Comprehensive DNA methylation profiling by MeDIP-NGS identifies potential genes and pathways for epithelial ovarian cancer.

Ovarian cancer, among all gynecologic malignancies, exhibits the highest incidence and mortality rate, primarily because it is often presents with non-specific or no symptoms during its early stages. For the advancement of Ovarian Cancer Diagnosis, it is crucial to identify the potential molecular signatures that could significantly differentiate between healthy and ovarian cancerous tissues and can be used further as a diagnostic biomarker for detecting ovarian cancer. In this study, we investigated the genome-wide methylation patterns in ovarian cancer patients using Methylated DNA Immunoprecipitation (MeDIP-Seq) followed by NGS. Identified differentially methylated regions (DMRs) were further validated by targeted bisulfite sequencing for CpG site-specific methylation profiles. Furthermore, expression validation of six genes by Quantitative Reverse Transcriptase-PCR was also performed. Out of total 120 differentially methylated genes (DMGs), 68 genes were hypermethylated, and 52 were hypomethylated in their promoter region. After analysis, we identified the top 6 hub genes, namely POLR3B, PLXND1, GIGYF2, STK4, BMP2 and CRKL. Interestingly we observed Non-CpG site methylation in the case of POLR3B and CRKL which was statistically significant in discriminating ovarian cancer samples from normal controls. The most significant pathways identified were focal adhesion, the MAPK signaling pathway, and the Ras signaling pathway. Expression analysis of hypermethylated genes was correlated with the downregulation of the genes. POLR3B and GIGYF2 turned out to be the novel genes associated with the carcinogenesis of EOC. Our study demonstrated that methylation profiling through MeDIP-sequencing has effectively identified six potential hub genes and pathways that might exacerbate our understanding of underlying molecular mechanisms of ovarian carcinogenesis.

Comparing carbon footprints of sheep farming systems in semi-arid regions of India: A life cycle assessment study.

Carbon foot prints (CFs) studies based on life cycle assessment between sheep farming systems and green house gases (GHG) emissions is one of the best indicators to quantify the amount of GHG emissions per kg of product. Therefore, a life cycle assessment (LCA) study was conducted for three different sheep farming systems i.e. intensive system (stall fed only), semi-intensive (grazing with supplementation) and extensive system (grazing only) under semiarid region of India to assess the carbon cost of sheep rearing. The total CFs were estimated to be 16.9, 15.8 and 17.1 kg CO2-eq in intensive, semi-intensive and extensive system of grazing indicating semi-intensive system to be most carbon (C) efficient. For 1kg mutton production in semi-intensive and intensive system, around 30% and 24% CFs were contributed from enteric fermentation and feed respectively, whereas, in extensive system, the contribution of enteric fermentation increased up to 50%. The carbon foot prints analysis gives an insight of carbon inputs used but the amount of CO2 sequestered in soil making LCA a holistic approach for estimating GHG emissions from livestock.

Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer.

Epithelial ovarian cancer (EOC) is the most aggressive and frequent malignancy detected among women worldwide. The pathophysiology of OC should, therefore be better understood to identify diagnostic, prognostic, and predictive novel biomarkers necessary for early detection, management, and prognostication. In this study, we aimed to investigate transcriptomic landscape and biomarker through RNA-seq data analysis. Further analysis by Protein Protein network identified top 10 Differentially Expressed Genes (DEGs). KEGG pathway enrichment analysis revealed the significant enrichment of DEGs in basal cell carcinoma, cell cycle and FoxO signalling pathway. The RNA-seq results of 10 DEGs were validated by QRT-PCR and TCGA database. Correlation studies were also performed between gene expression and clinical characteristics followed by survival analysis. Finally, 8 DEGs (CDKN1A, BCL6, CDC45, WNT2, TLR5, AQP5) including two novel DEGs (CSN1S1 and NKILA) were identified showing significant correlations with EOC characteristics. These may serve as interesting biomarkers and novel treatment targets and warrant further investigation into the functional outcome of EOC.

Point-of-care prognostication in moderate Covid-19: Analytical validation and prognostic accuracy of a soluble urokinase plasminogen activator receptor (suPAR) rapid test.

