple Selection Signals technique to identify the major candidate genes. In the genome of Sahiwal, a total of 70 genomic regions with 261 protein-coding genes were found. Milk production (NEK11, HMGCS1, BTN1A1,KCNH3), reproduction (SH3BGR, PSMG1, BRWD1,B3GALT5) and immune response genes (BPIFB1, MCOLN2) were more closely related to the Indian Sahiwal. Pakistani Sahiwal had genes closely linked with the dual-purpose meat (RALGAPA2, RIN2, CFAP61), and milk (SLC24A3 GALNT17, BACH2) traits. Our findings revealed differential patterns of selection signatures in transboundary Sahiwal cattle. Show less

This report aims to demonstrate the phenotypic, radiological, and genetic features of encephalocraniocutaneous lipomatosis (ECCL), a rare neurocutaneous disorder characterized by a distinct triad of congenital skin lesions, ocular anomalies, and central nervous system (CNS) abnormalities. The mosaic nature of ECCL puts the radiologist in a unique position to facilitate its prompt diagnosis. In the patient reported here, pulmonic stenosis and facial dysmorphism initially raised the suspicion of Noonan syndrome, which was unsupported by genetic testing. Serial imaging revealed multiple intracranial lipomas and glioma along with a clinically evident nevus psiloliparus, prompting further genetic evaluation. This identified a novel de novo variant in FGFR1 (c.1685A > C, p.Glu562Ala). The variant appeared heterozygous in blood and cheek swab cells derived DNA, contrasting with the typical mosaic nature of variants in ECCL. Show less

India accounts for 26 % of global tuberculosis (TB) cases, with delayed diagnosis of Mycobacterium tuberculosis (MTB) and drug resistance exacerbating disease transmission. Conventional drug susceptibility testing (DST) remains time-consuming, while molecular tools like the Xpert MTB/RIF assay-though rapid-are limited to detecting MTB and rifampicin (RIF) resistance. Testing for isoniazid (INH) and second-line drugs requires the costly Xpert MTB/XDR assay. Although line probe assays (LPAs) identifies first- and second-line drug resistance, their accessibility is restricted to specialized laboratories. This underscores the need for a rapid, cost-effective alternative to diagnose resistance to INH and fluoroquinolones (FQs). A cross-sectional study was performed at the Department of Microbiology, AIIMS Bhubaneswar, and the Intermediate Reference Laboratory (IRL), Cuttack, from March 2022 to April 2023. MTB isolates (n = 123) were analyzed using LPAs (Hain Lifescience's Genotype MTBDRplus and Genotype MTBDRsl) and multiplex allele-specific (MAS) PCR. The MAS-PCR targeted mutations in katG codon 315 and the inhA-15 promoter region for INH resistance, and gyrA codon 94 for FQ resistance. MAS-PCR identified INH resistance in 28/123 (22.76 %) isolates. Compared to LPA, MAS-PCR demonstrated sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of 80.77 %, 93.81 %, 77.78 %, 94.79 %, and 91.06 %, respectively, for INH resistance. For FQ resistance, MAS-PCR identified 19/123 (15.44 %) resistant isolates, with sensitivity, specificity, PPV, NPV, and accuracy of 87.50 %, 95.33 %, 73.68 %, 98.08 %, and 94.31 %, respectively, relative to LPA. MAS-PCR offers a rapid, technically feasible, and cost-effective method for detecting resistance to INH and FQs. Its high accuracy and affordability position it as a viable alternative in resource-limited settings, facilitating timely TB diagnosis and resistance management. Show less

