Search

Abstract Small non-coding RNAs (sncRNAs) derived from tRNAs are known as tRNA-derived small RNAs (tsRNAs). These tsRNAs are further categorized into tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), which play significant roles in the various molecular mechanisms underlying certain human diseases. However, the generation of tsRNAs and their potential roles during Dengue virus (DENV) infection is not yet known. Here, we performed small RNA sequencing to identify the generation and alterations in tsRNAs expression profiles of DENV-infected Huh7 cells. Upon DENV infection, tRNA fragmentation was found to be increased. We identified a significant number of differentially expressed tsRNAs during DENV infection. Interestingly, the 3′tRF population showed upregulation, while the i-tRF population exhibited downregulation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed to analyze the impact of differentially expressed tsRNAs on DENV pathogenesis. Our results suggest that differentially expressed tsRNAs are involved in transcriptional regulation via RNA polymerase II promoter and metabolic pathways. Overall, our study contributes significantly to our understanding of the roles played by tsRNAs in the complex dynamics of DENV infection.

Abstract Dengue viruses (DENV) are positive-stranded RNA viruses belonging to the Flaviviridae family. DENV is the causative agent of dengue, the most rapidly spreading viral disease transmitted by mosquitoes. Each year, millions of people contract the virus through bites from infected female mosquitoes of the Aedes species. In the majority of individuals, the infection is asymptomatic, and the immune system successfully manages to control virus replication within a few days. Symptomatic individuals may present with a mild fever (Dengue fever or DF) that may or may not progress to a more critical disease termed Dengue hemorrhagic fever (DHF) or the fatal Dengue shock syndrome (DSS). In the absence of a universally accepted prophylactic vaccine or therapeutic drug, treatment is mostly restricted to supportive measures. Similar to many other viruses that induce acute illness, DENV has developed several ways to modulate host metabolism to create an environment conducive to genome replication and the dissemination of viral progeny. To search for new therapeutic options, understanding the underlying host-virus regulatory system involved in various biological processes of the viral life cycle is essential. This review aims to summarize the complex interaction between DENV and the host cellular machinery, comprising regulatory mechanisms at various molecular levels such as epigenetic modulation of the host genome, transcription of host genes, translation of viral and host mRNAs, post-transcriptional regulation of the host transcriptome, post-translational regulation of viral proteins, and pathways involved in protein degradation.

SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5′ and 3′UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5′ and 3’UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5′ and 3′UTRs, using in-silico approaches. Our results suggest that 5′ and 3′UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.

Hundreds of tRNA genes and pseudogenes are encoded by the human genome. tRNAs are the second most abundant type of RNA in the cell. Advancement in deep-sequencing technologies have revealed the presence of abundant expression of functional tRNA-derived RNA fragments (tRFs). They are either generated from precursor (pre-)tRNA or mature tRNA. They have been found to play crucial regulatory roles during different pathological conditions. Herein, we briefly summarize the discovery and recent advances in deciphering the regulatory role played by tRFs in the pathophysiology of different human diseases.

Dengue is potentially a life-threatening arthropod-borne viral infection for which there are no known therapeutic agents till date. Early stage diagnosis of dengue infection is still lacking. Diagnosis is only made after severe manifestations and later stages of infection. Timely prognosis can prevent dengue related mortalities. The nucleic acid-based therapy has potential to emerge as a promising approach for early diagnosis and treatment of this viral infection. Many studies have been carried out suggested the regulatory role of ncRNAs thereby revealing the importance of protein-RNA and RNA-RNA interactions during infection. Various regulatory RNAs are either expressed by mammalian cells or generated by viral RNA have reported to play important roles in viral life cycle including dengue virus. Thus exploring host-virus interaction will pave the novel path for understanding the pathophysiology of febrile infection in dengue. Rapid advances in sequencing techniques along with significant developments in the field of RNA studies has made RNA therapeutics as one of the promising approaches as antiviral targets. The idea of RNA based therapies has been greatly backed by a Hepatitis C virus drug, Miravirsen which has successfully completed phase II clinical trial. In the present review, we will discuss the implications of different non-coding RNAs in dengue infection. Differential expression of small ncRNA may serve as a reliable biomarker of disease severity during different stages of infection and can also play regulatory roles in disease progression.