The soluble urokinase plasminogen activator receptor (suPAR) has been proposed as a biomarker for risk stratification of patients presenting with acute infections. However, most studies evaluating suPAR have used platform-based assays, the accuracy of which may differ from point-of-care tests capable of informing timely triage in settings without established laboratory capacity. Using samples and data collected during a prospective cohort study of 425 patients presenting with moderate Covid-19 to two hospitals in India, we evaluated the analytical performance and prognostic accuracy of a commercially-available rapid diagnostic test (RDT) for suPAR, using an enzyme-linked immunosorbent assay (ELISA) as the reference standard. Our hypothesis was that the suPAR RDT might be useful for triage of patients presenting with moderate Covid-19 irrespective of its analytical performance when compared with the reference test. Although agreement between the two tests was limited (bias = -2.46 ng/mL [95% CI = -2.65 to -2.27 ng/mL]), prognostic accuracy to predict supplemental oxygen requirement was comparable, whether suPAR was used alone (area under the receiver operating characteristic curve [AUC] of RDT = 0.73 [95% CI = 0.68 to 0.79] vs. AUC of ELISA = 0.70 [95% CI = 0.63 to 0.76]; p = 0.12) or as part of a published multivariable prediction model (AUC of RDT-based model = 0.74 [95% CI = 0.66 to 0.83] vs. AUC of ELISA-based model = 0.72 [95% CI = 0.64 to 0.81]; p = 0.78). Lack of agreement between the RDT and ELISA in our cohort warrants further investigation and highlights the importance of assessing candidate point-of-care tests to ensure management algorithms reflect the assay that will ultimately be used to inform patient care. Availability of a quantitative point-of-care test for suPAR opens the door to suPAR-guided risk stratification of patients with Covid-19 and other acute infections in settings with limited laboratory capacity.

Drip irrigation and sulphur fertilization influenced fodder yield, quality and water use efficiency of groundnut in arid region.

Availability of ample and nutritious fodder for livestock is always a challenge in arid region. Choice of crops such as groundnut that can fulfil the requirement of fodder with its crop residues along with human needs can be a viable option to bridge the gap between availability and requirement of fodder. The fodder yield and quality largely depend on soil moisture and nutrient supply especially sulphur (S), a key nutrient for improving groundnut fodder quality. However, no researchers have given emphasis on coupling effect of drip irrigation (DI) and sulphur on fodder yield, quality, digestibility and water use efficiency (WUE). Therefore, the study was conducted to determine the effects of different regimes of DI and S on productivity and quality of fodder. Results revealed that higher regimes of DI i.e. 0.8 +1.0 PE(pan evaporation) and 1.0 PE level of irrigation along with 40 kg S ha-1 significantly improved the yield, primary quality traits (crude protein, ether extract and ash), digestibility indices and significant reduction in Fibers which indicates improvement in quality of fodder. Fodder productivity was 27.0 and 25.6% higher in 1.0 PE and 0.8+1.0 PE level of irrigation, respectively, as compared to 0.6 PE level (lower water regime) of irrigation, although 0.6 PE level of irrigation recorded higher WUE and was at par with 0.8 PE and 0.6 +1.0 PE level of DI. By changing the levels of DI from 1.0 PE to 0.8+1.0 PE, considerable water can be saved without affecting the yield and quality of fodder. Similarly, crop responded to S up to 60 kg ha-1 but at par with 40 kg S ha-1 indicating that application of extra S after 40 kg did not warrant any extra benefit in terms of fodder yield, WUE and quality of fodder. Thus, adjusting the PE levels of DI for water saving and optimal S application can be a sustainable strategy to improve the productivity and quality of groundnut fodder in arid region.

Eco-friendly phytofabrication of Ficus Benjamina L. based ZnO-doped g-C3N4 nanocomposites for remarkable photocatalysis and antibacterial applications.

