BackgroundFrom bat wings to whale flippers, limb diversification has been crucial to the evolutionary success of mammals. We performed the first transcriptome-wide study of limb development in multiple species to explore the hypothesis that mammalian limb diversification has proceeded through the differential expression of conserved shared genes, rather than by major changes to limb patterning. Specifically, we investigated the manner in which the expression of shared genes has evolved within and among mammalian species.ResultsWe assembled and compared transcriptomes of bat, mouse, opossum, and pig fore- and hind limbs at the ridge, bud, and paddle stages of development. Results suggest that gene expression patterns exhibit larger variation among species during later than earlier stages of limb development, while within species results are more mixed. Consistent with the former, results also suggest that genes expressed at later developmental stages tend to have a younger evolutionary age than genes expressed at earlier stages. A suite of key limb-patterning genes was identified as being differentially expressed among the homologous limbs of all species. However, only a small subset of shared genes is differentially expressed in the fore- and hind limbs of all examined species. Similarly, a small subset of shared genes is differentially expressed within the fore- and hind limb of a single species and among the forelimbs of different species.ConclusionsTaken together, results of this study do not support the existence of a phylotypic period of limb development ending at chondrogenesis, but do support the hypothesis that the hierarchical nature of development translates into increasing variation among species as development progresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0902-6) contains supplementary material, which is available to authorized users.

African American (AA) men are more likely to be diagnosed with and die from prostate cancer (PCa) than European American (EA) men. Despite the central role of the androgen receptor (AR) transcription factor in PCa, little is known about the contribution of epigenetics to observed racial disparities. We performed AR ChIP-seq on primary prostate tumors from AA and EA men, finding that sites with greater AR binding intensity in AA relative to EA PCa are enriched for lipid metabolism and immune response genes. Integration with transcriptomic and metabolomic data demonstrated coinciding upregulation of lipid metabolism gene expression and increased lipid levels in AA PCa. In a metastatic prostate cancer cohort, upregulated lipid metabolism associated with poor prognosis. These findings offer the first insights into ancestry-specific differences in the PCa AR cistrome. The data suggest a model whereby increased androgen signaling may contribute to higher levels of lipid metabolism, immune response, and cytokine signaling in AA prostate tumors. Given the association of upregulated lipogenesis with PCa progression, our study provides a plausible biological explanation for the higher incidence and aggressiveness of PCa observed in AA men.

Castration-resistant prostate cancer (CRPC) remains highly lethal and in need of novel, actionable therapeutic targets. The pioneer factor GATA2 is a significant prostate cancer (PC) driver and linked to poor prognosis. GATA2 directly promotes androgen receptor (AR) gene expression (both full-length and splice-variant) and facilitates AR binding to chromatin, recruitment of coregulators, and target gene transcription. Unfortunately, there is no clinically applicable GATA2 inhibitor available at the moment. Using a bioinformatics algorithm, we screened in silico 2,650 clinically relevant drugs for a potential GATA2 inhibitor. Validation studies used cytotoxicity assays (MTT), global gene expression analysis, reporter assay, reverse phase protein array analysis (RPPA), and immunoblotting. We examined target engagement via cellular thermal shift assay (CETSA), ChIP-qPCR, and GATA2 DNA-binding assay. We identified the vasodilator dilazep as a potential GATA2 inhibitor and confirmed on-target activity via CETSA. Dilazep exerted anticancer activity across a broad panel of GATA2-dependent PC cell lines in vitro and in a PDX model in vivo. Dilazep inhibited GATA2 recruitment to chromatin and suppressed the cell cycle program, transcriptional programs driven by GATA2, AR, and c-MYC, and the expression of several oncogenic drivers, including AR, c-MYC, FOXM1, CENPF, EZH2, UBE2C, and RRM2, as well as of several mediators of metastasis, DNA damage repair and stemness. In conclusion, we provide, via an extensive compendium of methodologies, proof-of-principle that a small molecule can inhibit GATA2 function and suppress its downstream AR, c-MYC, and other PC-driving effectors. We propose GATA2 as a therapeutic target in CRPC.

