Noncoding RNAs in Alzheimer's Disease: Overview of Functional and Therapeutic Significance

Alzheimer's disease (AD) is a multifactorial disorder resulting from the complex interaction between genetic, epigenetic, and environmental factors. It represents an impending epidemic and lacks effective pharmacological interventions. The emergence of high throughput sequencing techniques and comprehensive genome evaluation has uncovered a diverse spectrum of non-- coding RNA (ncRNA) families. ncRNAs are the critical modulators of an eclectic array of biological processes and are now transpiring as imperative players in diagnosing and treating various diseases, including neurodegenerative disorders. Several ncRNAs are explicitly augmented in the brain, wherein they potentially regulate cognitive abilities and other functions of the central nervous system. Growing evidence suggests the substantial role of ncRNAs as modulators of tau phosphorylation, Aβ production, neuroinflammation, and neuronal survival. It indicates their therapeutic relevance as a biomarker and druggable targets against AD. The current review summarizes the existing literature on the functional significance of ncRNAs in AD pathogenesis and its imminent implications in clinics.

Epigenetics of Alzheimer’s Disease: Past, Present and Future

Alzheimer’s disease (AD) exemplifies a looming epidemic lacking effective treatment and manifests with the accumulation of neurofibrillary tangles, amyloid-β plaques, neuroinflammation, behavioral changes, and acute cognitive impairments. It is a complex, multifactorial disorder that arises from the intricate interaction between environment and genetic factors, restrained via epigenetic machinery. Though the research progress has improved the understanding of clinical manifestations and disease advancement, the causal mechanism of detrimental consequences remains undefined. Despite the substantial improvement in recent diagnostic modalities, it is challenging to distinguish AD from other forms of dementia. Accurate diagnosis is a major glitch in AD as it banks on the symptoms and clinical criteria. Several studies are underway in exploring novel and reliable biomarkers for AD. In this direction, epigenetic alterations have transpired as key modulators in AD pathogenesis with the impeding inferences for the management of this neurological disorder. The present chapter aims to discuss the significance of epigenetic modifications reported in the pathophysiology of AD such as DNA methylation, hydroxy-methylation, methylation of mtDNA, histone modifications, and noncoding RNAs. Additionally, the chapter also describes the possible therapeutic avenues that target epigenetic modifications in AD.

Systematic Analysis of the Therapy Resistance Genes and their Prognostic Relevance in Cervical Cancer

INTRODUCTION

Critical issues in the therapeutic management of cervical cancer (CC) include therapy resistance and treatment failure. The development of therapy resistance is a multifaceted, progressive process, including genetic and epigenetic abnormalities. The present study aimed to identify genes that may contribute to therapy resistance in CC.

MATERIALS AND METHODS

We have created an extensive list of the genes in cancer that are therapy-resistant using a text-mining approach. The list was compared with the TCGA-CESC dataset to identify the differentially expressed therapy resistance genes (DETRGs) in CC. We used online resources (UALCAN, DNMIVD, cBio- Portal, HCMDB, OncoDB, ShinyGO, HPA, KM Plotter, TIMER, and DGIdb) to determine the potential association between methylation and expression of therapy resistance genes with the prognosis and clinical outcomes in CC.

RESULTS

The systematic analysis identified 71 out of 91 DETRGs showed aberrant DNA methylation. The overlapping analysis identified 25 genes to show an inverse correlation between methylation and expression. Further, differential expression or methylation could be helpful in CC staging, HPV association, prediction of metastasis and prognosis. The study identified seven driver genes in CC. The PPIN identifies ten hub genes (HGs) associated with CC staging, cancer hallmarks, and prognosis to affect long-term survival.

CONCLUSION

Our thorough investigation uncovered several novel genes and pathways that might contribute to therapy resistance in CC. The genes identified in our study may serve as a biomarker, prognostic indicator, and therapeutic target in CC.