The research reported here emphasizes the phytoextract route synthesized ZnO-doped g-C3N4 (GCN) for its photocatalytic activity, which helps to ensure a sustained & healthy environment. The leaf extract solution of Ficus Benjamina L. was used for the synthesis of ZnO nanoparticles, and GCN was prepared via urea using a thermal polymerization process. The flower extract functions as both stabilizers and capping agents during the process of synthesis of ZnO nanoparticles. The synthesized nanocomposites were then calcined at 400 °C and were further characterized with spectroscopy (UV-Vis), diffracted pattern (XRD), and infrared spectroscopy (FTIR). Further, the photocatalytic activity of auramine orange (AO) and methylene blue (MB) dye from phytoextract route synthesized pure ZnO NPs, GCN-Pure, and composites with varied millimolar concentrations of ZnO nanoparticles with GCN of the constant amount was checked. After the complete analysis, it was observed that the series that was prepared of ZnO-GCN nanocomposites showed notable enhancement in the degradation pattern of the methylene blue dye. Apparently, 1.5 mmol (mM) ZnO-GCN presented greater degradation patterns for Auramine orange and Methylene blue dye as compared to other nanocomposites that were synthesized. The observed increased photocatalytic activity has a conceivable explanation. The antibacterial activity studies of the prepared nanocomposites were also performed against the E. coli strain showing an enhanced zone of inhibition towards it.

Effectiveness of Adjunctive High-Dose Infliximab Therapy to Improve Disability-Free Survival Among Patients With Severe Central Nervous System Tuberculosis: A Matched Retrospective Cohort Study.

BACKGROUND: Few treatment options exist for patients with severe central nervous system (CNS) tuberculosis (TB) worsening due to inflammatory lesions, despite optimal antitubercular therapy (ATT) and steroids. Data regarding the efficacy and safety of infliximab in these patients are sparse. METHODS: We performed a matched retrospective cohort study based on Medical Research Council (MRC) grading system and modified Rankin Scale (mRS) scores comparing 2 groups of adults with CNS TB. Cohort A received at least 1 dose of infliximab after optimal ATT and steroids between March 2019 and July 2022. Cohort B received only ATT and steroids. Disability-free survival (mRS score ≤2) at 6 months was the primary outcome. RESULTS: Baseline MRC grades and mRS scores were similar between the cohorts. Median duration before initiation of infliximab therapy from start of ATT and steroids was 6 (IQR: 3.7-13) months and for neurological deficits was 4 (IQR: 2-6.2) months. Indications for infliximab were symptomatic tuberculomas (20/30; 66.7%), spinal cord involvement with paraparesis (8/30; 26.7%), and optochiasmatic arachnoiditis (3/30; 10%), worsening despite adequate ATT and steroids. Severe disability (5/30 [16.7%] and 21/60 [35%]) and all-cause mortality (2/30 [6.7%] and 13/60 [21.7%]) at 6 months were lower in cohort A versus cohort B, respectively. In the combined study population, only exposure to infliximab was positively associated (aRR: 6.2; 95% CI: 2.18-17.83; P = .001) with disability-free survival at 6 months. There were no clear infliximab-related side effects noted. CONCLUSIONS: Infliximab may be an effective and safe adjunctive strategy among severely disabled patients with CNS TB not improving despite optimal ATT and steroids. Adequately powered phase 3 clinical trials are required to confirm these early findings.

Leukotriene A4 hydrolase (LTA4H rs17525495) gene polymorphisms and paradoxical reactions in extrapulmonary tuberculosis.

Paradoxical reactions (PRs) are poorly studied complex immunological phenomena, among patients with tuberculosis (TB). When PRs involves critical structures like the central nervous system (CNS), immunomodulatory therapy is often required. Predictors for PRs in TB to pre-empt appropriate treatment strategies in high-risk groups are lacking. TT genotype of Leukotriene A4 hydrolase (LTA4H) promoter region rs17525495 polymorphisms are associated with exaggerated immune responses in Tuberculous meningitis (TBM), the most severe form of extrapulmonary tuberculosis (EPTB). The association of these polymorphisms with PRs is not known. We evaluated this plausibility among 113 patients with EPTB, at high risk of PRs. Majority [81 (71.7%)] had disseminated tuberculosis with prominent CNS [54 (47.8%)] and lymph node involvement [47 (41.6%)]. Human immunodeficiency Virus (HIV) co-infection was seen among 23 (20.3%) patients. PRs were noted in 38.9% patients, at a median duration of 3 months (IQR 2-4). LTA4H rs17525495 single nucleotide polymorphism (SNP) analysis showed 52 (46%) patients had CC, 43 (38.1%) had CT and 18 (15.9%) had TT genotypes. There was no statistically significant difference in occurrence [CC 38.5% vs CT 39.5% vs TT 38.7%] and time of onset [median (IQR)] of PRs across the genotypes [CC 3 (1-4.7), CT 3 (2-5), TT 2 (2-3)]. PRs was shown to be significantly linked with HIV co-infection (RR 0.6, 95% CI 0.29-1.28), culture positivity (RR 0.5, 95% CI 0.28-1.14), TB Lymphadenitis (RR 0.7, 95% CI 0.44-1.19) and CNS involvement RR 2.1, 95% CI 1.27-3.49) in the univariate analysis (p < 0.2). On multivariate analysis, CNS involvement alone was associated with PRs (aRR 3.8 (1.38-10.92); p < 0.01). PRs were associated with CNS involvement but not with LTA4H rs17525495 polymorphisms.

