A5087101932- COVID-19 Clinical Research Studies
- Muscle Physiology and Disorders
- SARS-CoV-2 and COVID-19 Research
- Genetic Neurodegenerative Diseases
- Long-Term Effects of COVID-19
- Cancer Genomics and Diagnostics
- Cancer Cells and Metastasis
- Genetic factors in colorectal cancer
- Bioinformatics and Genomic Networks
- Ferroptosis and cancer prognosis
- Colorectal Cancer Treatments and Studies
- Biomedical Text Mining and Ontologies
- Cancer Immunotherapy and Biomarkers
- Botulinum Toxin and Related Neurological Disorders
- PI3K/AKT/mTOR signaling in cancer
- Bacillus and Francisella bacterial research
- Immune Cell Function and Interaction
- Advanced Breast Cancer Therapies
- Biotin and Related Studies
- Cardiac Fibrosis and Remodeling
- Inflammatory mediators and NSAID effects
- Dermatological and COVID-19 studies
- Cancer-related Molecular Pathways
- Adipose Tissue and Metabolism
- Tissue Engineering and Regenerative Medicine
University of California, San Diego
2016-2025
UC San Diego Health System
2025
La Jolla Bioengineering Institute
2016-2024
Dr. Hari Singh Gour University
2024
Dayananda Sagar University
2024
San Diego Supercomputer Center
2024
Arizona State University
2010
Mangalore Institute of Oncology
2009
Abstract Background Given the differences in embryonic origin, vascular and nervous supplies, microbiotic burden, main physiological functions of left right colons, tumor location is increasingly suggested to dictate behavior affecting pathology, progression prognosis. Right-sided colon cancers arise cecum, ascending colon, hepatic flexure and/or transverse while left-sided splenic flexure, descending, sigmoid colon. In contrast prior reports, we attempt delineate programs tumorigenesis...
Tissue extracellular matrix (ECM) provides structural support and creates unique environments for resident cells (Bateman JF, Boot-Handford RP, Lamandé SR.
The mechanisms underlying the immune remodeling and severity response in coronavirus disease 2019 (COVID-19) are yet to be fully elucidated. Our comprehensive integrative analyses of single-cell RNA sequencing (scRNAseq) data from four published studies, patients with mild/moderate severe infections, indicate a robust expansion mobilization innate highlight by which low-density neutrophils megakaryocytes play crucial role cross talk between lymphoid myeloid lineages. We also document marked...
Triple-negative breast cancer is a prevalent subtype with the lowest 5-year survival. Several factors contribute to its treatment response, but inherent molecular and cellular tumor heterogeneity are increasingly acknowledged as crucial determinants. Spatial transcriptomic profiling was performed on FFPE tissues from retrospective, treatment-naive group of women differential prognoses (17 >15 years survival-good prognosis (GPx) 15 <3 survival-poor (PPx)) using GeoMX ® Digital Profiler....
Abstract Background: Pregnancy-associated triple negative breast cancer (PA-TNBC) is one of the highest-risk cancers, marked by an aggressive phenotype that lacks targeted treatment options. Although pregnancy thought to decrease long-term risk, studies have shown cancers diagnosed immediately following post-lactational involution a 2-3x greater risk metastasis and death than other cancers. The molecular basis for this not fully understood. Methods: Spatial transcriptomics using GeoMx...
Background. EpiphaNet (http://epiphanet.uth.tmc.edu) is an interactive knowledge discovery system, which enables researchers to explore visually sets of relations extracted from MEDLINE using a combination language processing techniques. In this paper, we discuss the theoretical and methodological foundations evaluate utility models that underlie it for literature‐based discovery. addition, present summary results drawn qualitative analysis over six hours interaction with system by basic...
This study provides global transcriptomic profiling and analysis of botulinum toxin A (BoNT-A)-treated muscle over a 1-year period.Microarray was performed on rat tibialis anterior muscles from 4 groups (n = 4/group) at 1, 4, 12, 52 weeks after BoNT-A injection compared with saline-injected rats 12 weeks.Dramatic transcriptional adaptation occurred 1 week paradoxical increase in expression slow immature isoforms, activation genes competing pathways repair atrophy, impaired mitochondrial...
Objective: Recently emerged beta-coronavirus SARS-CoV-2, has resulted in the current pandemic designated COVID-19. COVID-19 manifests as severe illness exhibiting systemic inflammatory response syndrome, acute respiratory distress syndrome (ARDS), thrombotic events, and shock, exacerbated further by co-morbidities age. Recent clinical evidence suggests that development of ARDS subsequent pulmonary failure result from a complex interplay between cell types (endothelial, epithelial immune)...
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disorder with its primary insult on the skeletal muscle. Severe muscle wasting, chronic inflammation and fibrosis characterize dystrophic Here we identify dysregulated pathways in DMD utilizing a co-expression network approach as described Weighted Gene Co-expression Network Analysis (WGCNA). Specifically, utilize WGCNA's "preservation" statistics to gene modules that exhibit weak conservation of topology within healthy networks....
Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive BC subtype characterized by significant molecular and clinical heterogeneity, influenced genetic, phenotypic, environmental factors, as well interactions of the tumor with its surrounding milieu. A racial disparity has been observed between African American (AA) European (EA) women regarding incidence progression TNBC. TNBC frequently occurs in young parous who self-identify AA harbor a germline BRCA1 mutation....
Abstract Background While mechanisms contributing to the progression and metastasis of colorectal cancer (CRC) are well studied, stage-specific have been less comprehensively explored. This is focus this manuscript. Methods Using previously published data for CRC (Gene Expression Omnibus ID GSE21510), we identified differentially expressed genes (DEGs) across four stages disease. We then generated unweighted weighted correlation networks each stages. Communities within these were detected...
Diseases affecting skeletal muscle exhibit considerable heterogeneity in intensity, etiology, phenotypic manifestation and gene expression. Systems biology approaches using network theory, allows for a holistic understanding of functional similarities amongst diseases. Here we propose co-expression based, theoretic approach to extract from 20 heterogeneous diseases comprising dystrophinopathies, inflammatory myopathies, neuromuscular, metabolic Utilizing this framework identified seven...
Assessment of cellular immunity to the SARS-CoV-2 coronavirus is great interest in chronically immunosuppressed transplant recipients (Tr), who are predisposed infections and vaccination failures. We evaluated CD154-expressing T-cells induced by spike (S) antigenic peptides 204 subjects-103 COVID-19 patients 101 healthy unexposed subjects. Sreactive CD154+T-cell frequencies were a) higher 42 Tr sampled pre-pandemic, compared with NT (p=0.02), b) lower (p<0.0001) accompanied S-reactive B-cell...
Abstract Assessment of T-cell immunity to the COVID-19 coronavirus requires reliable assays and is great interest, given uncertain longevity antibody response. Some recent reports have used immunodominant spike (S) antigenic peptides anti-CD28 co-stimulation in varying combinations assess SARS-CoV-2. These may cause hyperstimulation could overestimate antiviral chronically immunosuppressed transplant recipients, who are predisposed infections vaccination failures. Here, we evaluate...
Botulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications. The goal of this study was to utilize co-expression network theory analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression for 2000 genes (extracted using ranking heuristic) served as the basis analysis. Using weighted gene analysis (WGCNA), we identified 19 co-expressed modules, further hierarchically clustered into five groups. Quantifying average expression and...
Trastuzumab therapy in HER2+ breast cancer patients has mixed success owing to acquired resistance therapy. A detailed understanding of downstream molecular cascades resulting from trastuzumab is yet emerge. In this study, we investigate the cellular mechanisms underlying using trastuzumab-sensitive and -resistant cells (BT474 BT474R) treated with endogenous ligands EGF HRG across time. We probe early receptor organization through microscopy signaling events multiomics measurements assess...
Abstract The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes progression, treatment resistance, ultimately death. Tissue injury microenvironmental changes can cause adult differentiated cells acquire a plastic “developmentally unstable hybrid state” (DUHCS) enabling transdifferentiation into other types effect repair. Yet, the relevant mechanisms enable...
Abstract BACKGROUND: Triple-Negative Breast Cancer (TNBC) is a highly aggressive subtype of breast cancer and only ~40% TNBC patients achieve pathological complete response (pCR) following neoadjuvant chemotherapy (NACT). Since molecular heterogeneity may contribute to variable responses NACT, we aimed deconvolute TNBC’s histological spatial transcriptomics (ST) patterns. METHODS: In total, 90 pre-treatment biopsies were collected from NACT-treated archival samples the ongoing FORCE...
Abstract The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes progression, treatment resistance, ultimately death. Tissue injury microenvironmental changes can cause adult differentiated cells acquire a plastic “developmentally unstable hybrid state” (DUHCS) enabling transdifferentiation into other types effect repair. Yet, the relevant mechanisms enable...
Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive BC subtype characterized by significant molecular and clinical heterogeneity, influenced genetic, phenotypic, environmental factors, as well interactions of the tumor with its surrounding milieu. In recent past, gene expression-based subtyping methods have provided a functional understanding for observed diversity/heterogeneity. this study, we propose approach to reclassifying TNBC while considering cellular...
An understanding of mechanisms underlying colorectal cancer (CRC) development and progression is yet to be fully elucidated. This study aims employ network theoretic approaches analyse single cell transcriptomic data from CRC better characterize its sided-ness.
ABSTRACT A diagnosis of synchronous tumors is always questionable when they show similar histology. We present a case tumors, i.e. melanoma (MM) arising from the scalp and angiosarcoma (AS) cheek in patient Xeroderma pigmentosum (XP). The presence melanin AS led to differential possibility transdifferentiation malignant first instance. Immunohistochemistry (IHC) was negative for markers (Melan A, SOX-10 & S 100) positive vascular (ERG, CD31 CD34) ruling out concluding swelling as...
Summary The adult mammary gland is maintained by lineage-restricted progenitor cells through pregnancy, lactation, involution, and menopause. Injury resolution, transplantation-associated reconstitution, tumorigenesis are unique exceptions, wherein basal gain the ability to reprogram a luminal state. Here, we leverage newly developed cell-identity reporter mouse strains, time-resolved single-cell epigenetic transcriptomic analyses decipher molecular programs underlying basal-to-luminal fate...