Ed Reznik

@iskander But tRNAs are typically not polyadenylated right? Not in your library

@EdReznik + tRNAs! But the noise introduced from sample condition + prep methods make this unusable in practice (when comparing across diverse sample origins)

Trick I've found useful for analyzing tumor RNA: zero out mitochondrial genes (including mt-tRNA), NUMTs, rRNA, rRNA pseudogenes, & MALAT1/NEAT1. Renormalize TPM (so values add up to 10^6). Cleans up noise from sample degradation, enrichment method, &c Does this have a name?

@iskander mtDNA encodes just 13 proteins that ultimately determine the most basic metabolic decision for a cell, to respire or ferment. i think that's as basic a feature of tumor biology as you're going to get.

@EdReznik Sometimes 5%, sometimes 30%! rRNA variance is even crazier, can get up to 90% depending on enrichment and sample degradation For my use cases though that’s pure noise, deflating TPMs of informative markers that are actually useful for reasoning about tumor biology

@notSoJunkDNA @iskander yes, mtdna is polyadenylated

@iskander should it be called "in silico poly-A enrichment"? most of the genes you propose to erase are not polyadenylated, are they?

Thrilled to receive the Gerstner Physician Scholars’ grant! The grant will support our work for the next 3 years on mitochondrial DNA mutations in cancer. Very thankful for the mentorship from Craig Thompson, @EdReznik, @motzermd, @arihakimi and many others! @MSK_DeptOfMed

Thanks to the many, many people who helped and guided along the way, and to the funders, esp @psscra for their investment in this high-risk science before we had anything to tangible to show for it, and to @CancerGrand + CANCAN for supporting new ideas in cachexia science

Lots of implications from this, but the biggest one is that we firmly believe a framework like this could be used to pioneer a precision medicine trial for cancer cachexia, matching tx to subtype.

Very excited to report on our lab’s unexpected adventure into subtyping cancer cachexia by way of anatomy, where we study the evolution of the bodies (not the genomes!) of patients with cancer during profound weight loss. Led by Sonia Boscenco. medrxiv.org/content/10.648…

I don’t post much anymore but thought I would take a moment to share my feelings on an issue that has been papered over by the negative impact that external forces have had on science and scientists: the toxicity of our own interactions within the scientific community. (1/10)

@MSKCancerCenter @EileenMOReilly @AACR What an absolute delight to see such a giant in the field giving a poster.

MSK gastrointestinal medical oncologist Dr. @EileenMOReilly speaks to a crowd about her late-breaking poster research on “Daraxonrasib monotherapy as first-line (1L) treatment for patients with metastatic #pancreatic adenocarcinoma (mPDAC)” at #AACR26. @aacr

I just want to say, for all those applying to PhD programs now in computational and systems biology: I would never have been admitted if I were to apply today. I don't even think I'd earn an interview. You are incredible and admission is not a judgement on your awesomeness.

Congratulations to this year’s recipients of the Memorial Sloan Kettering Cancer Center (MSK) 2025 Paul Marks Prize for Cancer Research: Dr. @AbdelWahablab, of @MSKCancerCenter; Dr. Andrea Ablasser, of @EPFL_en; and Dr. @cncurtis, of @StanfordMed. The prize, named in honor of MSK’s past President Emeritus, the late Paul Marks, recognizes a new generation of leaders who are making significant contributions to the understanding of cancer or are improving the treatment of the disease. Learn more about the winners: bit.ly/4hI5TOU

A special thanks as usual to our labs and to the patients and their families who contributed to this work.

They also open up an exciting line of inquiry into rRNA mutations themselves, the phenotypes of which we are only beginning to understand.

Together with @mito_oncogene, today we report in Nature Genetics a peculiar + exciting discovery: positive selection of mutations to mitochondrial ribosomal RNA in cancer. Led by Sonia Boscenco, Jacqueline Tait-Mulder, and Minsoo Kim nature.com/articles/s4158…