Pyoderma gangrenosum (PG) is a rare, noninfectious, truly nongangrenous, autoinflammatory condition marked by neutrophilic dermatosis. It is characterized by the rapid onset of painful, full-thickness, ulcerative skin lesions with distinctive violaceous and undermined borders. PG is commonly associated with autoimmune and hematologic disorders, namely, inflammatory bowel disease (IBD) and monoclonal gammopathy of undetermined significance (MGUS). However, it has less commonly been reported in association with lymphoplasmacytic lymphoma (LPL) and rarely with its subtype, Waldenström macroglobulinemia (WM). This case unfolds the story of a 72-year-old female patient with a complex medical and primarily cutaneous oncological history, who initially developed painful lesions on her shins suspected to be PG with a superimposed infection. During extensive infectious, rheumatologic, and oncologic workup revealing an IgM monoclonal gammopathy and antibiotic-resistant infections, her condition quickly deteriorated with altered mental status and eventual cardiopulmonary arrest 2 months after the initial PG diagnosis. This case highlights the importance of close follow-up after PG identification for unusual underlying malignancies and suggests that even an indolent malignancy like WM can contribute to aggressive clinical decline in this setting. Show less

With increasing life expectancy, the prevalence of cardiovascular disease (CVD) accompanied by comorbidities is rising, presenting a growing challenge for healthcare systems. Understanding shared genetic factors underlying CVD and its comorbid conditions may facilitate the development of more effective strategies for prevention and treatment. In this study, we investigated genetic correlations between CVD and common comorbidities using genome-wide association study (GWAS) summary statistics from the FinnGen R12 release, comprising data from 500,000 Finnish individuals. Following standard quality control procedures, we examined 19 disease endpoints using linkage disequilibrium score regression (LDSC) to estimate heritability and pairwise genetic correlations. Disease traits with significant heritability (z-score ≥ 4) and Bonferroni-corrected significant correlations (adjusted Out of the 19 diseases, four CVDs (transient ischemic attack, atrial fibrillation, myocardial infarction and heart failure) and seven comorbidities (type 2 diabetes, asthma, obesity, depression, chronic obstructive pulmonary disease, gingivitis and hypertension) showed statistically significant genetic correlations. A multivariate GWAS of the LGF identified 141 novel associated loci across 29 independent SNPs. These loci overlapped with 16 protein-coding genes, including These findings underscore a shared genetic architecture between CVD and its comorbidities. We provide genetic evidence supporting the re-evaluation of these gene targets in the context of integrated, holistic and multi-disease treatment strategies. The online version contains supplementary material available at 10.1186/s12920-025-02279-1. Show less

HNSCC is a highly aggressive cancer of the head and neck region, and there is an urgent need to find novel potential targets for its diagnosis and treatment. Long non-coding RNAs (lncRNAs) have emerged as important therapeutic and diagnostic targets for multiple cancers, including HNSCC. LINC01518 promotes the proliferation of oesophageal cancer cells, but the involvement of LINC01518 in HNSCC pathophysiology is unknown. We show that LINC01518 expression is significantly upregulated in high-grade HNSCC tumor samples in comparison to normal tissue, and transforming growth factor- β (TGF-β) promotes LINC01518 expression in HNSCC cell lines. Loss-of-function studies suggest that LINC01518 promotes cell proliferation, migration, and invasion in HNSCC cells. In addition, LINC01518 depletion sensitizes HNSCC cells to cisplatin-mediated apoptosis. Mechanistically, LINC01518 acts as a competitive endogenous RNA and binds to miR-1-3p and miR-216b-5p, resulting in up-regulation of their target genes Slug and GRP78, respectively. Our findings suggest that LINC01518 is an attractive therapeutic target for HNSCC. Show less

This work involved the preparation of pristine and iron nanoparticle-loaded biochar from a water chestnut shell to remove diclofenac sodium (DCF) containing effluent of pharmaceutical origin. To create suitable forecasting equations for the modelling of the DCF adsorption onto the adsorbent, response surface methodology (RSM) was used. The parameters, e.g. pH, adsorbent mass, DCF concentration and contact time, were used for the modeling of adsorption. The RSM model predicts that for 98.0% DCF removal, the ideal conditions are pH 6, an adsorbent dose of 0.5 g L Show less