Background: Prostate cancer (PC) is the single most common and second most lethal cancer in men. Despite therapeutic advances in androgen receptor (AR)-targeting agents, progression to lethal, drug-resistant, castration-resistant prostate cancer (CRPC) remains a major clinical problem. Thus, there is an unmet need for novel treatment approaches and novel, druggable therapeutic targets in metastatic CRPC. Profiling of PC patient samples shows increases in two master regulators of lipogenesis-sterol regulatory binding proteins 1 and 2 (SREBP1 and SREBP2)-and their transcriptional targets. Overexpression of SREBP1 and SREBP2 and their target genes has been associated with tumor aggressiveness, poor clinical outcomes, and drug resistance in PC. The activation and nuclear translocation of SREBPs is tightly regulated by SREBP cleavage-activating protein (SCAP). We propose targeting SCAP will simultaneously block the activation and subsequent activity of all three SREBPs and that this represents a promising therapeutic strategy to treat CRPC. Methods: To increase our understanding of SREBP biology in PC cells, we defined the cistrome of SREBPs across multiple PC cell lines via ChIP-Seq. We compared the transcriptomic profiles of genetic targeting of SREBP via siRNA and pharmacological targeting via the novel SCAP inhibitor, SCAPi. We evaluated the effect of SCAPi on cell viability, cell invasion, and AR-signaling in multiple PC cell lines using immunoblotting, luciferase reporters, flow cytometry, MTT, and invasion assays. Additionally, we will evaluate the anticancer activity and safety profile of our novel SCAPi using CDX mouse models. Results: We found that inhibition of SCAP via siRNA and via SCAPi both yielded similar gene signatures, particularly the perturbation of cell cycle and lipogenesis genes. SCAPi dramatically reduces cell viability, migration, invasion, and expression of both AR- and SREBP-target genes in multiple PC cell lines. Through flow cytometry (Annexin V) and western blots (cleaved PARP) we found SCAPi induces apoptosis within 48 hours in PC cells. Pilot studies in tumor-bearing mice show SCAPi significantly increases survival without inducing animal weight loss. Conclusions: There is a critical need for novel targets in PC, and dysregulated lipogenesis is an untargeted oncogenic pathway. Our work furthers the field’s understanding of hijacked lipogenesis in PC and paves the way for a first-in-class inhibitor of lipogenesis to treat lethal PC. Citation Format: Dallin Lowder, Jin Na Shin, Maria E. Ruiz-Echartea, Darlene Skapura, Jenny Deng, Aleksandra Rusin, Christel Davis, Erik Ehli, Cristian Coarfa, Michael Ittmann, Salma Kaochar. Developing a lipogenesis inhibitor for prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 442.

Supplementary Figure from The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response

<div>Abstract<p>African-American (AA) men are more likely to be diagnosed with and die from prostate cancer than European American (EA) men. Despite the central role of the androgen receptor (AR) transcription factor in prostate cancer, little is known about the contribution of epigenetics to observed racial disparities. We performed AR chromatin immunoprecipitation sequencing on primary prostate tumors from AA and EA men, finding that sites with greater AR binding intensity in AA relative to EA prostate cancer are enriched for lipid metabolism and immune response genes. Integration with transcriptomic and metabolomic data demonstrated coinciding upregulation of lipid metabolism gene expression and increased lipid levels in AA prostate cancer. In a metastatic prostate cancer cohort, upregulated lipid metabolism associated with poor prognosis. These findings offer the first insights into ancestry-specific differences in the prostate cancer AR cistrome. The data suggest a model whereby increased androgen signaling may contribute to higher levels of lipid metabolism, immune response, and cytokine signaling in AA prostate tumors. Given the association of upregulated lipogenesis with prostate cancer progression, our study provides a plausible biological explanation for the higher incidence and aggressiveness of prostate cancer observed in AA men.</p>Significance:<p>With immunotherapies and inhibitors of metabolic enzymes in clinical development, the altered lipid metabolism and immune response in African-American men provides potential therapeutic opportunities to attenuate racial disparities in prostate cancer.</p></div>

Supplementary Figure from The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response

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