Recapitulation of patient-specific 3D chromatin conformation using machine learning

Xu, Duo; Forbes, Andre Neil; Cohen, Sandra; Palladino, Ann; Karadimitriou, Tatiana; Khurana, Ekta

doi:10.1016/j.crmeth.2023.100578

Cited by 6 publications

(1 citation statement)

References 80 publications

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“… 5 However, ATAC-seq alone is not enough to differentiate between poised vs. active enhancers or the gene targets that the enhancer regulates. In this issue of Cell Reports Methods , Khurana and colleagues present differential gene targets of accessible chromatin (DGTAC), 6 which offers a possible solution to the problem for identifying long-range interactions between enhancers and genes in cancer patient samples.…”

Section: Main Textmentioning

confidence: 99%

Predicting patient-specific enhancer-promoter interactions

Baur,

Roy

2023

Cell Reports Methods

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Section: Main Textmentioning

confidence: 99%

Predicting patient-specific enhancer-promoter interactions

Baur,

Roy

2023

Cell Reports Methods

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The 30th Annual Prostate Cancer Foundation Scientific Retreat Report

Miyahira,

Soule

2024

The Prostate

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BackgroundThe 30th Annual Prostate Cancer Foundation (PCF) Scientific Retreat was held at the Omni La Costa Resort in Carlsbad, CA, from October 26 to 28, 2023. A hybrid component was included for virtual attendees.MethodsThe Annual PCF Scientific Retreat is a leading international scientific conference focused on pioneering, unpublished, and impactful studies across the spectrum of basic through clinical prostate cancer research, as well as research from related fields with significant potential for improving prostate cancer research and patient outcomes.ResultsThe 2023 PCF Retreat concentrated on key areas of research, including: (i) the biology of cancer stem cells and prostate cancer lineage plasticity; (ii) mechanisms of treatment resistance; (iii) emerging AI applications in diagnostic medicine; (iv) analytical and computational biology approaches in cancer research; (v) the role of nerves in prostate cancer; (vi) the biology of prostate cancer bone metastases; (vii) the contribution of ancestry and genomics to prostate cancer disparities; (viii) prostate cancer 3D genomics; (ix) progress in new targets and treatments for prostate cancer; (x) the biology and translational applications of tumor extracellular vesicles; (xi) updates from PCF TACTICAL Award teams; (xii) novel platforms for small molecule molecular glues and binding inhibitors; and (xiii) diversity, equity and inclusion strategies for advancing cancer care equity.ConclusionsThis meeting report summarizes the presentations and discussions from the 2023 PCF Scientific Retreat. We hope that sharing this information will deepen our understanding of current and emerging research and drive future advancements in prostate cancer patient care.

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A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations

Saldana-Guerrero,

Montano-Gutierrez,

Boswell

et al. 2024

Nat Commun

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Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.

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Recapitulation of patient-specific 3D chromatin conformation using machine learning

Cited by 6 publications

References 80 publications

Predicting patient-specific enhancer-promoter interactions

Predicting patient-specific enhancer-promoter interactions

The 30th Annual Prostate Cancer Foundation Scientific Retreat Report

A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations

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