Browsing by Author "Freedman, Jennifer A"

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    A widespread length-dependent splicing dysregulation in cancer.
    (Science advances, 2022-08) Zhang, Sirui; Mao, Miaowei; Lv, Yuesheng; Yang, Yingqun; He, Weijing; Song, Yongmei; Wang, Yongbo; Yang, Yun; Al Abo, Muthana; Freedman, Jennifer A; Patierno, Steven R; Wang, Yang; Wang, Zefeng
    Dysregulation of alternative splicing is a key molecular hallmark of cancer. However, the common features and underlying mechanisms remain unclear. Here, we report an intriguing length-dependent splicing regulation in cancers. By systematically analyzing the transcriptome of thousands of cancer patients, we found that short exons are more likely to be mis-spliced and preferentially excluded in cancers. Compared to other exons, cancer-associated short exons (CASEs) are more conserved and likely to encode in-frame low-complexity peptides, with functional enrichment in GTPase regulators and cell adhesion. We developed a CASE-based panel as reliable cancer stratification markers and strong predictors for survival, which is clinically useful because the detection of short exon splicing is practical. Mechanistically, mis-splicing of CASEs is regulated by elevated transcription and alteration of certain RNA binding proteins in cancers. Our findings uncover a common feature of cancer-specific splicing dysregulation with important clinical implications in cancer diagnosis and therapies.
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    Adaptive stress response genes associated with breast cancer subtypes and survival outcomes reveal race-related differences.
    (NPJ breast cancer, 2022-06) Al Abo, Muthana; Gearhart-Serna, Larisa; Van Laere, Steven; Freedman, Jennifer A; Patierno, Steven R; Hwang, Eun-Sil Shelley; Krishnamurthy, Savitri; Williams, Kevin P; Devi, Gayathri R
    Aggressive breast cancer variants, like triple negative and inflammatory breast cancer, contribute to disparities in survival and clinical outcomes among African American (AA) patients compared to White (W) patients. We previously identified the dominant role of anti-apoptotic protein XIAP in regulating tumor cell adaptive stress response (ASR) that promotes a hyperproliferative, drug resistant phenotype. Using The Cancer Genome Atlas (TCGA), we identified 46-88 ASR genes that are differentially expressed (2-fold-change and adjusted p-value < 0.05) depending on PAM50 breast cancer subtype. On average, 20% of all 226 ASR genes exhibited race-related differential expression. These genes were functionally relevant in cell cycle, DNA damage response, signal transduction, and regulation of cell death-related processes. Moreover, 23% of the differentially expressed ASR genes were associated with AA and/or W breast cancer patient survival. These identified genes represent potential therapeutic targets to improve breast cancer outcomes and mitigate associated health disparities.
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    Changing the landscape of non-small cell lung cancer disparities.
    (Journal of cancer biology, 2021-01) Odera, Joab O; Abo, Muthana Al; Patierno, Steven R; Clarke, Jeffrey M; Freedman, Jennifer A
    In the United States, lung and bronchus cancers are the second most common types of cancer and are responsible for the largest number of deaths from cancer, with African Americans suffering disproportionately from lung and bronchus cancers. This disparity likely results from a complex interplay among social, psycho-social, lifestyle, environmental, health system, and biological determinants of health. Toward improving outcomes for lung cancer patients of all races and ethnicities and mitigating lung cancer disparities, in this commentary, we bring forward biological factors that contribute to lung cancer disparities, efforts to identify, functionally characterize, and modulate novel ancestry-related RNA splicing-related targets in lung cancer for precision intervention, and translational and clinical research needs to improve outcomes for lung cancer patients of all races and ethnicities and mitigate lung cancer disparities.
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    Characterization of a castrate-resistant prostate cancer xenograft derived from a patient of West African ancestry.
    (Prostate cancer and prostatic diseases, 2021-10-13) Patierno, Brendon M; Foo, Wen-Chi; Allen, Tyler; Somarelli, Jason A; Ware, Kathryn E; Gupta, Santosh; Wise, Sandra; Wise, John P; Qin, Xiaodi; Zhang, Dadong; Xu, Lingfan; Li, Yanjing; Chen, Xufeng; Inman, Brant A; McCall, Shannon J; Huang, Jiaoti; Kittles, Rick A; Owzar, Kouros; Gregory, Simon; Armstrong, Andrew J; George, Daniel J; Patierno, Steven R; Hsu, David S; Freedman, Jennifer A

    Background

    Prostate cancer is a clinically and molecularly heterogeneous disease, with highest incidence and mortality among men of African ancestry. To date, prostate cancer patient-derived xenograft (PCPDX) models to study this disease have been difficult to establish because of limited specimen availability and poor uptake rates in immunodeficient mice. Ancestrally diverse PCPDXs are even more rare, and only six PCPDXs from self-identified African American patients from one institution were recently made available.

    Methods

    In the present study, we established a PCPDX from prostate cancer tissue from a patient of estimated 90% West African ancestry with metastatic castration resistant disease, and characterized this model's pathology, karyotype, hotspot mutations, copy number, gene fusions, gene expression, growth rate in normal and castrated mice, therapeutic response, and experimental metastasis.

    Results

    This PCPDX has a mutation in TP53 and loss of PTEN and RB1. We have documented a 100% take rate in mice after thawing the PCPDX tumor from frozen stock. The PCPDX is castrate- and docetaxel-resistant and cisplatin-sensitive, and has gene expression patterns associated with such drug responses. After tail vein injection, the PCPDX tumor cells can colonize the lungs of mice.

    Conclusion

    This PCPDX, along with others that are established and characterized, will be useful pre-clinically for studying the heterogeneity of prostate cancer biology and testing new therapeutics in models expected to be reflective of the clinical setting.
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    Single-nucleotide polymorphisms of stemness genes predicted to regulate RNA splicing, microRNA and oncogenic signaling are associated with prostate cancer survival.
    (Carcinogenesis, 2018-07) Freedman, Jennifer A; Wang, Yanru; Li, Xuechan; Liu, Hongliang; Moorman, Patricia G; George, Daniel J; Lee, Norman H; Hyslop, Terry; Wei, Qingyi; Patierno, Steven R
    Prostate cancer (PCa) is a clinically and molecularly heterogeneous disease, with variation in outcomes only partially predicted by grade and stage. Additional tools to distinguish indolent from aggressive disease are needed. Phenotypic characteristics of stemness correlate with poor cancer prognosis. Given this correlation, we identified single-nucleotide polymorphisms (SNPs) of stemness-related genes and examined their associations with PCa survival. SNPs within stemness-related genes were analyzed for association with overall survival of PCa in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Significant SNPs predicted to be functional were selected for linkage disequilibrium analysis and combined and stratified analyses. Identified SNPs were evaluated for association with gene expression. SNPs of CD44 (rs9666607), ABCC1 (rs35605 and rs212091) and GDF15 (rs1058587) were associated with PCa survival and predicted to be functional. A role for rs9666607 of CD44 and rs35605 of ABCC1 in RNA splicing regulation, rs212091 of ABCC1 in miRNA binding site activity and rs1058587 of GDF15 in causing an amino acid change was predicted. These SNPs represent potential novel prognostic markers for overall survival of PCa and support a contribution of the stemness pathway to PCa patient outcome.