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Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majournie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Methylation Screening Array (MSA), to focus on human trait screening and discovery. This array utilizes extensive data from previous Infinium platform-based epigenome-wide association studies (EWAS). It incorporates knowledge from the latest single-cell and cell type-resolution whole genome methylome profiles. The MSA is engineered to achieve scalable screening of epigenetics-trait association in an ultra-high sample throughput. Our design encompassed diverse human trait associations, including those with genetic, cellular, environmental, and demographical variables and human diseases such as genetic, neurodegenerative, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity for cell-type deconvolution and supporting 5-hydroxymethylation profiling in diverse human tissues. Our first atlas data using this platform uncovered the complex chromatin and tissue contexts of DNA modification variations and genetic variants linked to human phenotypes.
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Affiliation(s)
- David C Goldberg
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Cameron Cloud
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | - Elliot Kim
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | | | | | | | | | | | | | - Jared B Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Dutta S, Bhattacharya S, Harris H, Islam R, Bodas S, Polavaram N, Mishra J, Das D, Seshacharyulu P, Kalluchi A, Pal A, Kohli M, Lele S, Muders M, Batra S, Ghosh P, Datta K, Rowley M. Understanding the role of Pax5 in development of taxane-resistant neuroendocrine like prostate cancers. RESEARCH SQUARE 2023:rs.3.rs-3464475. [PMID: 38168280 PMCID: PMC10760218 DOI: 10.21203/rs.3.rs-3464475/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Resistance to the current Androgen Receptor Signaling Inhibitor (ARSI) therapies has led to higher incidences of therapy-induced neuroendocrine-like prostate cancer (t-NEPC). This highly aggressive subtype with predominant small cell-like characteristics is resistant to taxane chemotherapies and has a dismal overall survival. t-NEPCs are mostly treated with platinum-based drugs with a combination of etoposide or taxane and have less selectivity and high systemic toxicity, which often limit their clinical potential. During t-NEPC transformation, adenocarcinomas lose their luminal features and adopt neuro-basal characteristics. Whether the adaptive neuronal characteristics of t-NEPC are responsible for such taxane resistance remains unknown. Pathway analysis from patient gene-expression databases indicates that t-NEPC upregulates various neuronal pathways associated with enhanced cellular networks. To identify transcription factor(s) (TF) that could be important for promoting the gene expression for neuronal characters in t-NEPC, we performed ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq in our NE-like cell line models and analyzed the promoters of transcriptionally active and significantly enriched neuroendocrine-like (NE-like) cancer-specific genes. Our results indicate that Pax5 could be an important transcription factor for neuronal gene expression and specific to t-NEPC. Pathway analysis revealed that Pax5 expression is involved in axonal guidance, neurotransmitter regulation, and neuronal adhesion, which are critical for strong cellular communications. Further results suggest that depletion of Pax5 disrupts cellular interaction in NE-like cells and reduces surface growth factor receptor activation, thereby, sensitizing them to taxane therapies. Moreover, t-NEPC specific hydroxymethylation of Pax5 promoter CpG islands favors Pbx1 binding to induce Pax5 expression. Based on our study, we concluded that continuous exposure to ARSI therapies leads to epigenetic modifications and Pax5 activation in t-NEPC, which promotes the expression of genes necessary to adopt taxane-resistant NE-like cancer. Thus, targeting the Pax5 axis can be beneficial for reverting their taxane sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Muders
- Rudolf Becker Laboratory for Prostate Cancer Research, Center of Pathology, University of Bonn Medical Center
| | - Surinder Batra
- University of Nebraska Medical Center, Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases
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