Integrated bioinformatic analysis to understand the association between phthalate exposure and breast cancer progression

Phthalates have been extensively used as plasticizers while manufacturing plastic-based consumer products. Estradiol mimicking properties and association studies suggest phthalates may contribute to breast cancer (BC). We performed an in-silico analysis and functional studies to understand the association between phthalate exposure and BC progression. Search for phthalate-responsive genes using the comparative toxicogenomics database identified 20 genes as commonly altered in response to multiple phthalates exposure. Of the 20 genes, 12 were significantly differentially expressed between normal and BC samples. In BC samples, 9 out of 20 genes showed a negative correlation between promoter methylation and its expression. AHR, BAX, BCL2, CAT, ESR2, IL6, and PTGS2 expression differed significantly between metastatic and non-metastatic BC samples. Gene set enrichment analysis identified metabolism, ATP-binding cassette transporters, insulin signaling, and type II diabetes as highly enriched pathways. The diagnostic assessment based on 20 genes expression suggested a sensitivity and a specificity >0.91. The aberrantly expressed phthalate interactive gene influenced the overall survival of BC patients. Drug-gene interaction analysis identified 14 genes and 523 candidate drugs, including 19 BC treatment-approved drugs. Di(2-ethylhexyl) phthlate (DEHP) exposure increased the growth, proliferation, and migration of MCF-7 and MDA-MB-231 cells in-vitro. DEHP exposure induced morphological changes, actin cytoskeletal remodeling, increased ROS content, reduced basal level lipid peroxidation, and induced epithelial to mesenchymal transition (EMT). The present approach can help to explore the potentially damaging effects of environmental agents on cancer risk and understand the underlined pathways and molecular mechanisms.

Mitigation of arsenic induced developmental cardiotoxicity by ferulic acid in zebrafish

We investigated whether ferulic acid (FA), a nutraceutical could mitigate the arsenic (As) induced cardiotoxicity. Zebrafish larvae (60 and 72 h post-fertilization [hpf]) were used to study the effect of FA on As at different time points (24 and 48 h after exposure). The FA exposure was given as pre-treatment (60 hpf) and simultaneous treatment (72 hpf) to translate the results for As contaminated areas. To accomplish this, the lethality assay was done, and based on the results, the dosage for As (1 mM) and FA (30 μM) was fixed. The FA intervention (30 μM) as 12 h pre-treatment (60 hpf) and simultaneous treatment along with As (72 hpf) decreased the As content in zebrafish larvae as evidenced by inductively coupled plasma-mass spectrometry. As exposure showed congenital deformities especially cardiac malformations in zebrafish larvae after 24 and 48 h. These teratogenic effects induced by As were reduced by FA supplementation in both groups. Also, o-dianisidine staining demonstrated that As treated larvae encountered abnormal cardiac function with reduced blood circulation, while FA supplementation reversed these effects. The acetylcholinesterase activity, a biomarker of As-induced cardiotoxicity was also found to be decreased in As group, which was rescued by FA. The modulation in the expression of the genes involved in cardiogenesis (nkx2.5, bmp2b, gata4, gata5, myh6, myl7, and tnnt2) further confirmed the ameliorative effect of FA on As induced malformations.

Analysis of Nuclear Encoded Mitochondrial Gene Networks in Cervical Cancer

BACKGROUND

Cervical cancer (CC) is one of the most common female cancers in many developing and underdeveloped countries. High incidence, late presentation, and mortality suggested the need for molecular markers. Mitochondrial defects due to abnormal expression of nuclear-encoded mitochondrial genes (NEMG) have been reported during cancer progression. Nevertheless, the application of NEMG for the prognosis of CC is still elusive. Herein, we aimed to investigate the associations between NEMG and CC prognosis.

MATERIALS AND METHODS

The differentially expressed genes (DEG) in the TCGA-CESC dataset and NEMGs were retrieved from TACCO and Mitocarta2.0 databases, respectively. The impact of methylation on NEMG expression were predicted using DNMIVD and UALCAN tools. HCMDB tool was used to predict genes having metastatic potential. The prognostic models were constructed using DNMIVD, TACCO, GEPIA2, and SurvExpress. The functional enrichment analysis (FEA) was performed using clusterProfiler. The protein-protein interaction network (PPIN) was constructed to identify the hub genes (HG) using String and CytoHubba tools. Independent validation of the HG was performed using Oncomine and Human Protein Atlas databases. The druggable genes were predicted using DGIdb.

RESULTS

Among the 52 differentially expressed NEMG, 15 were regulated by DNA methylation. The expression level of 16, 10, and 7 has the potential for CC staging, prediction of metastasis, and prognosis. Moreover, 1 driver gene and 16 druggable genes were also identified. The FEA identified the enrichment of cancer-related pathways, including AMPK and carbon metabolism in cancer. The combined expression of 10 HG has been shown to affect patient survival.