The interaction between stromal and tumor cells in tumor microenvironment is a crucial factor in Mantle cell lymphoma (MCL) progression and therapy resistance. We have identified a long non-coding RNA, CERS6-AS1, upregulated in MCL and associated with poor overall survival. CERS6-AS1 expression was elevated in primary MCL within stromal microenvironment and in a subset of MCL cells adhered to stromal layer. These stromal-adhered MCL-subsets exhibited cancer stem cell signatures than suspension counterparts. Mechanistically, we found that downregulating CERS6-AS1 in MCL reduced Fibroblast Growth Factor Receptor-1 (FGFR1), expression attributed to loss of its interaction with RNA-binding protein nucleolin. In addition, using in-silico approach, we have discovered a direct interaction between nucleolin and 5'UTR of FGFR1, thereby regulating FGFR1 transcript stability. We discovered a positive association of CERS6-AS1 with cancer stem cell signatures, and Wnt signaling. Building on these, we explored potential therapeutic strategies where combining nucleolin-targeting agent with FGFR1 inhibition significantly contributed to reversing cancer stem cell signatures and abrogated primary MCL cell growth on stromal layer. These findings provide mechanistic insights into regulatory network involving CERS6-AS1, nucleolin, and FGFR1 axis-associated crosstalk between tumor cells and stromal cell interaction and highlights therapeutic potential of targeting a non-coding RNA in MCL. Show less

The exposure of broiler chickens to high ambient temperatures causes heat stress (HS), negatively affecting their health and production performance. To mitigate heat stress in broilers, various strategies, including dietary, managerial, and genetic interventions, have been extensively tested with varying degrees of efficacy. For sustainable broiler production, it is imperative to develop an innovative approach that effectively mitigates the adverse effects of HS. Our previous studies have provided valuable insights into the effects of prehatch embryonic thermal manipulation (TM) and posthatch baicalein supplementation on embryonic thermotolerance, metabolism, and posthatch growth performance. This follow-up study investigated the effect of these interventions on gluconeogenesis and lipid metabolism in the liver, as well as muscle proliferation and regeneration capacity in heat-stressed broiler chickens. A total of six-hundred fertile Cobb 500 eggs were incubated for 21 d. After candling, 238 eggs were subjected to TM at 38.5°C with 55% relative humidity (RH) from embryonic day (ED) 12 to 18. These eggs were transferred to the hatcher and kept at a standard temperature (37.5°C) from ED 19 to 21, while 236 eggs were incubated at a controlled temperature (37.5°C) till hatch. After hatching, 180 day-old chicks from both groups were raised in 36 pens treatment (n = 10 birds/pen, 6 replicates per treatment). The treatments were: 1) Control, 2) TM, 3) Control heat stress (CHS), 4) Thermal manipulation heat stress (TMHS), 5) Control heat stress supplement (CHSS), and 6) Thermal manipulation heat stress supplement (TMHSS). Baicalein was added to the treatment group diets starting from d 1. All birds were raised under the standard environment for 21 d, followed by chronic heat stress from d 22 to 35 (32-33 ⁰C for 8 h) in the CHS, TMHS, CHSS, and TMHSS groups. A thermoneutral (22-24⁰C) environment was maintained in the Control and TM groups. RH was constant (50 ± 5%) throughout the trial. In the liver, TM significantly increased (P < 0.05) IGF2 expression. Baicalein supplementation significantly increased (P < 0.05) HSF3, HSP70, SOD1, SOD2, TXN, PRARα, and GHR expression. Moreover, the combination of TM and baicalein supplementation significantly increased (P < 0.05) the expression of HSPH1, HSPB1, HSP90, LPL, and GHR. In the muscle, TM significantly increased (P < 0.05) HSF3 and Myf5 gene expression. TM and baicalein supplementation significantly increased (P < 0.05) the expression of MyoG and significantly (P < 0.05) decreased mTOR and PAX7. In conclusion, the prehatch TM of embryos and posthatch baicalein supplementation mitigated the deleterious effects of HS on broiler chickens by upregulating genes related to liver gluconeogenesis, lipid metabolism, and muscle proliferation. Show less