Diagnostics and Therapeutic Potential of miR-205 and miR-34a in Ovarian Cancer Management: A miRNA-Target-Based Analysis.

Epithelial ovarian cancer (EOC) treatment strategies mainly focused on surgery combined with chemotherapy. Recent targeted therapy techniques emerge as milestone and could be used for management of ovarian cancer (OC) progression with more efficacy. The aim is to evaluate the therapeutic and diagnostic potential of microRNA (miRNA) in management of EOC using in silico and quantitative real-time PCR (qRT-PCR) expression analysis. We performed functional enrichment and miRNA-Target genes expression analysis in 48 EOC and 22 normal tissue samples using qRT-PCR and correlated with miRNA expression data in matched samples to evaluate the diagnostic and therapeutic potential of miRNA in OC management. In silico functional enrichment analysis revealed miRNA association with disease. Target genes of miRNAs participate in several biologically important pathways leading to cancer progression. Targets of miRNA-205 and miRNA-34a were significantly downregulated, and upregulated, respectively, in EOC. Moreover, significant negative correlation between relative expression of miRNA-205 and target genes (BCL2, ZEB1, E2F1, and TP53) was observed with r = -0.813; r = -0.755; r = -0.559; and r = -0.767, respectively. Similarly, miRNA-34a also showed higher negative correlation with target genes (MDM4, MAPK3, BRCA1, AREG) with r = -0.840; r = -0.870; r = -0.622; and r = -0.623, respectively. In addition, receiver operating characteristics analysis of combined miRNA panel, miRNA-205-Target gene panel, and miRNA-34a-Target gene panel exhibited higher diagnostics value with area under the curve (AUC) of 92.7 (p < 0.0001), 94.8 (p < 0.0001), and 98.3 (p < 0.0001), respectively. Negative Correlation between miRNA and target genes expression data in matched samples highlights therapeutic potential of miRNA in EOC management. Moreover, combined diagnostic potential of miRNA-target gene panel could predict risk of EOC with higher AUC, sensitivity, and specificity.

Survival analysis and prognostic factors of the carcinoma of gallbladder.

BACKGROUND: The present study aims to evaluate the survival status of patients with gallbladder cancer (GBC) and explore the prognostic factors for the improvement and preventions. METHODS: The study consists of 176 patients with clinically diagnosed gallbladder cancer; the study was conducted between 2019 and 2021 registered at Kamala Nehru Memorial Cancer Hospital, Prayagraj, India. The survival rates were analyzed by the Kaplan-Meier method; survival rate difference was analyzed by log-rank test, prognosis factors; and hazard ratio for mortality outcomes was estimated using Cox regression method. RESULTS: The overall median survival time of patients was 5 months with the 1-year, 2-year, and 3-year survival rates of 24.4%, 8.5%, and 4.5%, respectively. The 3-year survival for patients with jaundice was 2.9%, liver infiltration (4.2%), gallstones (0.8%), and with advanced tumor grade (1.4%). Elderly GBC patients had lower survival rates (3.8%), while the 3-year overall survival for patients residing in urban areas dropped to zero. No patients in the tumor stage (T3/T4) and with distance metastasis stage survived in 3 years, while only 1.1% of patients with advanced nodal stage survived. On receiving surgery and radiation therapy, the 3-year survival rate increased to 19.5% and 35%, respectively. The results of multivariate analysis showed that urban region (HR = 1.568, p = 0.040), gallstone or not (1.571, p = 0.049), N stage (HR = 1.468, p = 0.029), and M stage (HR = 2.289, p < 0.0001) were independent risk factors for prognosis, while surgery or not (HR = 0.573, p = 0.030) was the protective factor for the prognosis of GBC. CONCLUSION: The overall survival of GBC in the Gangetic belt is poor. The geographical region of patients, gallstones, and N and M stage was the risk factors for prognosis, while surgery or not was the protective factor for the prognosis of GBC.