CONCLUSION

Our findings suggest that the abnormal expression of NEMGs may play a critical role in CC development and progression. The genes identified in our study may serve as a prognostic indicator and therapeutic target in CC.
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Exploring the role of macular thickness as a potential early biomarker of neurodegeneration in acute schizophrenia

OBJECTIVE

The retina has been investigated as a gateway to assess the neurodegenerative changes in the brain. Schizophrenia is also conceptualized as a neurodegenerative disorder like Alzheimer's and Parkinson's disease. The current literature suggests reduced retinal nerve fibre layer (RNFL) thickness and macular thickness (MT), as a marker of neurodegeneration, in patient suffering from chronic schizophrenia. This study aims to compare RNFL thickness and MT in acute schizophrenic patients with age and sex matched healthy controls.

METHODS

Twenty acutely ill schizophrenic patients and 20 normal controls were included in the study after proper informed consent. RNFL thickness and MT was measured using spectral domain Optical Coherence Tomography after clinical psychological assessment and ocular examination.

RESULTS

The two groups were comparable in terms of socio-demographic variables. The average RNFL thickness of patients and healthy controls was 102.11 ± 29.18 µm and 105.14 ± 27.35 µm, respectively. Central macular thickness was 181.12 ± 13.63 µm in patients and 234.58 ± 10.71 µm in controls. There was a statistically significant reduction in thickness of macula (p < 0.05) but not for RNFL (p = 0.339).

CONCLUSION

The study concludes that macular thinning rather than reduced RNFL is an early manifestation in acute schizophrenia patients and can be considered as a potential early biomarker of neurodegeneration in schizophrenia.

Integrated bioinformatic analysis of miR-15a/16-1 cluster network in cervical cancer

The miR-15a/16-1 cluster is abnormally expressed in cervical cancer (CC) tissues and plays a vital role in cervical carcinogenesis. We aimed to evaluate the miR-15a/16-1 expression in healthy and cancerous cervical tissues, identify the associated networks, and to test its prognostic significance. miR-15a/16-1-MC expressions were analyzed in TCGA-CESC datasets by UALCAN, GEPIA2, and Datasetviewer. miR-15a/16-1 validated targets were extracted from mirTarBase and in silico functional analysis of the target genes were performed using WebGestalt. The interaction networks were constructed by the miRNet, STRING, and NetworkAnalyst tools. The prognostic significance and metastatic potential of the target genes were predicted using UALCAN and HCMDB. The FDA approved drugs to target miR-15a/16-1 and target gene network in CC were performed using DGIdb, STITCH and PanDrugs. TCGA-CESC and GEO data analysis suggested significant overexpression of miR-15a/16-1 in CC samples. The Kaplan-Meier survival analysis showed that miR-15a and its four target genes (BCL2, CCNE1, NUP50, and RBPJ) influence the overall survival of CC patients. Among the 66 differentially expressed target genes, 12 of them are linked to head, neck, or lung metastasis. Functional enrichment analysis predicted the association of this cluster with p53 signaling, human papillomavirus infection, PI3-AKT signaling pathway, and pathways in cancer. Drug-gene interaction analysis showed 52 potential FDA approved drugs to interact with the miR-15a/16-1 target genes. Nine of the 52 drugs are currently used as a chemotherapeutic agent for the treatment of CC patients. The present study shows that miR-15a/16-1 expression can be used as a clinical marker and target for therapy in CC.

Molecular landscape of recurrent cervical cancer

Cervical cancer (CC) is a major gynecological problem in developing and underdeveloped countries. Despite the significant advancement in early detection and treatment modalities, several patients recur. Moreover, the molecular mechanisms responsible for CC recurrence remains obscure. The patients with CC recurrence often show poor prognosis and significantly high mortality rates. The clinical management of recurrent CC depends on treatment history, site, and extent of the recurrence. Owing to poor prognosis and limited treatment options, recurrent CC often presents a challenge to the clinicians. Several in vitro, in vivo, and patient studies have led to the identification of the critical molecular changes responsible for CC recurrence. Both aberrant genetic and epigenetic modifications leading to altered cell signaling pathways have been reported to impact CC recurrence. Researchers are currently trying to dissect the molecular pathways in CC and translate these findings for better management of disease. This article attempts to review the existing knowledge of disease relapse, accompanying challenges, and associated molecular players in CC.