In this study, comparative analysis of skeletal muscle transcriptome was carried out for four biological replicates of Aseel, a fighter type breed and Punjab Brown, a meat type breed of India. The profusely expressed genes in both breeds were related to muscle contraction and motor activity. Differential expression analysis identified 961 up-regulated and 979 down-regulated genes in Aseel at a threshold of log Show less

Alzheimer's disease (AD) is the prime cause of 65-80% of dementia cases and is caused by plaque and tangle deposition in the brain neurons leading to brain cell degeneration. β-secretase (BACE-1) is a key enzyme responsible for depositing extracellular plaques made of β-amyloid protein. Therefore, efforts are being applied to develop novel BACE-1 enzyme inhibitors to halt plaque build-up. In our study, we analyzed some Elenbecestat analogues (a BACE-1 inhibitor currently in clinical trials) using a structure-based drug design and scaffold morphing approach to achieve a superior therapeutic profile, followed by in silico studies, including molecular docking and pharmacokinetics methodologies. Among all the designed compounds, SB306 and SB12 showed good interactions with the catalytic dyad motifs (Asp228 and Asp32) of the BACE-1 enzyme with drug-likeliness properties and a high degree of thermodynamic stability confirmed by the molecular dynamic and stability of the simulated system indicating the inhibitory nature of the SB306 and SB12 on BACE 1. Show less

Herpetic stromal keratitis (HSK) is a painful and vision-impairing disease caused by recurrent HSV-1 infection of the cornea. The virus replication in the corneal epithelium and associated inflammation play a dominant role in HSK progression. Current HSK treatments targeting inflammation or virus replication are partially effective and promote HSV-1 latency, and long-term use can cause side effects. Thus, understanding molecular and cellular events that control HSV-1 replication and inflammation is crucial for developing novel HSK therapies. In this study, we report that ocular HSV-1 infection induces the expression of IL-27, a pleiotropic immunoregulatory cytokine. Our data indicate that HSV-1 infection stimulates IL-27 production by macrophages. Using a primary corneal HSV-1 infection mouse model and IL-27 receptor knockout mice, we show that IL-27 plays a critical role in controlling HSV-1 shedding from the cornea, the optimum induction of effector CD4+ T cell responses, and limiting HSK progression. Using in vitro bone marrow-derived macrophages, we show that IL-27 plays an antiviral role by regulating macrophage-mediated HSV-1 killing, IFN-β production, and IFN-stimulated gene expression after HSV-1 infection. Furthermore, we report that IL-27 is critical for macrophage survival, Ag uptake, and the expression of costimulatory molecules involved in the optimum induction of effector T cell responses. Our results indicate that IL-27 promotes endogenous antiviral and anti-inflammatory responses and represents a promising target for suppressing HSK progression. Show less

Dendritic cells (DCs) undergo rapid metabolic reprogramming to generate signal-specific immune responses. The fine control of cellular metabolism underlying DC immune tolerance remains elusive. We have recently reported that NCoR1 ablation generates immune-tolerant DCs through enhanced IL-10, IL-27 and SOCS3 expression. In this study, we did comprehensive metabolic profiling of these tolerogenic DCs and identified that they meet their energy requirements through enhanced glycolysis and oxidative phosphorylation (OXPHOS), supported by fatty acid oxidation-driven oxygen consumption. In addition, the reduced pyruvate and glutamine oxidation with a broken TCA cycle maintains the tolerogenic state of the cells. Mechanistically, the AKT-mTOR-HIF-1α-axis mediated glycolysis and CPT1a-driven β-oxidation were enhanced in these tolerogenic DCs. To confirm these observations, we used synthetic metabolic inhibitors and found that the combined inhibition of HIF-1α and CPT1a using KC7F2 and etomoxir, respectively, compromised the overall transcriptional signature of immunological tolerance including the regulatory cytokines IL-10 and IL-27. Functionally, treatment of tolerogenic DCs with dual KC7F2 and etomoxir treatment perturbed the polarization of co-cultured naïve CD4 Show less

