Feel free to reach out here (or via email) with any questions.

Although the main conclusion's are unchanged, the preprint contains updates pertaining to individual essential lncRNAs. In parallel, we are working with the journal to correct the scientific record, but we wanted to share the updated work with the community as quickly as possible.

In the preprint, all results have been updated with proper filtering to eliminate guide RNAs with potential off-targets in other transcripts. Where needed, we performed new experiments and updated computational analyses. The study’s main conclusions are unchanged.

We have updated our lncRNA study with the properly filtered library: doi.org/10.6084/m9.figshare.30370171

Most importantly, we want to thank Rita Cha & the group of Roland Rad for bringing these issues to our attention. We are very grateful for the help we received to correct and update the study.

And here's some of the main take-aways from the study: bsky.app/profile/nevi...

What sad news… Sayan was such a wonderful human being. Thank you for sharing.

@gamzeandgursoy.bsky.social is our local expert on genome privacy — maybe she can comment! In the meantime, here's her excellent recent review: pubmed.ncbi.nlm.nih.gov/35508070/

Thank you for following along and please check out the paper 📜 for more details.

The link in the first bleat (not skeet!) above is open-access. Also, you can find PDFs for this study and all others from our lab here: sanjanalab.org/papers.html

I also want to highlight a similar study of the MYC locus in the context of different lymphomas (from
@russelljhryan.bsky.social & team), which has many complementary discoveries to our work: www.biorxiv.org/content/10.1...

Also I am very grateful to noncoding genomics funding from the MacMillan Center for the Study of the Noncoding Cancer Genome at NYGC, NHGRI and NCI. Without funding from these sources, this work would not have been possible.

Thanks also to co-authors @johnomix.bsky.social, Simon Müller, Alex Mendez-Mancilla, Evan Geller and Noa Liscovitch-Brauer. Many amazing labmates past and present contributed!

This study was led by a stellar team 💫: Staff scientist Christina Caragine and PhD student
Vicky Le. The idea for a "noncoding Cancer DepMap" started with some of my first students, Meer Mustafa and Bianca Diaz. Big shout-out to Meer & Bianca for their early contributions!

Given MYC's prime role in the progression of SO many different cancers, we hope these these tumor-specific regulators yield potential therapeutic targets for this “undruggable” oncogene. 💊 CRE discovery from saturation CRISPR screens presents an important step towards this ultimate goal.

In parallel with CREs from the CRISPR screen, we took an even broader approach: Using expression data from thousands of tumors and normal tissues, we found many TFs with cancer-specific MYC-correlated expression (>5-fold higher cancer vs. normal tissue).

Getting back to the MYC story, we next wondered whether the CREs we identified bind specific TFs. We looked for those TFs whose expression was correlated with MYC expression and where binding sites could be identified in the CREs.