Transcriptional and Epigenetic Regulation of Human CD4+ T Helper Lineage Specification

Activated T helper (Th) cells have ability to differentiate into functionally distinct Th1, Th2 and Th17 subsets through a series of overlapping networks that include signaling and transcriptional control and the epigenetic mechanisms to direct immune responses. However, inappropriate execution in the differentiation process and abnormal function of these Th cells can lead to the development of several immune mediated diseases. Therefore, the thesis aimed at identifying genes and gene regulatory mechanisms responsible for Th17 differentiation and to study epigenetic changes associated with early stage of Th1/Th2 cell differentiation. Genome wide transcriptional profiling during early stages of human Th17 cell differentiation demonstrated differential regulation of several novel and currently known genes associated with Th17 differentiation. Selected candidate genes were further validated at protein level and their specificity for Th17 as compared to other T helper subsets was analyzed. Moreover, combination of RNA interference-mediated downregulation of gene expression, genome-wide transcriptome profiling and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq), combined with computational data integration lead to the identification of direct and indirect target genes of STAT3, which is a pivotal upstream transcription factor for Th17 cell polarization. Results indicated that STAT3 directly regulates the expression of several genes that are known to play a role in activation, differentiation, proliferation, and survival of Th17 cells. These results provide a basis for constructing a network regulating gene expression during early human Th17 differentiation. Th1 and Th2 lineage specific enhancers were identified from genome-wide maps of histone modifications generated from the cells differentiating towards Th1 and Th2 lineages at 72h. Further analysis of lineage-specific enhancers revealed known and novel transcription factors that potentially control lineage-specific gene expression. Finally, we found an overlap of a subset of enhancers with SNPs associated with autoimmune diseases through GWASs suggesting a potential role for enhancer elements in the disease development. In conclusion, the results obtained have extended our knowledge of Th differentiation and provided new mechanistic insights into dysregulation of Th cell differentiation in human immune mediated diseases.Siirretty Doriast

Ayurvedic Amalaki Rasayana and Rasa-Sindoor suppress neurodegeneration in fly models of Huntington’s and Alzheimer’s diseases

We examined two Ayurvedic Rasayana formulations, claimed to facilitate ‘healthy ageing’, for their role in neuroprotection in fly models of polyQ (127Q and Huntington’s) and Alzheimer’s disorders. Our earlier findings showed that dietary supplement of Amalaki Rasayana, a preparation derived from Indian gooseberry fruits, and Rasa-Sindoor, an organo-metallic Bhasma prepared from mercury and sulphur, improves general well-being of fruit flies. Here we show that dietary supplement of either of these formulations during larval period substantially suppressed neurodegeneration in fly models of polyQ and Alzheimer’s disorders without any side-effects. Dietary Amalaki Rasayana or Rasa-Sindoor prevented accumulation of inclusion bodies and heat shock proteins, suppressed apoptosis, elevated the levels of heterogeneous nuclear ribonucleoproteins and cAMP response element binding protein and at the same time improved the ubiquitin–proteasomal system for better protein clearance in affected cells. Our studies suggest, the potential of these Ayurvedic formulations in providing a holistic relief from the increasingly common neurodegenerative disorders

Molecular Modelling a Key Method for Potential Therapeutic Drug Discovery

The well-defined and characterized 3D crystal structure of a protein is important to explore the topological and physiological features of the protein. The distinguished topography of a protein helps medical chemists design drugs on the basis of the pharmacophoric features of the protein. Structure-based drug discovery, specifically for pathological proteins that cause a higher risk of disease, takes advantage of this fact. Current tools for studying drug-protein interactions include physical, chromatographic, and electrophoretic methods. These techniques can be separated into either non-spectroscopic (equilibrium dialysis, ultrafiltration, ultracentrifugation, etc.) or spectroscopic (Fluorescence spectroscopy, NMR, X-ray diffraction, etc.) methods. These methods, however, can be time-consuming and expensive. On the other hand, in silico methods of analyzing protein-drug interactions, such as docking, molecular simulations, and High-Throughput Virtual Screenings (HTVS), are heavily underutilized by core drug discovery laboratories. These kinds of approaches have a great potential for the mass screening of potential small drugs molecules. Studying protein-drug interactions is of particular importance for understanding how the structural conformation of protein elements affect overall ligand binding affinity. By taking a bioinformatics approach to analyzing drug-protein interactions, the speed with which we identify potential drugs for genetic targets can be greatly increased