Epithelial-to-mesenchymal transition (EMT) is a key cellular process involved in the various biological processes ranging from embryonic development, wound healing, and cancer metastasis. EMT is the key player in cancer progression to a metastatic state. The transformed tumor cells acquire the migratory property and invade surrounding tissues, which ultimately leads to cancer metastasis via EMT. Epithelial cells undergo certain phenotypic changes to acquire mesenchymal status. At a molecular level, this transition process is elicited by several signaling cascades that include cytokines and a group of transcription factors like Twist, snail, and Zeb1/2. Emerging evidence suggests that various non-coding RNAs (ncRNAs) play a significant role in modulating EMT-associated transcription factors (EMT-TFs) and molecular signaling at the transcriptional and post-transcriptional level and thus, regulating the EMT process. Various noncoding-RNAs like miRNAs, piRNAs, tsRNAs, lncRNAs, T-UCRs, CircRNAs, eRNAs, snoRNAs can either promote or can inhibit the process of EMT and thus modulates cancer progression. Here we review the recent research advances in delineating the role of various non-coding RNAs in the EMT, cancer, and metastasis process as well as their potential roles as biomarkers and therapeutic targets.

In 2020, a novel strain of coronavirus (COVID-19) has led to a significant morbidity and mortality worldwide. As of the date of this writing, a total of 116 M cases has been diagnosed worldwide leading to 2.5 M deaths. The number of mortalities is directly correlated with the rise of innate immune cells (especially macrophages) in the lungs that secrete inflammatory cytokines (IL-1β and IL-6) leading to the development of “Cytokine Storm Syndrome” (CSS), multi-organ-failure and death. Given that currently the treatment of this condition is rare and release of effective vaccine might be months away, here, we review the plants and their pharmacologically active-compounds as potential phytopharmaceuticals for the virus induced inflammatory response. Experimental validation of the effectiveness of these natural compounds to prevent or reduce the cytokine storm might be beneficial as an adjunct treatment of SARS-CoV-2.

Abstract Osteoporosis is a systemic-skeletal disorder characterized by enhanced fragility of bones leading to increased rates of fractures and morbidity in large number of populations. Probiotics are known to be involved in management of various-inflammatory diseases including osteoporosis. But no study till date had delineated the immunomodulatory potential of Lactobacillus rhamnosus (LR) in bone-health. In the present study, we examined the effect of probiotic-LR on bone-health in ovariectomy (Ovx) induced postmenopausal mice model. In the present study, we for the first time report that LR inhibits osteoclastogenesis and modulates differentiation of Treg-Th17 cells under in vitro conditions. We further observed that LR attenuates bone loss under in vivo conditions in Ovx mice. Both the cortical and trabecular bone-content of Ovx+LR treated group was significantly higher than Ovx-group. Remarkably, the percentage of osteoclastogenic CD4+Rorγt+Th17 cells at distinct immunological sites such as BM, spleen, LN and PP were significantly reduced, whereas the percentage of anti-osteoclastogenic CD4+Foxp3+Tregs and CD8+Foxp3+Tregs were significantly enhanced in LR-treated group thereby resulting in inhibition of bone loss. The osteoprotective role of LR was further supported by serum cytokine data with a significant reduction in osteoclastogenic cytokines (IL-6, IL-17 and TNF-α) along with enhancement in anti-osteoclastogenic cytokines (IL-4, IL-10, IFN-γ) in LR treated-group. Altogether, the present study for the first time establishes the osteoprotective role of LR on bone health, thus highlighting the immunomodulatory potential of LR in the treatment and management of various bone related diseases including osteoporosis.

