Atomic Force Microscopy: a tool to unveil the mystery of biological systems

This article focuses on one of the promising and emerging nanolevel imaging techniques: Atomic Force Microscopy (AFM). In recent studies, AFM has been extensively used to understand intricate biological phenomena like prokaryotic and eukaryotic genome organization, different DNA transaction activities, protein chaperoning and also protein-nucleic acid organization in viruses

The role of divergent noncoding gene in triple-negative breast Cancer

Breast cancer is the second leading cause of cancer mortality in women after lung cancer. Breast cancer is grouped into different molecular subtypes; triple-negative breast cancer (TNBC) accounts for 20%. TNBC is a highly aggressive histologic subtype; the lack of unique therapeutic targets makes it harder to treat. Recent studies have implicated genes involved in cancers that are transcribed using a process known as divergent transcription. The expression of these genes is tightly regulated; however, many escape regulation and become aberrantly expressed in tumors. Interestingly, our genomic analysis suggests that several of these genes encode noncoding transcripts. Analysis of transcriptome from different tissue types, including cancer and normal, revealed that many are upregulated in various cancers. Selected divergent transcript, such as lncRNA67, has been completely characterized (transcription start and stop site, 5’ cap, polyA tail, and exon/intron structure) and cloned. In functional assays, overexpression of lncRNA67 regulates gene expression, cell proliferation, and tumor growth. Our molecular analyses indicate that lncRNA67 plays a vital role in triple-negative breast cancer biology. Collectively, our results suggest that divergent transcripts are an integral component of cancer biology and present a new repertoire of diagnostic and potential therapeutic targets

The role of a cancer testis-antigen in regulating tumor growth and oncogenic pathways in triple-negative breast cancer.

Breast cancer is the second leading cause of cancer-related deaths in women, after lung cancer. Unfortunately, it is the primary cause of death among Hispanic women. Approximately 10-20% of breast cancers are classified as basal (triple-negative) subtypes, which are challenging to treat due to the absence of specific targets. Triple-negative breast cancer is a highly aggressive and lethal type of tumor, particularly among Hispanic women, with a poor prognosis compared to other breast cancer subtypes. Therefore, it is crucial to identify new molecules with therapeutic and prognostic values to treat this evolving disease. Multiple studies have demonstrated that X-linked genes are associated with cancer. Although these genes are tightly regulated and expressed only in immune-privileged organs, many become abnormally expressed in tumors. Our genomic analysis has revealed that newly annotated X-linked genes previously thought to be gene deserts in the human genome are highly antigenic and cancer testis-antigens (CT genes). However, little information exists about their expression and role in triple-negative breast cancer. To fill this gap, we have used an integrated genomic approach to identify testis-tissue-specific genes differentially expressed in this type of breast cancer. Additionally, we have discovered a highly immunogenic cancer-testis gene using cutting-edge technology-driven (Global Run-On Sequencing) gene expression analysis. With cell- , mouse-based, and genomic approaches, we have mechanistically found that this CT gene modulates gene expression, immune response, and tumor growth in triple-negative breast cancer. This finding can potentially revolutionize the diagnosis and treatment of this type of breast cancer

Human positive coactivator 4 controls heterochromatinization and silencing of neural gene expression by interacting with REST/NRSF and CoREST

The highly abundant, multifunctional transcriptional positive coactivator 4 (PC4) plays important roles in transcription, replication and DNA repair. Our recent work showed that PC4 is a bona fide non-histone component of chromatin. Here, we report that knockdown of PC4 dramatically alters heterochromatin organization of the genome, accompanied by increased H3K9 (histone H3 at lysine residue 9)/14 acetylation, H3K4 trimethylation and reduction in the level of H3K9 dimethylation. These posttranslational modifications of histone H3 result in overexpression of normally silenced genes (e.g., neural genes) located in heterochromatin. The results of ChIP (chromatin immunoprecipitation) and re-ChIP assays showed that overexpression of a neuronal-specific gene is accompanied by histone hyperacetylation. We further show that PC4 interacts with heterochromatin protein 1α , REST/NRSF (RE1-silencing transcription factor/neuron-restrictive silencer factor) and CoREST to establish the repressed state of neural genes in nonneuronal cells. Thus, PC4 plays a crucial role in maintaining a dynamic chromatin state and heterochromatin gene silencing

Implications of enhancer transcription and eRNAs in cancer

Despite extensive progress in developing anti-cancer therapies, therapy resistance remains a major challenge that promotes disease relapse. The changes that lead to therapy resistance can be intrinsically present or may be initiated during treatment. Genetic and epigenetic heterogeneity in tumors make it more challenging to deal with therapy resistance. Recent advances in genome-wide analyses have revealed that the deregulation of distal gene regulatory elements, such as enhancers, appears in several pathophysiological conditions, including cancer. Beyond the conventional function of enhancers in recruiting transcription factors to gene promoters, enhancer elements are also transcribed into noncoding RNAs known as enhancer RNAs (eRNA). Accumulating evidence suggests that uncontrolled enhancer activity with aberrant eRNA expression promotes oncogenesis. Interestingly, tissue-specific, transcribed eRNAs from active enhancers can serve as potential therapeutic targets or biomarkers in several cancer types. This review provides a comprehensive overview of the mechanisms of enhancer transcription and eRNAs as well as their potential roles in cancer and drug resistance

Harnessing the Immune System with Cancer Vaccines: From Prevention to Therapeutics

Prophylactic vaccination against infectious diseases is one of the most successful public health measures of our lifetime. More recently, therapeutic vaccination against established diseases such as cancer has proven to be more challenging. In the host, cancer cells evade immunologic regulation by multiple means, including altering the antigens expressed on their cell surface or recruiting inflammatory cells that repress immune surveillance. Nevertheless, recent clinical data suggest that two classes of antigens show efficacy for the development of anticancer vaccines: tumor-associated antigens and neoantigens. In addition, many different vaccines derived from antigens based on cellular, peptide/protein, and genomic components are in development to establish their efficacy in cancer therapy. Some vaccines have shown promising results, which may lead to favorable outcomes when combined with standard therapeutic approaches. This review provides an overview of the innate and adaptive immune systems, their interactions with cancer cells, and the development of various different vaccines for use in anticancer therapeutics

Curcumin-glucoside, A Novel Synthetic Derivative of Curcumin, Inhibits alpha-Synuclein Oligomer Formation: Relevance to Parkinson's Disease

alpha-Synuclein aggregation is centrally implicated in Parkinson's disease (PD). It involves multi-step nucleated polymerization process via the formation of dimers, soluble toxic oligomers and insoluble fibrils. In the present study, we synthesized a novel compound viz., Curcumin-glucoside (Curc-gluc), a modified form of curcumin and studied its anti-aggregating potential with alpha-synuclein. Under aggregating conditions in vitro, Curc-gluc prevents oligomer formation as well as inhibits fibril formation indicating favorable stoichiometry for inhibition. The binding efficacies of Curc-gluc to both alpha-synuclein monomeric and oligomeric forms were characterized by micro-calorimetry. It was observed that titration of Curc-gluc with alpha-synuclein monomer yielded very low heat values with low binding while, in case of oligomers, Curc-gluc showed significant binding. Addition of Curc-gluc inhibited aggregation in a dose-dependent manner and enhanced alpha-synuclein solubility, which propose that Curc-gluc solubilizes the oligomeric form by disintegrating preformed fibrils and this is a novel observation. Overall, the data suggest that Curc-gluc binds to alpha-synuclein oligomeric form and prevents further fibrillization of alpha-synuclein; this might aid the development of disease modifying agents in preventing or treating PD