Stress and Molecular Drivers for Cancer Progression: A Longstanding Hypothesis

Stress management is becoming very important part of cancer patient care. Chronic stressors lead to boost tumorigenesis and promote cancer development, recurrence, and drug resistant leading to poor health outcomes. The Hypothalamic-Pituitary-Adrenal (HPA) axis, which is activated by stress, also regulates Hypothalamic-Pituitary-Thyroid (HPT) axis. Stress related changes in immune function and inflammatory response also leads to reduced immune surveillance resulting in tumorigenesis. This article explores the hormonal axis impacted by stress and how chronic stress can lead to poor outcome of a cancer patient

PHARMACEUTICAL POTENTIAL OF LABORATORY GROWN CULTURES OF BLUE-GREEN ALGAE: A COMPREHENSIVE REVIEW AND FUTURE POSSIBILITIES

COVID-19 pandemic has taught the world researchers the urgent need for new sources and novel pharmaceuticals not only for existing diseases but also for both seasonal epidemics and future pandemics. Pharmaceutical drug discoveries for the past fifty years depended deeply on the procedure of empirical transmission of a huge number of pure bioactive compounds to provide new leads. The screening of extracts or isolating compounds is a common way to discover novel biologically active molecules. Most of the valuable Blue-Green algal metabolites are concentrated in their biomass. For existence in nature, Blue-Green algae (BGA) secrete and contain various organic substances like proteins, fatty acids, vitamins, pigments, primary and secondary metabolites, and these compounds are explored for potential biological activities such as antibacterial, antifungal, antiviral (including the anti-SARS-CoV-2 virus that causes COVID-19), anticancer, antioxidant, antidiabetic, protease inhibitory activity, anti-inflammatory activity, etc. Due to their diverse application, pharmaceutical companies have shown commercial interest in the Blue-green algal group for the discovery and development of novel molecules to combat deadly diseases for the benefit of society and mankind. The current review paper highlights and discusses the diverse pharmaceutical potential of laboratory-grown cultures of BGA along with comprehensive and current knowledge on bioactive compounds discovered by researchers globally

Long non-coding RNA (lncRNA) as a new biomarker for hepatocellular carcinoma (HCC) drug resistance

Background: Hepatocellular carcinoma (HCC) is the 4th leading cause of cancer-related deaths worldwide and the 6th most common cancer worldwide. When HCC progresses to advanced stages, drug resistance becomes a major hurdle and leaves clinicians with limited therapeutic options. Long non-coding RNAs (lncRNAs) have shown to promote drug resistance in various cancers. The goal of our research is to explain the molecular role of lncRNAs in HCC drug resistance and compile a comprehensive list of studied lncRNAs involved in HCC drug resistance. Methods: To compile a list of lncRNA involved in HCC drug resistance we performed an advanced search on Lnc2Cancer, a database that provides experimentally supported associations between lncRNA and human cancer, using the following filters: “hepatocellular carcinoma”, “drug clinical application”, “lncRNA”, “all biological function”, and “all regulatory mechanism.” Results: We identified 12 lncRNAs that are involved in HCC drug resistance: Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT 1), Keap1 Regulation-Associated LncRNA (KRAL), Transcribed Ultra-conserved Region 338 (TUC338), Long intergenic non-protein coding RNA, regulator of reprogramming (linc-ROR), Linc-VLDLR, Highly Upregulated in Liver Cancer (HULC), HCC associated long non-coding RNA (HANR), LncRNA Regulator of AKT Signaling Associated with HCC and RCC (LncARSR), Taurine up-regulated gene 1 (TUG1), H19, NR2F1 Antisense RNA 1 (NR2F1-AS1), and HOX Transcript Antisense RNA (HOTAIR). Conclusions: Our review demonstrates that lncRNAs involved in HCC drug resistance participate in various mechanistic categories such as autophagy, epithelial-mesenchymal transition, and efflux pump upregulation. There is a need to uncover novel lncRNA biomarkers for both the early detection of HCC and to create drug strategies for clinicians when predicting chemoresistance

Performing a High-Throughput Virtual Screening (HVTS) to identify potential therapeutic targets of YB-1 protein