Discoveries in the last few years have emphasized the existence of an enormous breadth of communication between osteo-immune systems. These discoveries fuel novel approaches for the treatment of several bone pathologies including osteoporosis. Bifidobacterium longum (BL) is a preferred probiotic of choice due to its varied immunomodulatory potential in alleviating various inflammatory diseases. Here, we evaluate the effect of BL in an ovariectomy (ovx)-induced post-menopausal osteoporotic mouse model. Our in vitro findings reveal that BL suppresses the differentiation and functional activity of RANKL-induced osteoclastogenesis in both mouse bone marrow cells and human PBMCs. Strikingly, BL-induced Bregs were found to be significantly more efficient in suppressing osteoclastogenesis and modulating Treg–Th17 cell balance with respect to control Bregs in vitro. Our in vivo µCT and bone mechanical strength data further confirm that BL supplementation significantly enhanced bone mass and bone strength, along with improving the bone microarchitecture in ovx mice. Remarkably, alterations in frequencies of CD19+CD1dhiCD5+IL-10+ Bregs, CD4+Foxp3+IL-10+ Tregs, and CD4+Rorγt+IL-17+ Th17 cells in distinct lymphoid organs along with serum-cytokine data (enhanced anti-osteoclastogenic cytokines IFN-γ and IL-10 and reduced osteoclastogenic-cytokines IL-6, IL-17, and TNF-α) strongly support the immunomodulatory potential of BL. Altogether, our findings establish a novel osteo-protective and immunomodulatory potential of BL in augmenting bone health under osteoporotic conditions.

Introduction: Combination of Angiotensin Receptor and Neprilysin Inhibitors (ARNI) has become the mainstay drug in treatment of Heart Failure (HF) with reduced Ejection Fraction (HFrEF). However, there are very few studies to evaluate the extent and spectrum of benefit of ARNI therapy in Indian HFrEF patients. Aim: To observe the benefits of sacubitril/valsartan (ARNI) therapy on left ventricle function, parameters of cardiac remodelling, N terminal pro Brain-natriuretic peptide (NT-proBNP), rate of rehospitalisation for HF and detailed subgroup analysis in symptomatic HFrEF patients who are already receiving optimal medical therapy. Materials and Methods: This longitudinal study was conducted at Cardiology Department of Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India, from September 2018 to August 2020. Total 200 patients of HFrEF with previous echocardiographic records of past six months, who did not show any further improvement in left ventricle dysfunction or cardiac dimensions were included in the study out of these 200 patients, 174 (87%) completed the one year follow-up. Patients were started on ARNI initially from 100 mg/day and up titrated to 400 mg/day. At each follow-up (6 weeks, 4 months, 6 months, 9 months and 1 year) clinical examination, New York Heart Association (NYHA) functional class, 2D Echocardiography and NT-ProBNP were done. Echocardiographic parameters of Cardiac Reverse Remodelling (CRR) i.e., Left Ventricular Ejection Fraction (LVEF), Left Ventricular End Diastolic Diameter (LVEDD), Left Ventricle End-Systolic Diameter (LVESD) were recorded at each follow-up. All categorical variables were shown in the form of frequency, mean with standard deviation and percentage. Intergroup comparison between different time periods was done by one-way Analysis of Variance (ANOVA) and paired t-test. A p-value

Increasing evidence in recent years has suggested that regulatory B cells (Bregs) are one of the crucial modulators in various inflammatory disease conditions. However, no study to date has investigated the significance of Bregs in modulating osteoclastogenesis. To the best of our knowledge, in the present study, we for the first time examined the anti-osteoclastogenic potential of Bregs under in vitro conditions and observed that Bregs suppress RANKL-induced osteoclastogenesis in a dose-dependent manner. We further elucidated the mechanism behind the observed suppression of osteoclasts differentiation via Bregs. Our results clearly suggested that the observed anti-osteoclastogenic property of Bregs is mediated via the production of IL-10 cytokine. Next, we explored whether Bregs have any role in mediating inflammatory bone loss under post-menopausal osteoporotic conditions in ovx mice. Remarkably, our in vivo data clearly suggest that the frequencies of both CD19+IL-10+ Bregs and CD19+CD1dhiCD5+IL-10+ “B10” Bregs were significantly reduced in case of osteoporotic mice model. Moreover, we also found a significant reduction in serum IL-10 cytokine levels in osteoporotic mice, thereby further supporting our observations. Taken together, the present study for the first time establishes the direct role of regulatory B cells in modulating osteoclastogenesis in vitro. Further, our in vivo data suggest that modulations in the percentage of Bregs population along with its reduced potential to produce IL-10 might further exacerbate the observed bone loss in ovx mice.

