A5042749306- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Cancer, Hypoxia, and Metabolism
- Radiomics and Machine Learning in Medical Imaging
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- Glioma Diagnosis and Treatment
- Bayesian Methods and Mixture Models
- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
- Cancer, Lipids, and Metabolism
- Molecular Biology Techniques and Applications
- MicroRNA in disease regulation
- Statistical Methods in Clinical Trials
- Cancer Immunotherapy and Biomarkers
- Optimal Experimental Design Methods
- Histone Deacetylase Inhibitors Research
- Cell Image Analysis Techniques
- Immune Cell Function and Interaction
- Genetic factors in colorectal cancer
- Glutathione Transferases and Polymorphisms
Indiana University School of Medicine
2017-2025
Indiana University – Purdue University Indianapolis
2018-2025
Oregon Health & Science University
2025
Ural Federal University
2024
University of Indianapolis
2019-2024
Indiana University Health
2021-2024
Indiana University Melvin and Bren Simon Comprehensive Cancer Center
2021-2024
Indiana Cancer Consortium
2022-2024
Sichuan University
2018-2024
Stanford University
2024
Most patients with pancreatic adenocarcinoma (PDAC) suffer cachexia; some do not. To model heterogeneity, we used patient-derived orthotopic xenografts. These phenocopied donor weight loss. Furthermore, muscle wasting correlated mortality and murine IL-6, human IL-6 associated the greatest cachexia. In cell culture mice, PDAC cells elicited adipocyte expression plus receptor (IL6R) in myocytes blood. induced lipolysis steatosis, dysmetabolism, wasting. Depletion of from malignant halved...
The metabolic heterogeneity and interplay between cells are known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we yet establish systematic understanding intra-tissue cooperative mechanisms. To mitigate this knowledge gap, developed novel computational method, namely, flux estimation analysis (scFEA), infer cell-wise fluxome from RNA-sequencing (scRNA-seq) data. scFEA is empowered by...
Pancreatic cancer is a solid tumour that often fatal. Hence, there an urgent need to identify new drug targets for this disease. Highly proliferating cells have increased demand nutrients and, therefore, up-regulate selective amino acid transporters. Here, we investigated which transporters are up-regulated in pancreatic and whether any of these has potential as target fatal disease.The expression was analysed using publicly available microarray datasets, the findings with transporter...
Immune evasion is a pivotal event in tumor progression. To eliminate human cancer cells, current immune checkpoint therapy set to boost CD8+ T cell–mediated cytotoxicity. However, this action eventually dependent on the efficient recognition of tumor-specific antigens via cell receptors. One primary mechanism by which cells evade surveillance downregulate their antigen presentation. Little progress has been made toward harnessing potential therapeutic targets for enhancing presentation cell....
Abstract Aims In addition to giving optimal medical and device therapy, promoting self‐care of chronic heart failure (CHF) patients also plays an important role in comprehensive disease management for better outcomes. The study was aimed investigate whether short message service (SMS) would help improve death or readmission‐free survival behaviour CHF patients. Methods results This a randomized controlled trial. Between December 2011 September 2015, admitted with decompensated tertiary...
Abstract Background Recent advances in kernel-based Deep Learning models have introduced a new era medical research. Originally designed for pattern recognition and image processing, are now applied to survival prognosis of cancer patients. Specifically, versions the Cox proportional hazards trained with transcriptomic data predict outcomes Methods In this study, broad analysis was performed on TCGA cancers using variety Learning-based models, including Cox-nnet, DeepSurv, method proposed by...
Gastric cancer is one of the most prevalent and aggressive cancers worldwide, its molecular mechanism remains largely elusive. Here we report genomic landscape in primary gastric adenocarcinoma human, based on complete genome sequences five pairs matching normal samples. In total, 103,464 somatic point mutations, including 407 nonsynonymous ones, were identified recurrent mutations harbored by Mucins (MUC3A MUC12) transcription factors (ZNF717, ZNF595 TP53). 679 rearrangements detected,...
Abstract Histologically normal tissue adjacent to the tumor can provide insight of microenvironmental alterations surrounding cancerous lesion and affecting progression disease. However, little is known about molecular changes governing cancer initiation in cancer-free breast tissue. Here, we employed laser microdissection whole-transcriptome profiling epithelium prior post diagnosis identify earliest carcinogenesis. Furthermore, a comprehensive analysis three compartments (microdissected...
