Inhibition of PERK-mediated unfolded protein response acts as a switch for reversal of residual senescence and as senolytic therapy in glioblastoma.

Background: Glioblastoma due to recurrence is clinically challenging with 10-15 months overall survival. Previously we showed that therapy-induced senescence (TIS) in glioblastoma reverses causing recurrence. Here, we aim to delineate the TIS reversal mechanism for potential therapeutic intervention to prevent glioblastoma (GBM) recurrence.

Comparison of outcomes of percutaneous deep venous arterialization in multiple practice settings.

Objective: We compared the efficacy of percutaneous deep venous arterialization (pDVA) in patients with no-option chronic limb-threatening ischemia in the hospital vs in office-based laboratory (OBL) settings.

Methods: A retrospective chart review was performed of all patients who underwent pDVA using off-the-shelf devices from January 2018 to March 2023 in a hospital and an OBL. We identified 73 eligible patients, 41 from a hospital setting (59% male; median age, 72 years; interquartile range, 18 years) and 32 from an OBL setting (59% males; 67 years; interquartile range, 16 years).

Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model.

Chromosome instability (CIN) is frequently observed in many tumors. The breakage-fusion-bridge (BFB) cycle has been proposed to be one of the main drivers of CIN during tumorigenesis and tumor evolution. However, the detailed mechanisms for the individual steps of the BFB cycle warrants further investigation.

Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome.

Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant mutations in combination with their functional and biochemical residue context as determined by protein structures and somatic mutation propensity within conserved PFAM domains, integrating the CADD scoring scheme.

Association of with human thyroid cancer.

Introduction: The diverse subtypes of thyroid carcinoma have distinct clinical outcomes despite a comparable spectrum of underlying genetic alterations. Beyond genetic alterations, sparse efforts have been made to characterize the microbes associated with thyroid cancer. In this study, we examine the microbial profile of thyroid cancer.

Influence of pathogens on host genome and epigenome in development of head and neck cancer.

Background: Head and neck cancer (HNSCC) is a heterogeneous group of cancers, affecting multiple regions such as oral cavity, pharynx, larynx, and nasal region, each showing a distinct molecular profile. HNSCC accounts for more than 6 million cases worldwide, soaring mainly in the developing countries.

Recent Findings: The aetiology of HNSCC is complex and multifactorial, involving both genetic and environmental factors.

The Molecular and Cellular Basis of Hutchinson-Gilford Progeria Syndrome and Potential Treatments.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare, autosomal-dominant, and fatal premature aging syndrome. HGPS is most often derived from a de novo point mutation in the gene, which results in an alternative splicing defect and the generation of the mutant protein, progerin. Progerin behaves in a dominant-negative fashion, leading to a variety of cellular and molecular changes, including nuclear abnormalities, defective DNA damage response (DDR) and DNA repair, and accelerated telomere attrition.

Progesterone modulates the DSCAM-AS1/miR-130a/ESR1 axis to suppress cell invasion and migration in breast cancer.

Background: A preoperative-progesterone intervention increases disease-free survival in patients with breast cancer, with an unknown underlying mechanism. We elucidated the role of non-coding RNAs in response to progesterone in human breast cancer.

Methods: Whole transcriptome sequencing dataset of 30 breast primary tumors (10 tumors exposed to hydroxyprogesterone and 20 tumors as control) were re-analyzed to identify differentially expressed non-coding RNAs followed by real-time PCR analyses to validate the expression of candidates.

TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants.

Cancer is a somatic disease. The lack of Indian-specific reference germline variation resources limits the ability to identify true cancer-associated somatic variants among Indian cancer patients. We integrate two recent studies, the GenomeAsia 100K and the Genomics for Public Health in India (IndiGen) program, describing genome sequence variations across 598 and 1029 healthy individuals of Indian origin, respectively, along with the unique variants generated from our in-house 173 normal germline samples derived from cancer patients to generate the Tata Memorial Centre-SNP database (TMC-SNPdb) 2.

ADAM10 facilitates rapid neural stem cell cycling and proper positioning within the subventricular zone niche via JAMC/RAP1Gap signaling.

