Twitter Beğeni Hilesi

What if we could inducibly create thousands of structural variants and ecDNAs in human cells and see which ones survive? biorxiv.org/content/10.110… I’m excited to share our story on scrambling the human genome by combining prime editing, repetitive elements, and recombinases. A🧵

Yet again--to nobody's surprise--Jay Shendure & co blow several fields'-worth of minds in a single paper 🤯🤯 Remarkable combination of cool tech + important but understudied problem Tech like this will transform our understanding of how SVs impact cellular phenotypes & fitness!

Long awaited preprint came out! It seems that a DNA double-strand break in chr17p, often near or within TP53, could be the initiator of osteosarcomagenesis. It creates a dicentric chromosome, which can lead to various genomic events, including chromothripsis and focal amps.

I am delighted to share my recent work, the product of an excellent collaboration with Kaiyuan Zhu and Jens Luebeck in the Bafna lab, that describes CoRAL: our tool for reconstructing focal amplifications, like ecDNA, from long-read data: biorxiv.org/content/10.110…

This collaboration was initiated in the very first week when I joined @UTSWNews. I gave a talk on #ecDNA and Ben Drapkin approached me saying that we should check it in his PDX models, and bingo, ecDNA with MYCs are prevalent in chemo-resistant small cell lung cancer!

Quick backgrounder / primer on ecDNA as it relates to cancer research from 2022 by Chris Bailey news.cancerresearchuk.org/2022/11/11/thi… Cancer Grand Challenges #CGCSummit (PP)

So excited to have this preprint out! Severus is a new tool for somatic SV calling in cancer using long reads. It supports tumor/normal analysis, takes advantage of long-read phasing and can cluster and annotate complex SV events. medrxiv.org/content/10.110…

Low depth WGS 🧬 harnessing precision medicine in glioblastoma 🧠: this Letter to the Editor in Annals of Oncology reports on the identification of ncogenic extrachromosomal DNA using FFPE samples Imran Noorani @charlesswanton Mischel Lab annalsofoncology.org/article/S0923-…

Our study on disentangling complex amplicons in Esophageal adenocarcinoma is now online Nature Communications ! We combined short reads, Oxford Nanopore long reads and scDNA-seq to understand the mechanisms behind these complex amplicons. Rebecca Fitzgerald Lab Karol Nowicki-Osuch nature.com/articles/s4146…

1/5 Today, I’m sharing 7yrs of work. I believe we discovered a comprehensive mapping from protein structure to glycan structure, a genetic encoding for specific glycans, and a new paradigm in extracellular biology. biorxiv.org/content/10.110… #Glycotime

Congrats #CancerGrandChallenges team #eDyNAmiC on their latest paper in eLife - the journal! 📢 They've uncovered how ecDNA-containing tumours up-regulate DNA damage and repair, cell cycle control, and mitotic processes, but down-regulate global immune regulation 👇 elifesciences.org/articles/88895

🔥Excited to share Mădălina Giurgiu Decoil out today Genome Research If you have Nanopore genome sequencing and want to study the structural heterogeneity of ecDNA, try it. Thank you to all the collaborators Cancer Grand Challenges team eDyNAmiC, Max Delbrück Center Charité - Universitätsmedizin Berlin Memorial Sloan Kettering Cancer Center

📢 eDyNAmiC exploits CRISPR-C to examine ecDNA biogenesis, finding: 1⃣ Circularisation is efficient 2⃣ Ligation events rely on distinct repair pathways to those forming the chromosomal scar 3⃣ Support for the dissociation model of excisional ecDNA formation More in Cancer Discovery 👇

🚨 Excited to share our latest paper in Cell identifying how under-replicated chromosomes in micronuclei become shattered by the Fanconi anemia pathway during mitosis. This work was led by UTSW Graduate School of Biomedical Sciences student Justin Engel. 🧵 (1/13): cell.com/cell/fulltext/…