The biclustering of large-scale gene expression data holds promising potential for detecting condition-specific functional modules (i.e. biclusters). However, existing methods do not adequately address a comprehensive detection all significant bicluster structures and have limited power when applied to generated by RNA-Sequencing (RNA-Seq), especially single-cell RNA-Seq (scRNA-Seq) data, where massive zero low values are observed.We present new algorithm, QUalitative BIClustering algorithm...
Host defense and inflammation are regulated by the NF-κB essential modulator (NEMO), a scaffolding protein with broad immune cell tissue expression profile. Hypomorphic mutations in inhibitor of kinase regulatory subunit gamma (IKBKG) encoding NEMO typically present immunodeficiency. Here, we characterized pediatric autoinflammatory syndrome 3 unrelated male patients distinct X-linked IKBKG germline that led to overexpression isoform lacking domain encoded exon 5 (NEMO-Δex5). This failed...
Abstract Heat shock factor 1 (HSF1) is a stress-responsive transcription that promotes cancer cell malignancy. To provide better understanding of the biological processes regulated by HSF1, here we developed an HSF1 activity signature (HAS) and found it was negatively associated with antitumor immune cells in breast tumors. Knockdown decreased tumor size caused influx several cells, most notably CD8+ T cells. Depletion rescued reduction growth HSF1-deficient tumors, suggesting prevents...
We present a computational study of tissue transcriptomic data 14 cancer types to address: what may drive cell division? Our analyses point that persistent disruption the intracellular pH by Fenton reactions be at root development. Specifically, we have statistically demonstrated take place in cytosol and mitochondria across all types, based on gene-expression integrated via Michaelis–Menten equation. In addition, shown (i) disease cells will continuously increase their pH, which respond...
Abstract A key challenge in modeling single-cell RNA-seq data is to capture the diversity of gene expression states regulated by different transcriptional regulatory inputs across individual cells, which further complicated largely observed zero and low expressions. We developed a left truncated mixture Gaussian (LTMG) model, from kinetic relationships inputs, mRNA metabolism abundance single cells. LTMG infers multi-modalities meanwhile, dropouts expressions are treated as truncated....
It has been observed that both cancer tissue cells and normal proliferating (NPCs) have the Warburg effect. Our goal here is to demonstrate they do this for different reasons. To accomplish this, we analyzed transcriptomic data of over 7000 control tissues 14 types in TCGA five NPC GEO. analyses reveal NPCs accumulate large quantities ATPs produced by respiration process before starting effect, raise intracellular pH from ∼6.8 ∼7.2 prepare cell division energetically. Once cycle starts,...
Activation of the epithelial-to-mesenchymal transition (EMT) program is a critical mechanism for initiating cancer progression and migration. Colorectal cancers contain many genetic epigenetic alterations that can contribute to EMT. Mutations activating PI3K/AKT signaling pathway are observed in >40% patients with colorectal contributing increased invasion metastasis. Little known about how oncogenic pathways such as synergize chromatin modifiers activate EMT program. Lysine-specific...
Abstract We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression tumor samples, through a community-wide DREAM Challenge. assess six published and 22 community-contributed methods using in vitro silico transcriptional profiles admixed cancer healthy cells. Several predict most cell types well, though they either were not trained to all functional CD8+ T states or do so with low accuracy. address this gap, including deep learning-based approach, whose...
Glutamine and glutamate are known to play important roles in cancer biology. However, no detailed information is available terms of their levels involvement various biological processes across different types, whereas such knowledge could be critical for understanding the distinct characteristics types. Our computational study aimed examine functional glutamine
Objective: Accumulated evidence highlights the biological significance of oxidative stress in tumorigenicity and progression colorectal cancer (CRC). Our study aimed to establish a reliable stress-related signature predict patients' clinical outcomes therapeutic responses. Methods: Transcriptome profiles features CRC patients were retrospectively analyzed from public datasets. LASSO analysis was used construct an overall survival, disease-free disease-specific progression-free survival....
Abstract Background Genome-wide association studies have identified several breast cancer susceptibility loci. However, biomarkers for risk assessment are still missing. Here, we investigated cancer-related molecular changes detected in tissues from women at high prior to disease manifestation. Disease-free tissue cores donated by healthy ( N = 146, median age 39 years) were processed both methylome (MethylCap) and transcriptome (Illumina’s HiSeq4000) sequencing. Analysis of microarray...
Antigen processing and presentation via major histocompatibility complex (MHC) molecules are central to immune surveillance. Yet, quantifying the dynamic activity of MHC class I II antigen remains a critical challenge, particularly in diseases like cancer, infection autoimmunity where these pathways often disrupted. Current methods fall short providing precise, sample-specific insights into presentation, limiting our understanding evasion therapeutic responses. Here, we present PSAA...