Retrospective analysis of the role of retrobulbar amphotericin-B injection in the management of COVID-19 associated rhino-orbito-cerebral-mucormycosis.

Introduction: Rhino-orbito-cerebral-mucormycosis (ROCM) is the most common form of mucormycosis observed during the second wave of COVID-19 where a steep rise in the number of cases was seen. The orbital form is almost always associated with fungal sinusitis. Among the various treatment modalities available, the role of retrobulbar Amphotericin-B injections is under-reported. This study is conducted to determine the role of transcutaneous retrobulbar amphotericin-B (TRAMB) in the management of COVID-19 associated ROCM. Methods: a retrospective analysis of 61 patients of COVID-19 associated ROCM was done, who met the inclusion criteria and presented to a tertiary care center, between May to August 2021. These patients were administered TRAMB (deoxycholate/emulsion form) along-with systemic amphotericin B. All the patients were evaluated for clinical improvement. Results: out of 61 patients, 58 (95.08%) showed overall improvement. 40 patients (65.57%) stabilized or improved clinically and 3 patients succumbed to the illness due to advanced systemic mucormycosis and acute kidney failure. Sixteen out of 58 patients underwent orbital exenteration. Out of remaining 43 patients, 35 showed complete recovery of orbital and ocular disease and the disease stabilized in eight patients. Seven patients demonstrated TRAMB associated ocular complications which however completely resolved in six patients. Conclusion: to the best of the author´s knowledge, regression of orbital mucormycosis with improvement in ptosis, proptosis, ocular motility and stabilization of visual acuity are scarcely reported in literature. Further TRAMB as a globe non-deforming treatment modality is an option available for ROCM.

Use of Ceftriaxone as a Predictor of Good Outcome in Stroke Patients: A Retrospective Chart Review.

Background: Whether ceftriaxone (CEFT) has any added advantage other than its antibiotics effect in stroke as a neuroprotective agent is not known, and this forms the base of this study. Purpose: We tried to assess the predictive role of the use of CEFT with respect to outcome in stroke patients. Methods: A retrospective chart review was conducted from a stroke registry over consecutive stroke patients admitted at a tertiary teaching institute from January 2017 to December 2018. Patients were categorized into three groups on the basis of antibiotics they received; patients without antibiotic treatment (NAB), piperacillin plus tazobactam treatment, and the CEFT treatment group. The outcome was assessed by the modified Rankin Scale at three months in good (0-3) and poor outcomes (4-6). Results: A total of 390 stroke patients were analyzed with ages ranging between 20 and 95 years and 151 of them were females. It was found that the severity at three months was significantly lower in those patients who were given CEFT antibiotic (P = 0.04; OR = 0.626; 95% CI [0.396, 0.990]). Conclusion: Stroke patients in CEFT-treated group have a better outcome compared to piperacillin-tazobactam therapy or without antibiotics use at three months. This study indicates the possibility of an additional neuroprotective effect of CEFT apart from its antibacterial property.

Host Biomarkers Reflect Prognosis in Patients Presenting With Moderate Coronavirus Disease 2019: A Prospective Cohort Study.

Efficient resource allocation is essential for effective pandemic response. We measured host biomarkers in 420 patients presenting with moderate coronavirus disease 2019 and found that different biomarkers predict distinct clinical outcomes. Interleukin (IL)-1ra, IL-6, IL-10, and IL-8 exhibit dose-response relationships with subsequent disease progression and could potentially be useful for multiple use-cases.

Metabolic Pathways, Enzymes, and Metabolites: Opportunities in Cancer Therapy.