Immunophenotyping by flow cytometry (FCM) is a useful diagnostic tool for the evaluation of mature B-cell neoplasms (MBN). Here, CD200 expression may play a significant role and improve the distinction between various MBNs, but any potential as a prognostic marker is yet to be established. The present prospective study was conducted on all the suspected cases of MBNs. Immunophenotyping was done using a BD FACS Canto FCM using a panel of 4 to 6 color combinations of monoclonal antibodies; CD45, CD34, CD5, CD19, CD20, CD22, CD23, CD79b, FMC7, CD10, CD38, ZAP70, CD200, IgG, IgM, CD25, CD103, CD2, CD3, CD11c as well as κ and λ light chains. CD200 expression was compared in different subgroups. Of the total of 130 cases included in the study, CD200 was positive in 118 cases (90%). CD200 was expressed in 100% of the cases of CLL(86 cases), atypical CLL(06 cases), HCL(14 cases), FL(02 cases), SMZL(04 cases), LPL (01 case), and low-grade NHL (05 cases), with the highest intensity of fluorescence in HCL followed by CLL. All the cases of MCL and PLL were exclusively negative for CD200. In conclusion, the results of the present study support inclusion of this marker in the flow cytometric panels for the differential diagnosis of MBNs. Show less

Fetal alcohol spectrum disorders (FASDs) are associated with systemic inflammation and neurodevelopmental abnormalities. Several candidate genes were found to be associated with fetal alcohol exposure (FAE)-associated behaviors, but a sex-specific complete transcriptomic analysis was not performed at the adult stage. Recent studies have shown that they are regulated at the developmental stage. However, the sex-specific role of RNA in FAE offspring brain development and function has not been studied yet. Here, we carried out the first systematic RNA profiling by utilizing a high-throughput transcriptomic (RNA-seq) approach in response to FAE in the brain cortex of male and female offspring at adulthood (P60). Our RNA-seq data analysis suggests that the changes in RNA expression in response to FAE are marked sex-specific. We show that the genes Muc3a, Pttg1, Rec8, Clcnka, Capn11, and pnp2 exhibit significantly higher expression in the male offspring than in the female offspring at P60. FAE female mouse brain sequencing data also show an increased expression of Eno1, Tpm3, and Pcdhb2 compared to male offspring. We performed a pathway analysis using a commercial software package (Ingenuity Pathway Analysis). We found that the sex-specific top regulator genes (Rictor, Gaba, Fmri, Mlxipl) are highly associated with eIF2 (translation initiation), synaptogenesis (the formation of synapses between neurons in the nervous system), sirtuin (metabolic regulation), and estrogen receptor (involved in obesity, aging, and cancer) signaling. Taken together, our transcriptomic results demonstrate that FAE differentially alters RNA expression in the adult brain in a sex-specific manner. Show less

Congenital myasthenic syndromes (CMS) are rare, heterogeneous, and often treatable genetic disorders depending on the underlying molecular defect. We performed a detailed clinical evaluation of seven patients from five unrelated families. Exome sequencing was performed on five index patients. Clinically significant variants were identified in four CMS disease-causing genes: COLQ (3/7), CHRNE (2/7), DOK7 (1/7), and RAPSN (1/7). We identified two novel variants, c.930₉₃₃delCATG in DOK7 and c.1016₁₀₃₂ + 2dup in CHRNE . A common pathogenic variant, c.955-2A>C, has been identified in COLQ -related CMS patients. Homozygosity mapping of this COLQ variant in patients from two unrelated families revealed that it was located in a common homozygous region of 3.2 Mb on chromosome 3 and was likely to be inherited from a common ancestor. Patients with COLQ variants had generalized muscle weakness, those with DOK7 and RAPSN variants had limb-girdle weakness, and those with CHRNE variants had predominant ocular weakness. Patients with COLQ and DOK7 variants showed improvement with salbutamol and CHRNE with pyridostigmine therapy. This study expands the mutational spectrum and adds a small but significant cohort of CMS patients from India. We also reviewed the literature to identify genetic subtypes of CMS in India. Show less

