Biology subjects

Weiser, N. E.

Publications and source records attributed to Weiser, N. E..

4 recordsLinked to original sources

bioRxiv2026

scAmp analyzes focal gene amplifications at single-cell resolution

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common driver of tumor progression and is associated with acquired drug resistance and poor patient survival. While whole genome sequencing (WGS) studies have revealed the landscape of genes amplified on ecDNA in tumors, it remains challenging to study the subclonal heterogeneity and functional (e.g., transcriptomic) consequences of ecDNA on tumors. To address this, we introduce scAmp: a probabilistic algorithm for detecting and analyzing ecDNA from single-cell datasets. We demonstrate scAmps improved accuracy over WGS approaches on well-characterized cell-lines and its applicability to clinical histopathology. We further showcase scAmp by analyzing 73 patient tumors profiled with single-cell ATAC-seq, where we analyze the subclonal evolution of ecDNA+ subclones and identify the effect of ecDNA amplifications on the chromatin accessibility landscape of cancer cells. Together, we anticipate that scAmp will broadly enable further studies - both retrospective and prospective - that dissect critical questions of how ecDNA affect cancer cells and the tumors in which they reside.

cancer biology↗

bioRxiv2024

MORC-1 is a key component of the C. elegans CSR-1 germline gene licensing mechanism

The Argonaute CSR-1 is essential for germline development in C. elegans. Mutation of csr-1 downregulates thousands of germline-expressed genes, leading to the model that the CSR-1-mediated small RNA pathway promotes, or "licenses," gene expression by an unknown mechanism. CSR-1 also silences a limited number of genes through its canonical endonucleolytic "slicer" activity. We show that the GHKL-type ATPase MORC-1, a CSR-1 slicing target, over-accumulates at CSR-1 "licensed" target genes in csr-1(-), which correlates with ectopic gain of H3K9me3, H3K36me3 loss, and gene downregulation. Loss of morc-1 rescues csr-1(-) defects, while overexpressing MORC-1 in the germline of wild-type worms is sufficient to cause sterility and downregulate CSR-1 targets. These results show that MORC-1 overexpression in csr-1(-) is a primary driver of the CSR-1-mediated gene licensing mechanism. One-Sentence SummaryMORC-1 acts downstream of CSR-1 to regulate germline chromatin states and is a key component of the gene licensing mechanism.

molecular biology↗

bioRxiv2024

Enhancer activation from transposable elements in extrachromosomal DNA

Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoral heterogeneity in aggressive cancers. While transposable element (TE) reactivation is common in cancer, its role on ecDNA remains unexplored. Here, we map the 3D architecture of MYC-amplified ecDNA in colorectal cancer cells and identify 68 ecDNA-interacting elements (EIEs)--genomic loci enriched for TEs that are frequently integrated onto ecDNA. We focus on an L1M4a1#LINE/L1 fragment co-amplified with MYC, which functions only in the ecDNA amplified context. Using CRISPR-CATCH, CRISPR interference, and reporter assays, we confirm its presence on ecDNA, enhancer activity, and essentiality for cancer cell fitness. These findings reveal that repetitive elements can be reactivated and co-opted as functional rather than inactive sequences on ecDNA, potentially driving oncogene expression and tumor evolution. Our study uncovers a mechanism by which ecDNA harnesses repetitive elements to shape cancer phenotypes, with implications for diagnosis and therapy.

genetics↗

bioRxiv2024

Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers

Extrachromosomal DNA (ecDNA) presents a major challenge for precision medicine, contributing to poor survival for patients with oncogene-amplified tumours. EcDNA renders tumours resistant to targeted treatments by facilitating massive transcription of oncogenes and rapid genome evolution. At present, there are no ecDNA- specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers, exposing an actionable vulnerability. Stepwise analyses of ecDNA transcription reveal landscapes of pervasive RNA transcription and associated single-stranded DNA, leading to excessive transcription replication conflicts and replication stress (RS) compared to chromosomal loci. Nucleotide incorporation onto growing DNA strands is markedly slower on ecDNA, and RS is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. Replication Protein A2 phosphorylated on serine 33, a mediator of DNA damage repair that binds single-stranded DNA, shows elevated localization on ecDNA in a transcription dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition abrogates the DNA replication check point, causing extensive and preferential tumour cell death in ecDNA-containing tumours as they enter S-phase. To exploit this vulnerability, we develop a highly selective, potent, and bioavailable oral CHK1 inhibitor, BBI-2779, and demonstrate that it preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containing FGFR2 on ecDNA, BBI-2779, suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. These results reveal transcription-replication conflict as an ecDNA-generated vulnerability that can be targeted as an ecDNA-directed therapy and suggest that synthetic lethality of excess can be exploited as a strategy for treating cancer.

cancer biology↗