Background: Hepatocellular carcinomas (HCCs) is a primary malignancy of the liver. Hispanic-Texans have several risk factors and disparities that compound the risk of HCC diagnosis and treatment. The most used chemotherapeutic drug against HCC is sorafenib, but many liver cancers have developed a resistance to this drug. The knockdown of Y-box binding protein-1 (YB-1) has been shown to greatly increase sensitivity to sorafenib. In this study, we will discuss identification of potential YB-1 inhibitors, which can lead to re-sensitization of liver cancer cells to sorafenib. Methodology: The RCSB protein data bank (pdb) was used to retrieve the crystal structure of YB1, while the DrugBank database was used to obtain a list of experimental and approved drugs. A multiple sequence alignment (MSA) of YB-1 & Lin28 was done by Clustal Omega. Biovia Discovery Studio 2020 was used to visualize 3D models and perform a High-Throughput Virtual Screening (HTVS), which includes rigid docking via the LibDock extension, flexible docking via the CDocker extension, and a pharmacokinetic profiling via an ADMET analysis. Results: The cold shock domain of YB-1 was found to be conserved with Lin28, as a known transcription factor. 22 drug candidates were identified through HTVS. The best six show a decent binding ability in both rigid and flexible dockings and have been previously tested in different cancer types to some extent. Conclusion: We were able to identify six potential drug candidates for inhibiting our protein of interest, YB-1. Studies are in progress to study them on sorafenib-resistant HCC cell lines

Role of POTE-2 in hepatocellular carcinoma progression.

Background: Hepatocellular carcinoma (HCC) accounts for 85-90% of primary liver cancers. The Hispanic population had an incidence of 21.2 per 100,000 in Texas. Particularly, the Rio Grande Valley (RGV) is an underserved area facing disparities that increase risk factors of HCC and thus, yielding higher incidence and mortality. Therefore, early, faster, and inexpensive diagnostic biomarkers and methods are crucial to under-resourced areas such as the RGV. Recently, we have identified an extracellular cancer antigen, POTE-2. Preliminary data indicates high POTE-2 expression in HCC tumors. In this study, we will discuss the role of POTE-2 in HCC progression and its associated regulatory pathways. Methods: The Cancer Genome Atlas (TCGA) database of HCC patients (n=371 tumor; n=50 normal) was analyzed. Liver cancer cells were procured from ATCC. POTE-2 mRNA and protein expression analyzed via RT-PCR and western blot. Absolute copy number was determined using Digital Droplet PCR. Lentiviral-based plasmids were used for overexpression and knockdown studies. Signaling pathways were analyzed using Proteome Profiler array. Results: Comprehensive analysis of TCGA database revealed high POTE-2 expression tumors with upregulation in all stages of HCC. POTE-2 expression increases with nodal metastatic status leading to poor survival. The protein expression for POTE-2 was significantly higher in SK-HEP1 compared to C3A cells. Lentiviral transduction showed significant overexpression and knockdown of the POTE-2 protein. Modulation of POTE-2 expression led to changes in lncRNA and kinase pathways. Conclusion: These studies will help discover novel mechanisms of POTE-2 protein function, signaling pathways and roles in liver cancer progression

Mucin MUC13 and YAP1 correlate with poor survival in colorectal cancer

Background: Metastatic disease contributes to over 90% of cancer-associated deaths. Colorectal cancer (CRC), the second lethal malignancy, has the greatest incidence and mortality rates in the Southern United States. Over 40-50% of CRC patients acquire metastasis at some point throughout their disease\u27s progression. CRC survival rate drops from 90%-14% when the disease is confined within the colon and therefore “early diagnosis” becomes imperative to determine timely and quality treatments. We have identified that MUC13 protein translocate to nucleus along with transcription factor Yes-Associated Protein 1 (YAP1) during anchorage independent conditions (metastatic phenotype). YAP1 is known to be overexpressed in CRC which promotes proliferation and survival of CRC cells. This study will provide information regarding MUC13 and YAP1 correlation and their role in CRC patient outcomes. Methods: The comparative analysis of MUC13 and YAP1 expression in CRC samples (Tissue Microarrays (TMA) of CRC patients (39 cases and 95 cores)) with Pathology grade, TNM Classification, Clinical stage, and Survival information were investigated using Immunohistochemistry (IHC) staining, followed by digital scanning by 3D-Histech scanner, and analysis using QuantCenter image analysis software. Results: IHC analysis revealed increased MUC13 expression in colon adenocarcinoma and metastatic adenocarcinoma compared to normal colon tissues. MUC13 expression was observed in nucleus, cytoplasm and membrane associated with mostly with poorly differentiated adenocarcinomas, while YAP1 was localized in the nucleus. The correlation of MUC13/YAP1 expression with patient outcome is in progress. Conclusion: This study will potentially establish a correlation between MUC13 and YAP1 with CRC patient outcome