A prospective study on prevalence of adverse drug reactions due to antibiotics usage in otolaryngology department of a tertiary care hospital in North India

Background: Polypharmacy, advancing age and longer duration of hospital stay are the factors responsible for adverse drug reactions (ADRs). This study has attempted to analyze the pattern of antimicrobial prescription in OPD & IPD of the Otolaryngology department and to detect, document, assess and report the suspected ADRs due to antibiotic use and preparation of guidelines to minimize the incidence of ADRs.Methods: A prospective study conducted at the TMMC&RC on patients aged >40 years, who visited the Otolaryngology department over a period of 5 months. Suspected ADRs were assessed for causality and severity using Naranjo’s probability scale and modified Hartwig’s criteria, respectively. Results: Out of 1200, 925 prescriptions were analyzed. Most patients were from 41-60 age (59.45%) followed by 61-80 age (37.29%) and least from >80 yr (3.24%). But the incidence of ADRs were found to be higher in patients of >80 yr age group n=8 (26.66%). The most commonly prescribed antibacterials were β-Lactams (64.61%). Out of 925 prescriptions studied, only 94 were found to have 154 ADRs. The most commonly identified ADRs were Gastrointestinal 47.40%, followed by Neurotoxicity 24.67%, cutaneous reactions 20.12%, Hepatic 4.54% and Kidney 3.24%. 74.67% of the ADRs were probable and 20.77% were possible type and only 4.54% were definite. 74.67% ADRs were found to be type A, and 25.32% type B.Conclusions: Our study showed that prevalence of ADRs was highest in elder age group and diarrhea was the most common ADR found. Therefore elderly patients should be given special attention when prescribing medications to avoid clinically significant harmful consequences. Minimizing unnecessary antibiotic use by even a small percentage could significantly reduce the immediate and direct risks of drug-related adverse events in individual patients

Assessment of hearing loss in multi-drug resistant tuberculosis (MDR-TB) patients undergoing Aminoglycoside treatment

Background: Incomplete treatments and treatment failures has led to Multi-drug resistant tuberculosis, which has emerged as a significant problem in treating tuberculosis and thus the second line drugs are used with the concomitant increase in the incidence of adverse effects.Methods: This prospective study was carried out from June 2009 to May 2014 in the department of ENT in collaboration with TB & Chest at Teerthanker Mahaveer Medical College & Research Centre. Out of 104, only 84 patients were included in our study. Patients were divided into three groups: group I (n=27) patients using Amikacin, group II (n=40) patients using kanamycin and group III (n=17) patients using streptomycin. Baseline pre-treatment pure tone audiometry was performed on all the patients and repeated every three months until completion of therapy.Results: Patients included were 15 to 55 years age with higher number of males (65%, n=55) than females (35%, n =29). Only 22.7% (n=19) of patients were found to be suffered from Hearing Loss. At the end of the study (at 12 month), Overall incidence of HFL was 58.0% (n=11) while incidence of Dead ear was 31.5% (n=6) and LFL was 10.5% (n=2). Amikacin was found to be more Ototoxic than Kanamycin and streptomycin.Conclusion: Aminoglycosides in MDR-TB patients may cause irreversible hearing loss involving higher frequencies and can become a hearing handicap as speech frequencies are too implied in more or less of the patients, thus underlining the need for regular audiologic evaluation in patients of MDR-TB during the treatment.

c.620C>T mutation in GATA4 is associated with congenital heart disease in South India

Background: Congenital Heart Diseases (CHDs) usually refer to abnormalities in the structure and/or function of the heart that arise before birth. GATA4 plays an important role in embryonic heart development, hence the aim of this study was to find the association of GATA4 mutations with CHD among the south Indian CHD patients. Method: GATA4 gene was sequenced in 100 CHD patients (ASD, VSD, TOF and SV) and 200 controls. Functional significance of the observed GATA4 mutations was analyzed using PolyPhen, SIFT, PMut, Plink, Haploview, ESE finder 3.0 and CONSITE. Results: We observed a total of 19 mutations, of which, one was in 5′ UTR, 10 in intronic regions, 3 in coding regions and 5 in 3′ UTR. Of the above mutations, one was associated with Atrial Septal Defect (ASD), two were found to be associated with Tetralogy of Fallot (TOF) and three (rs804280, rs4841587 and rs4841588) were strongly associated with Ventricular Septal Defect (VSD). Interestingly, one promoter mutation (−490 to 100 bp) i.e., 620 C>T (rs61277615, p-value = 0.008514), one splice junction mutation (G>A rs73203482; p-value = 9.6e-3, OR = 6.508) and one intronic mutation rs4841587 (p-value = 4.6e-3, OR = 4.758) were the most significant findings of this study. In silico analysis also proves that some of the mutations reported above are pathogenic. Conclusion: The present study found that GATA4 genetic variations are associated with ASD, TOF and VSD in South Indian patients. In silico analysis provides further evidence that some of the observed mutations are pathogenic

Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup

The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent

IL10 variant g.5311A is associated with Visceral Leishmaniasis in Indian population