Objectives: Direct oral anticoagulants (DOACs) are now replacing vitamin K oral anticoagulants (VKAs) owing to superior efficacy, rapid action, less bleeding, wider therapeutic range,and fewer food and drug interactions.Unfortunately, the available data on the use of DOACs, particularly dabigatran, for treatment of left ventricular thrombus (LVT) issparse.We have hereby presented the largest study on use of dabigatran in LVT. Methods: Retrospective data of patients having LVT as diagnosed by transthoracic echocardiography (TTE) was screened. Patients on dabigatran were included in the study and follow up data of 6 months was obtained through medical records. Results: f the 15 patients included in the study, the most frequent etiology was ischemic heart disease (67%), including 7 patients of STEMI (47%), followed by non-ischemic cardiomyopathy in 5 patients (33%). Only one patient, with STEMI, developed mild gastrointestinal bleeding at 3 months. Complete clot resolution was seen in 2 patients (13%) at first week of follow up and total 5 patients (33%) at the end of second week. The rate of clot resolution at 1 month, 3 months, and 6 months were 80%, 93% and 100%, respectively. The median duration required for complete clot resolution was 30 days (IQR=14-30). Conclusion: Dabigatran appears to be safe, highly efficacious and results in rapid LV clot resolution. DOACs may be a suitable alternative to warfarin in treatment of LV thrombus. However, larger studies are required to validate this hypothesis.

Background: Renal involvement in HIV patients is relatively common and quite broad. However, despite an increasingly large number of HIV patients in Asia, systematic studies of renal involvement are lacking. Objectives: The study was carried out to delineate the clinical spectrum of renal disease in HIV/AIDS patients hospitalised in a tertiary care centre. Patients and Methods: A total of 510 consecutive hospitalised HIV/AIDS with age >18years were included in the study. Detailed demographic, clinical and laboratory data including urinalysis was obtained from all participants. Results: Electrolyte disorders were seen in 71% of patients, with the most frequent being hyponatremia (61%). Acute renal failure was seen in 15.8% and CKD was found in 13% of HIV patients. Dipstick proteinuria of grade ≥1+ was seen in 147 patients (29% of total). CD4 count had a significant positive correlation with creatinine clearance, hyponatremia and total leukocyte count, and significant negative correlation with duration of disease and proteinuria. Conclusion: Electrolyte disorders and renal involvement are quite common in HIV/AIDS patients from India. Prompt diagnosis and management is required as their presence carry higher morbidity and mortality.

Background: Chronic kidney disease (CKD) has become epidemic in HIV/AIDS patients across Western and Eastern countries. HIV-associated nephropathy (HIVAN) has been consistently reported in studies from North America, Europe and African countries. However, studies from Asian countries are very sparse and differ strikingly in histological spectrum of renal disease, particularly in presence of HIVAN. Objectives: The study was carried out to in a teaching hospital from India to delineate the histological spectrum of renal disease and detect presence HIVAN in those with significant proteinuria (≥1gm/day). Patients and Methods: Urine analysis was done in 510 consecutive hospitalised HIV/AIDS patients after screening 640 such patients with age >18years. Patients with dipstick proteinuria ≥1+ were subjected to 24-hour urinary protein estimation. Renal biopsy was done in 10 patients with proteinuria ≥1gm/day. Results: Dipstick proteinuria ≥1+ was present in 29% patients. In patients undergoing kidney biopsy, the most frequent glomerular lesion was mesangial proliferative glomerulonephritis (30%) followed by HIVAN (20%). Tubulo-interstitial lesions were seen in 60% of biopsies. Pooled analysis of all the available kidney biopsy series from India revealed prevalence of HIVAN to be 16.5%. Conclusion: Contrary to the popular belief, HIVAN appears to be a common entity in this part of world too. High degree of clinical suspicion is required as diagnosis of HIVAN caries higher morbidity and mortality. Moreover, an early diagnosis and timely management can improve prognosis in such patients.

Background: Pulmonary embolism (PE) is a lethal clinical condition requiring immediate systemic thrombolysis to decrease mortality. Reteplase has been extensively used in acute myocardial infarction but studies in massive PE are rare. We have presented here efficacy and safety of reteplase in patients with high risk PE diagnosed on basis of bedside transthoracic echocardiography. Methods: This was retrospective study including 20 patients of massive PE undergoing thrombolysis with reteplase. Bedside TTE was used to evaluate presence of RV dysfunction and thrombi in these patients with hemodynamic compromise. Safety and efficacy outcomes were analysed till three months of follow up. Results: 12 patients (60%) included in the study were males and mean age was 41 ± 19 years. The dyspnoea, chest pain and haemoptysis improved in all patients after thrombolysis. At discharge, RV dilatation normalised, systolic pulmonary artery pressure decreased, systolic blood pressure significantly increased and hypoxemia had completely corrected. Two patients had minor self-limiting bleeding episodes in form of mild haematuria and oral bleeding. During the follow up period of 3 months all patients were clinically stable and there were no bleeding episodes or death. Moreover, there was no recurrence of PE and/or DVT. Conclusion: Reteplase is highly efficacious in massive pulmonary embolism and results in rapid clinical improvement. Moreover, it can be safely used without increased risk of significant bleeding or mortality. Although limited by retrospective nature, reteplase appears to be an attractive option for massive PE but large prospective studies are further required.