Metabolic reprogramming enables cancer cells to proliferate and produce tumor biomass under a nutrient-deficient microenvironment and the stress of metabolic waste. A cancer cell adeptly undergoes a variety of adaptations in metabolic pathways and differential expression of metabolic enzyme genes. Metabolic adaptation is mainly determined by the physiological demands of the cancer cell of origin and the host tissue. Numerous metabolic regulators that assist cancer cell proliferation include uncontrolled anabolism/catabolism of glucose metabolism, fatty acids, amino acids metabolism, nucleotide metabolism, tumor suppressor genes, microRNAs, and many regulatory enzymes and genes. Using this paradigm, we review the current understanding of metabolic reprogramming in tumors and discuss the new strategies of cancer metabolomics that can be tapped into for cancer therapeutics.

Investigating the Role of Glutathione S- Transferase Genes, Histopathological and Molecular Subtypes, Gene-Gene Interaction and Its Susceptibility to Breast Carcinoma in Ethnic North- Indian Population.

BACKGROUND: Breast Cancer (BC) is a genetically and clinically heterogeneous disease including complex interactions between gene-gene and gene-environment components. This study aimed, to explore whether the Glutathione S- transferase (GSTs) gene polymorphism has role in BC susceptibility. We further evaluated the frequency of four subtypes of BC based on molecular classification followed by microscopic histological analysis to study the grades of invasive ductal carcinoma (IDC). MATERIALS AND METHOD: Polymorphism in GST genes in North-Indian BC patients was assessed by multiplex-PCR and PCR-RFLP methods. 105 BC patients and 145 healthy controls were enrolled for this study. Data was analyzed by calculating the odds ratio (OR) and 95% CI from logistic regression analyses. RESULTS: Our findings revealed that GSTM1 null genotype (OR = 2.231; 95% CI = 1.332-3.737; p-value= 0.002) is significantly associated to BC risk in ethnic North- Indian population. However, the risk for BC susceptibility in North-Indians does not appear to be associated with GSTT1 null genotype. The GSTP1 (Val/Val) genotype (OR=1.545; CI=0.663-3.605; p-value= 0.314) was also found to be susceptible for BC risk. Combination of three high risk GST genotypes association exhibiting gene-gene interaction further confirmed the increased risk to BC in this region. CONCLUSIONS: The results of present study indicated that polymorphism in GSTM1 and rs1695 of GSTP1 genes may influence BC development among North-Indian women. Thus, the screening of GSTM1 and GSTP1 gene should be recommended for the earlier investigation for BC as a precautionary measure.

Higher order genes interaction in DNA repair and cytokine genes polymorphism and risk to lung cancer in North Indians.

Context: Lung cancer pathological process involves cumulative effects exerted by gene polymorphism(s), epigenetic modifications, and alterations in DNA repair machinery. Further, DNA damage due to oxidative stress, chronic inflammation, and the interplay between genetic and environmental factors is also an etiologic milieu of this malignant disease. Aims: The present study aims to assess the prognostic value of DNA repair, cytokines, and GST gene polymorphism in lung cancer patients who had not received any neoadjuvant therapy. Materials and Methods: In this case-control study, 127 cases and 120 controls were enrolled. DNA from the blood samples of both patients and controls was used to genotype XRCC1Arg399Gln, XPDLys751Gln, and interleukin-1 (IL-1ß) genes by polymerase chain reaction (PCR)-restriction fragment length polymorphism method, whereas multiplex PCR was performed to genotype GSTT1 and GSTM1. Results: Binary logistic regression analysis showed that XRCC1Arg399Gln-mutant genotype (Gln/Gln, odds ratio [OR] = 4.6, 95% confidence interval [CI]: 2.2-9.6) and GSTT1 null (OR = 2.7, 95% CI: 1.6-4.5) were linked to cancer susceptibility. Generalized multidimensional reduction analysis of higher order gene-gene interaction using cross-validation testing (CVT) accuracy showed that GSTT1 (CVT 0.62, P = 0.001), XPD751 and IL-1ß (CVT 0.6, P = 0.001), and XRCC1399, XPD751, and interleukin-1 receptor antagonists (IL-1RN) (CVT 0.98, P = 0.001) were single-, two-, and three-factor best model predicted, respectively, for lung cancer risk. Classification and regression tree analysis results showed that terminal nodes which contain XRCC1399-mutant genotype (AA) had increased the risk to lung cancer. Conclusion: The present study demonstrated that XRCC1399 (Gln/Gln), GSTT1, and IL-1RN allele I, I/II served as the risk genotypes. These genes could serve as the biomarkers to predict lung cancer risk.