Background: Visceral Leishmaniasis (VL) is a multifactorial disease, where the host genetics play a significant role in determining the disease outcome. The immunological role of anti-inflammatory cytokine, Interleukin 10 (IL10), has been well-documented in parasite infections and considered as a key regulatory cytokine for VL. Although VL patients in India display high level of IL10 in blood serum, no genetic study has been conducted to assess the VL susceptibility/resistance. Therefore, the aim of this study is to investigate the role of IL10 variations in Indian VL; and to estimate the distribution of disease associated allele in diverse Indian populations. Methodology: All the exons and exon-intron boundaries of IL10 were sequenced in 184 VL patients along with 172 ethnically matched controls from VL endemic region of India. Result and Discussion: Our analysis revealed four variations; rs1518111 (2195 A>G, intron), rs1554286 (2607 C>T, intron), rs3024496 (4976 T>C, 3’ UTR) and rs3024498 (5311 A>G, 3’ UTR). Of these, a variant g.5311A is significantly associated with VL (χ2 = 18.87; p = 0.00001). In silico approaches have shown that a putative micro RNA binding site (miR-4321) is lost in rs3024498 mRNA. Further, analysis of the above four variations in 1138 individuals from 34 ethnic populations, representing different social and linguistic groups who are inhabited in different geographical regions of India, showed variable frequency. Interestingly, we have found, majority of the tribal populations have low frequency of VL (‘A’ of rs3024498); and high frequency of leprosy (‘T’ of rs1554286), and Behcet’s (‘A’ of rs1518111) associated alleles, whereas these were vice versa in castes. Our findings suggest that majority of tribal populations of India carry the protected/less severe allele against VL, while risk/more severe allele for leprosy and Behcet’s disease. This study has potential implications in counseling and management of VL and other infectious diseases

Epigenetic-focused CRISPR/Cas9 screen identifies (absent, small, or homeotic)2-like protein (ASH2L) as a regulator of glioblastoma cell survival

Background: Glioblastoma is the most common and aggressive primary brain tumor with extremely poor prognosis, highlighting an urgent need for developing novel treatment options. Identifying epigenetic vulnerabilities of cancer cells can provide excellent therapeutic intervention points for various types of cancers. Method: In this study, we investigated epigenetic regulators of glioblastoma cell survival through CRISPR/Cas9 based genetic ablation screens using a customized sgRNA library EpiDoKOL, which targets critical functional domains of chromatin modifiers. Results: Screens conducted in multiple cell lines revealed ASH2L, a histone lysine methyltransferase complex subunit, as a major regulator of glioblastoma cell viability. ASH2L depletion led to cell cycle arrest and apoptosis. RNA sequencing and greenCUT&RUN together identified a set of cell cycle regulatory genes, such as TRA2B, BARD1, KIF20B, ARID4A and SMARCC1 that were downregulated upon ASH2L depletion. Mass spectrometry analysis revealed the interaction partners of ASH2L in glioblastoma cell lines as SET1/MLL family members including SETD1A, SETD1B, MLL1 and MLL2. We further showed that glioblastoma cells had a differential dependency on expression of SET1/MLL family members for survival. The growth of ASH2L-depleted glioblastoma cells was markedly slower than controls in orthotopic in vivo models. TCGA analysis showed high ASH2L expression in glioblastoma compared to low grade gliomas and immunohistochemical analysis revealed significant ASH2L expression in glioblastoma tissues, attesting to its clinical relevance. Therefore, high throughput, robust and affordable screens with focused libraries, such as EpiDoKOL, holds great promise to enable rapid discovery of novel epigenetic regulators of cancer cell survival, such as ASH2L. Conclusion: Together, we suggest that targeting ASH2L could serve as a new therapeutic opportunity for glioblastoma

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security

greenPipe: Datasets

Genome-wide localization of chromatin and transcription regulators can be detected by a variety of techniques. In 2021, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulators, which has a very high sensitivity, resolution, accuracy and reproducibility, whilst assuring specificity . This technique produces robust genomic profiles, which are accurate and unbiased towards open chromatin. This pipeline is developed specifically for greenCUT&RUN technique, but it is applicable to CUT&RUN or CUT&Tag also. This repository contains the indexed reference genome and test datasets. greenPipe can be downloaded from https://github.com/snizam001/greenPip

Epigenetic signatures of high altitude adaptation in Tibetan population

Genetic adaptations in high-altitude populations which provide them survival benefit/advantage in high altitude have been well documented. However, till date, very limited studies on the epigenetic adaptation in high altitude human population. Therefore, we aimed to study the high altitude adaptation in Tibetan population, with respect to epigenetic adaptation. DNA methylation is one of the major epigenetic marks, role of which has been suspected in a spectrum of gene-environment interaction and biological processes. The most common form of DNA methylation in vertebrates is 5-methylcytosine, mostly observed in CpG rich promoter region. Recent advancements in the field of DNA sequencing made it possible to analyse genome-wide methylation rapidly with high resolution, however, study of methylation at population level to explore population specific gene-environment interaction is not in long race.  Therefore, the present study has been designed to analyse DNA methylation signatures (using whole genome bisulfite sequencing) in Tibetan population (presently inhabiting Karnataka since last 50-60 years) but were native of Ladakh (above 5000 meters) since generations along with Indian populations who are living at low altitude (~10 meters). DNA was isolated from blood, collected from the subjects after informed consent. DNA was converted using bisulfite reagents and whole genome bisulfite sequencing (WGBS) was performed using Illumina-2500 platform (Medgenome Pvt. Ltd.). Analysis of WGBS data was performed using various statistical/bioinformatics tools such as bedtools, Bioconductor and R package to find out methylation sites that are significantly different. We observed 6 differentially methylated regions in Tibetans, highland population, of which, 5 were hypo methylated and one was hypermethylated. The present study reveals  differential hypo methylation of CYP2E1 and CRELD1 genes, previously reported to be involved in high altitude adaptation (Simonson et al., 2010; Dong et al., 2014), which would of greater interest. Besides this, we observed novel epigenetic differences in chromosome 7, 11 and 15. Our study, for the first time reveals genome wide level of methylation difference in Tibetan population (native of high altitude since generations) residing in low altitude with other mainland Indians of low altitude which could be important epigenetic markers of natural selection. Comparison with native high altitude Tibetan would make the scenario clearer, which is in the process