Background: Recent studies have shown EAT to be an indicator of cardiovascular risk and atherosclerotic plaque development. However, such data is sparse from Indian sub-continent. The present study evaluated the relationship of EAT as determined by echocardiography to the presence and severity of coronary artery disease (CAD). Materials and Methods: This was a cross-sectional observational study constituting 500 patients including 250 with angiographically normal coronary arteries (non-CAD group), and 250 patients with significant CAD on coronary angiogram (CAD group). CAD severity was assessed by Gensini and SYNTAX scores. Results: The mean systolic and diastolic EAT thickness in the CAD group (5.7 ± 1.5 mm and 4.3 ± 1.1 mm) were significantly higher than the non-CAD group (4.2 ± 1.2 mm and 3.2 ± 1.2 mm), both P < 0.001. EAT thickness showed a significant positive correlation with waist circumference, LDL-C levels, Gensini score, and SYNTAX score. On multivariate logistic regression analysis, both systolic and diastolic EAT thickness were found to be independent predictor of CAD in addition traditional risk factors. Receiver operating characteristics (ROC) analysis showed that systolic EAT thickness of 5 mm and diastolic EAT thickness of 4 mm had similar sensitivity (85% vs 83%, respectively) and specificity (70% vs 72%, respectively) to detect presence of CAD. Conclusion: Systolic and diastolic EAT thicknesses are increased in CAD patients and related to both presence and severity of CAD. EAT, being modifiable, may be an attractive target for future interventions to reduce CV risk and has potential to monitor the response to life-style modification and therapy. However, larger and prospective studies required to validate these findings.

Bohring-Opitz syndrome (BOS) is a rare, sporadic genetic disorder, characterized by feeding difficulties, developmental delay, flexion abnormalities, dysmorphic facial features and typical body posture (BOS posture). This syndrome is diagnosed on the basis of distinctive clinical features with or without confirmation by genetic studies. Cardiac abnormalities are seen in almost half of the patients, but are nonspecific. We present a case of a 3-week-old male baby with BOS who was referred to our hospital with congestive heart failure, seizures and failure to thrive. He was diagnosed to have double outlet right ventricle and aortopulmonary window (DORV and APW). To our knowledge, this is the first case of Bohring-Opitz Syndrome ever reported with such clinical presentation.

Harlequin ichthyosis (HI) is the most severe form of congenital ichthyosis and inherited in an autosomal recessive manner. The disease is marked by severe thickened and scaly skin on the entire body. It is a lethal disease, but patients can rarely survive for several months or years with treatment. We present here seven cases of HI, where cardiac evaluation was done by echocardiography. To our knowledge, this is the first study to report associated cardiac abnormalities in such patients.

Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3' untranslated region (3'UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3'UTR to non-productive isoforms with a long 3'UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5' splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3'UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm.

Abstract The molecular basis of a significant number of cases of isolated growth hormone deficiency remains unknown. We describe three sisters affected with severe isolated growth hormone deficiency and pituitary hypoplasia caused by biallelic mutations in the RNPC3 gene, which codes for a minor spliceosome protein required for U11/U12 small nuclear ribonucleoprotein (snRNP) formation and splicing of U12‐type introns. We found anomalies in U11/U12 di‐snRNP formation and in splicing of multiple U12‐type introns in patient cells. Defective transcripts include preprohormone convertases SPCS2 and SPCS3 and actin‐related ARPC5L genes, which are candidates for the somatotroph‐restricted dysfunction. The reported novel mechanism for familial growth hormone deficiency demonstrates that general mRNA processing defects of the minor spliceosome can lead to very narrow tissue‐specific consequences.