Selective permeability of the blood-brain barrier restricts the treatment efficacy of neurologic diseases. Berberine (BBR) and curcumin (CUR)-loaded transferosomes (TRANS) were prepared for the effective management of Alzheimer's disease (AD). The study involved the syntheses of BBR-TRANS, CUR-TRANS, and BBR-CUR-TRANS by the film hydration method. Vesicles were characterized to ensure the formation of drug-loaded vesicles and their in vivo performance. The particle sizes of BBR-TRANS, CUR-TRANS, and BBR-CUR-TRANS were 139.2 ± 7, 143.4 ± 8, and 165.3 ± 6.5 nm, respectively. The presence of diffused rings in the SED image indicates the crystalline nature of the payload. Low surface roughness in an AFM image could be associated with the presence of a surface lipid. BBR-CUR-TRANS showed 41.03 ± 1.22 and 47.79 ± 3.67% release of BBR and 19.22 ± 1.47 and 24.67 ± 1.94% release of CUR, respectively, in phosphate buffer saline (pH 7.4) and acetate buffer (pH 4.0). Formulations showed sustained release of both loaded drugs. BBR-TRANS, CUR-TRANS, and BBR-CUR-TRANS exhibited a lower percentage of hemolysis than pure BBR and CUR, indicating the safety of the payload from delivery vesicles. Lower percentages of binding were recorded from BBR-CUR-TRANS than BBR-TRANS and CUR-TRANS. Acetylcholinesterase inhibition activity of the prepared transferosomes was greater than that of pure drugs, which are thought to have good cellular penetration. The spatial memory was improved in treated mice models. The level of malondialdehyde decreased in AD animals treated with BBR-TRANS, CUR-TRANS, and BBR-CUR-TRANS, respectively, as compared to the scopolamine-induced AD animals. BBR-CUR-TRANS-treated animals showed the highest decrease in the NO level. The catalase level was significantly restored in scopolamine-intoxicated animals treated with BBR-TRANS, CUR-TRANS, and BBR-CUR-TRANS. The immunohistochemistry result suggested that the BBR-TRANS, CUR-TRANS, and BBR-CUR-TRANS have significantly decreased the regulation of expression of BACE-1 through antioxidant activity. In conclusion, the study highlights the utility of formulated transferosomes as promising carriers for the co-delivery of drugs to the brain. Show less

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Here, we review the impact of high-density lipoproteins (HDL) on sepsis from the perspective of biochemistry and pathophysiology, epidemiological research, and intervention studies in animals. Pathogen lipid moieties are major ligands for innate immunity receptors, such as toll-like receptors. The binding of pathogen-associated lipids to lipoproteins leads to sequestration, neutralization, and inactivation of their pro-inflammatory effects. Lipoproteins constitute an arm of the innate immune system. Pathogen-associated lipids can be removed from the body via the reverse lipopolysaccharide transport pathway in which HDL play a key role. Independent of the capacity for sequestration, the direct anti-inflammatory effects of HDL may counteract the development of sepsis. Mendelian randomization research using genetic variants associated with HDL cholesterol as an instrumental variable was consistent with a probable causal relationship between increased HDL cholesterol levels and decreased risk of infectious hospitalizations. Low HDL cholesterol independently predicts an adverse prognosis in sepsis both in observational epidemiology and in Mendelian randomization studies. Several HDL-associated enzymes, including phospholipid transfer protein (PLTP) and cholesterol ester transfer protein (CETP), undergo profound changes during sepsis. Potential HDL-directed interventions for treatment of sepsis include apolipoprotein A-I-based therapies, recombinant PLTP, and CETP inhibition. Show less