Low FODMAP in 2017: Lessons learned from clinical trials and mechanistic studies

Given the prevalence of irritable bowel syndrome (IBS) and the suboptimal response to most therapeutic approaches, there has been increasing interest in and adoption of dietary treatment strategies, such as the low Fermentable Oligo-, Di-, & Mono-Saccharides and Polyols (FODMAP) diet. FODMAPs are a diverse group of carbohydrates that exert effects in the gastrointestinal tract not only via fermentation but likely via alterations in the microbiota, metabolome, permeability, and intestinal immunity as well. Clinical evidence for efficacy of this diet is mounting, but there are significant questions regarding short- and long-term safety and effects on the microbiota and nutrition that remain unanswered. This review article interprets the recent findings reported in this issue of Neurogastroenterology and Motility and summarizes the mechanistic and clinical efficacy data of the low FODMAP diet in IBS patients to date.

Limited hepatitis B immunoglobulin with potent nucleos(t)ide analogue is a cost-effective prophylaxis against hepatitis B virus after liver transplantation

BACKGROUND

Prophylaxis against hepatitis B virus (HBV) recurrence after orthotopic liver transplantation (OLT) includes lifelong hepatitis B immunoglobulin (HBIG) and oral antiviral agent(s). In the presence of high-genetic-barrier nucleos(t)ide analogues, the need for lifelong HBIG is questioned. We evaluated the safety and cost-effectiveness of a limited HBIG course.

METHODS

OLT from 2006 to 2013 were reviewed. Patients with pre-OLT hepatitis B virus surface antigen who received HBV prophylaxis with 2 HBIG doses (anhepatic and first post-operative day; 10,000 units/dose) and potent nucleos(t)ide analogues were included. The primary end point was HBV recurrence (HBV-DNA detection).

RESULTS

Thirteen patients (primary transplants) were included, median Model for End-Stage Liver Disease score was 18, and there was no fulminant failure; HBV-DNA was detected in 4 patients at OLT. After OLT, 10 patients received entecavir and/or tenofovir. Median follow-up was 23 months. One recurrence occurred (7.7%) at month 13 (HBV-DNA: 14 IU/mL); the graft maintained excellent function. This minimal viremic expression is related to hepatocellular carcinoma recurrence with neoplastic replication carrying integrated HBV-DNA; thus, there is no defined HBV viral recurrence. No graft loss or patient death was related to HBV recurrence. The 1-year patient and graft survival rate was 84.6%. Cost-savings in the first year was $178,100 per patient when compared with Food and Drug Administration-approved HBIG dosing.

CONCLUSIONS

In the era of potent oral nucleos(t)ide analogues, a limited HBIG course appears to be cost-effective in preventing HBV recurrence.

Development of chitosan conjugated DNA vaccine against nodavirus in Macrobrachium rosenbergii (De Man, 1879)

The protective efficacy of a DNA construct containing extra small virus antisense (XSVAS) gene of nodavirus encapsulated with chitosan nanoparticles (NPs) was investigated in giant freshwater prawn Macrobrachium rosenbergii (De Man, 1879). The delivery was carried out using oral and immersion methods. A plasmid concentration of 100 ng μL(-1) when conjugated with chitosan NPs was found to be more effective in increasing the survivability of the infected prawn. The particle mean size, zeta potential and loading efficiency percentage were 297 nm, 27 mV and 85%, respectively. The ability of the chitosan to form a complex with the plasmid was studied by agarose gel electrophoresis. The NPs were characterized by atomic force microscopy (AFM). Persistence study showed the presence of the DNA construct up to 30th day post-treatment. The oral treatment was found to be better than the immersion treatment for delivery of the chitosan-conjugated DNA construct. This is probably the first report on the delivery of nanoconjugated DNA construct in M. rosenbergii, against nodavirus.

A COMPARATIVE STUDY OF MMPI PROFILES OF PSYCHIATRIC PG's v/s MEDICAL PG's

MMPI profiles of 10 psychiatric PG's have been compared with 10 medical PG's. The findings are discussed statistically and otherwise. Both the groups fall within the range of normal. Some interesting findings are not unexpected, if a larger section of population could be studied preferably over a span of few years.

A turbidimetric method for the screening of amylase-producing mutants of Aspergillus niger

The method is based on the assumption that extracellular amylase, which is produced by strains of Aspergillus niger in liquid culture, hydrolyses the starch in the media and brings about a corresponding decrease in the turbidity of the media. Mutant strains which produced different quantities of amylase exhibited different degrees of decrease in turbidity of the media. The results showed that a greater degree of decrease in turbidity was observed for a higher quantity of amylase produced.