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Jan 6, 2025 | 
digitalcommons.library.tmc.edu | Chad J. Creighton |Flora Zhang |Yiqun Zhang |Patricia D. Castro
KeywordsMale, Humans, DNA Methylation, Transcriptome, Black or African American, Epigenomics, Prostatic Neoplasms, RNA, Messenger, Gene Expression Regulation, Neoplastic, CpG Islands, Carrier Proteins, Nerve Tissue Proteins, Clinically localized prostate cancer, DNA methylation, gene expression, Genome-wide profiling, CpG methylation, African American menAbstractAfrican American (AA) men have the highest incidence and mortality rate from Prostate cancer (PCa) than any other racial/ethnic group.
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Jan 6, 2025 | 
digitalcommons.library.tmc.edu | Yiqun Zhang |Fengju Chen |Chad J. Creighton
KeywordsHumans, Neoplasms, Antineoplastic Agents, Transcriptome, metastasis, transcriptomics, patient-derived xenografts, PDX, molecular subtypes, pan-cancer, MYC, prostaglandins, EZH2, immune checkpointAbstractMolecular mechanisms underlying cancer metastasis span diverse tissues of origin. Here, we synthesize and collate the transcriptomes of patient-derived xenografts and patient tumor metastases, and these data collectively represent 38 studies and over 3,000 patients and 4,000 tumors.
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Jan 6, 2025 | 
digitalcommons.library.tmc.edu | Chad J. Creighton
KeywordsHumans, Female, Transcriptome, Gene Expression Profiling, Neoplasms, Gene Expression Regulation, Neoplastic, Breast NeoplasmsAbstractThe vast amount of gene expression profiling data of bulk tumors and cell lines available in the public domain represents a tremendous resource.
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Jan 6, 2025 | 
digitalcommons.library.tmc.edu | Fengju Chen |Yiqun Zhang |Fritz J Sedlazeck |Chad J. Creighton
KeywordsHumans, Transcriptome, Neoplasms, RNA, Germ Cells, cancer, structural variation, structural variants, germline, PCAWG, Pan-Cancer Analysis of Whole Genomes, Whole Genome Sequencing, GWAS, eQTL, expression quantitative trait lociAbstractGermline variation and somatic alterations contribute to the molecular profile of cancers. We combine RNA with whole genome sequencing across 1,218 cancer patients to determine the extent germline structural variants (SVs) impact expression of nearby genes.
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Jan 6, 2025 | 
digitalcommons.library.tmc.edu | Yiqun Zhang |Fengju Chen |Marija Balic |Chad J. Creighton
BACKGROUND: The differential gene expression profile of metastatic versus primary breast tumors represents an avenue for discovering new or underappreciated pathways underscoring processes of metastasis. However, as tumor biopsy samples are a mixture of cancer and non-cancer cells, most differentially expressed genes in metastases would represent confounders involving sample biopsy site rather than cancer cell biology.
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Jul 23, 2024 | 
digitalcommons.library.tmc.edu | Wen Bu |Chad J. Creighton |Kelsey S. Heavener |Carolina Marinovic Gutierrez |Carolina Campelo Gutiérrez
AbstractCRISPR-Cas9 has been used successfully to introduce indels in somatic cells of rodents; however, precise editing of single nucleotides has been hampered by limitations of flexibility and efficiency. Here, we report technological modifications to the CRISPR-Cas9 vector system that now allows homology-directed repair-mediated precise editing of any proto-oncogene in murine somatic tissues to generate tumor models with high flexibility and efficiency.
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Mar 4, 2024 | 00069-7?rss=yes&sz=64)
cell.com | Chad J. Creighton
Highlights•Combined RNA and germline SV analysis using the PCAWG consortium datasets•Several genes impacted by germline SVs could conceivably contribute to cancer•Several genes are essential in cell lines or involve patient survival associationsSummaryGermline variation and somatic alterations contribute to the molecular profile of cancers.
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Feb 13, 2024 | 
nature.com | Chandra sekhar amara |Andrea B. Apolo |Jianjun Gao |Yair Lotan |H. Courtney Hodges |Seth P Lerner | +5 more
AbstractSMARCB1 loss has long been observed in many solid tumors. However, there is a need to elucidate targetable pathways driving growth and metastasis in SMARCB1-deficient tumors. Here, we demonstrate that SMARCB1 deficiency, defined as genomic SMARCB1 copy number loss associated with reduced mRNA, drives disease progression in patients with bladder cancer by engaging STAT3. SMARCB1 loss increases the chromatin accessibility of the STAT3 locus in vitro.
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Jul 3, 2023 | 
nature.com | Deyong Jia |Chad J. Creighton
AbstractThe complement system is a major component of the innate immune system that works through the cytolytic effect of the membrane attack complex (MAC). Complement component 7 (C7) is essential for MAC assembly and its precisely regulated expression level is crucial for the cytolytic activity of MAC. We show that C7 is specifically expressed by the stromal cells in both mouse and human prostates. The expression level of C7 inversely correlates with clinical outcomes in prostate cancer.
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May 25, 2023 | 
biorxiv.org | Vasanthi Avadhanula |Chad J. Creighton |Richard Sucgang |Laura Ferlic-Stark
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