Inflammatory bowel disease (IBD) is characterized by gastrointestinal inflammation comprised of Crohn's disease and ulcerative colitis. Centers for Disease Control and Prevention report that 1.3% of the population of the United States (approximately 3 million people) were affected by the disease in 2015, and the number keeps increasing over time. IBD has a multifactorial etiology, from genetic to environmental factors. Most of the IBD treatments revolve around disease management, by reducing the inflammatory signals. We previously identified the surface layer protein A (SlpA) of Show less

Nonimmune hydrops fetalis (NIHF) has varied etiology. We assessed the etiological spectrum and evaluated the utility of fetal whole exome sequencing (fWES) for the diagnosis of NIHF. In this prospective cohort study, we evaluated antenatally diagnosed fetuses with NIHF between July 2018 and December 2019 according to the routine diagnostic algorithm. Fetuses that remained undiagnosed after routine NIHF workup were subjected to fetal chromosomal microarray and/or WES. Pregnancies were followed up for clinical outcomes. Of the 45 fetuses, consanguinity and recurrent hydrops fetalis were observed in 13.3% (6/45) and 28.8% (13/45), respectively. Overall, an etiological diagnosis was possible in 75.5% (34/45) of fetuses, while the cause remained unknown in 24.4% (11/45). A genetic etiology was identified in 46.6% (21/45): aneuploidy and monogenic disorders in 28.8% (13/45) and 17.8% (8/45), respectively. fWES on 19 fetuses detected disease-causing variants in 42.1% (8/19). Nine novel variants were detected in RAPSN, ASCC1, NEB, PKD1L1, GUSB, and PIEZO1. Only 8.8% (4/45) of the cohort survived without morbidity. This study describes the etiological spectrum and the disease-causing variants in an Indian cohort of hydropic fetuses. Show less

Retinoic acid-inducible gene I-like receptors (RLRs) are important cytosolic pattern recognition receptors (PRRs) that sense viral RNA before mounting a response leading to the activation of type I IFNs. Several viral infections induce epithelial-mesenchymal transition (EMT), even as its significance remains unclear. Here, we show that EMT or an EMT-like process is a general response to viral infections. Our studies identify a previously unknown mechanism of regulation of an important EMT-transcription factor (EMT-TF) Snail during RNA viral infections and describe its possible implication. RNA viral infections, poly(I·C) transfection, and ectopic expression of RLR components induced Snail levels, indicating that RLR pathway could regulate its expression. Detailed examination using mitochondrial antiviral signaling protein knockout (MAVS-KO) cells established that MAVS is essential in this regulation. We identified two interferon-stimulated response elements (ISREs) in the Show less

Triple-negative breast cancer is an aggressive type of breast cancer with high risk of recurrence. It is still poorly understood and lacks any targeted therapy, which makes it difficult to treat. Thus, it is important to understand the underlying mechanisms and pathways that are dysregulated in triple-negative breast cancer. To investigate the role of mitochondria in triple-negative breast cancer progression, we analysed previously reported gene expression data from triple-negative breast cancer cybrids with SUM-159 as the nuclear donor cell and SUM-159 or A1N4 (c-SUM-159, c-A1N4) as the mitochondrial donor cells and with 143B as the nuclear donor cell and MCF-10A or MDA-MB-231 (c-MCF-10A, c-MDA-MB-231) as the mitochondrial donor cells. The role of potential biomarkers in cell proliferation and migration was examined in SUM-159 and MDA-MB-231 cells using sulforhodamine B and wound healing assays. Rank product analysis of cybrid gene expression data identified 149 genes which were significantly up-regulated in the cybrids with mitochondria from the cancer cell line. Analysis of previously reported breast tumour gene expression datasets confirmed 9 of the 149 genes were amplified, up-regulated, or down-regulated in more than 10% of the patients. The genes included These results indicate that mitochondria-regulated nuclear gene expression helps breast cancer cells survive and proliferate, consistent with previous work focusing on an Src gene signature which is mitochondria regulated and drives malignancy in breast cancer cybrids. This is the first study to show that mitochondria in triple-negative breast cancer mediate significant up-regulation of a number of genes, and silencing of Show less