The mechanisms that regulate neural stem cell (NSC) lineage progression and maintain NSCs within different domains of the adult neural stem cell niche, the subventricular zone are not well defined. Quiescent NSCs are arranged at the apical ventricular wall, while mitotically activated NSCs are found in the basal, vascular region of the subventricular zone. Here, we found that ADAM10 (a disintegrin and metalloproteinase 10) is essential in NSC association with the ventricular wall, and via this adhesion to the apical domain, ADAM10 regulates the switch from quiescent and undifferentiated NSC to an actively proliferative and differentiating cell state.

Mitigating consumer privacy breach in smart grid using obfuscation-based generative adversarial network.

Smart meters allow real-time monitoring and collection of power consumption data of a consumer's premise. With the worldwide integration of smart meters, there has been a substantial rise in concerns regarding threats to consumer privacy. The exposed fine-grained power consumption data results in behaviour leakage by revealing the end-user's home appliance usage information.

is associated with inflammation and poor survival in early-stage HPV-negative tongue cancer.

Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, gallbladder, cervical, colorectal, and head and neck tumors. We identify known cancer-associated pathogens consistent with the literature.

IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome.

Background: Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate.

Results: We present an updated version of the SARS-CoV-2 analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2.

Molecular characterization of lung squamous cell carcinoma tumors reveals therapeutically relevant alterations.

Introduction: Unlike lung adenocarcinoma patients, there is no FDA-approved targeted-therapy likely to benefit lung squamous cell carcinoma patients.

Materials And Methods: We performed survival analyses of lung squamous cell carcinoma patients harboring therapeutically relevant alterations identified by whole exome sequencing and mass spectrometry-based validation across 430 lung squamous tumors.

Results: We report a mean of 11.

An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome.

The analysis of the SARS-CoV-2 genome datasets has significantly advanced our understanding of the biology and genomic adaptability of the virus. However, the plurality of advanced sequencing datasets-such as short and long reads-presents a formidable computational challenge to uniformly perform quantitative, variant or phylogenetic analysis, thus limiting its application in public health laboratories engaged in studying epidemic outbreaks. We present a computational tool, Infectious Pathogen Detector (IPD), to perform integrated analysis of diverse genomic datasets, with a customized analytical module for the SARS-CoV-2 virus.

A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2.

Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with synthesized viral transcripts.

Raman spectroscopy-based detection of RNA viruses in saliva: A preliminary report.

Several non-invasive Raman spectroscopy-based assays have been reported for rapid and sensitive detection of pathogens. We developed a novel statistical model for the detection of RNA viruses in saliva, based on an unbiased selection of a set of 65 Raman spectral features that mostly attribute to the RNA moieties, with a prediction accuracy of 91.6% (92.

Inhibition of SETMAR-H3K36me2-NHEJ repair axis in residual disease cells prevents glioblastoma recurrence.

Background: Residual disease of glioblastoma (GBM) causes recurrence. However, targeting residual cells has failed, due to their inaccessibility and our lack of understanding of their survival mechanisms to radiation therapy. Here we deciphered a residual cell-specific survival mechanism essential for GBM relapse.

Identifying cancer driver genes from functional genomics screens.

With the emerging advances made in genomics and functional genomics approaches, there is a critical and growing unmet need to integrate plural datasets in order to identify driver genes in cancer. An integrative approach, with the convergence of multiple types of genetic evidence, can limit false positives through a posterior filtering strategy and reduce the need for multiple hypothesis testing to identify true cancer vulnerabilities. We performed a pooled shRNA screen against 906 human genes in the oral cancer cell line AW13516 in triplicate.

Multi-State Energy Classifier to Evaluate the Performance of the NILM Algorithm.

With the large-scale deployment of smart meters worldwide, research in non-intrusive load monitoring (NILM) has seen a significant rise due to its dual use of real-time monitoring of end-user appliances and user-centric feedback of power consumption usage. NILM is a technique for estimating the state and the power consumption of an individual appliance in a consumer's premise using a single point of measurement device such as a smart meter. Although there are several existing NILM techniques, there is no meaningful and accurate metric to evaluate these NILM techniques for multi-state devices such as the fridge, heat pump, etc.