Travis Fleming

Amazing work @hemagene.bsky.social! He's a rising star for sure!

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

Out today in @science.org!
What if you could chart cells' regulatory programs at unprecedented resolution?
In my work with Jorge Martin-Rufino from the @bloodgenes.bsky.social lab, we dissect the genome’s control circuits and find where key genetic variation hides
bit.ly/3YhBMoO

MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in an aggressive subtype of acute myeloid leukemia (AML). Direct depletion of MECOM using an endogenous auxin...

A complementary pre-print was also posted from @delwelruud.bsky.social and @dpastoors.bsky.social further highlighting the importance of MECOM's repression of CEBPA in AML!
www.biorxiv.org/content/10.1...

A huge congrats to @dpastoors.bsky.social and @delwelruud.bsky.social for this fantastic work!

Thanks so much @dpastoors.bsky.social! Excited to see two great stories converging on the same biology :)

Congrats @tjflemin.bsky.social, @bloodgenes.bsky.social and coauthors! I feel like preprint directly ties together #HemeSky 's favorite two transcription factors: MECOM and CEBPA. As to why these two: I'm heavily biased as our complementary work will also be on biorxiv soon (monday!!)

Thank you so much! @ernstlaboratory.bsky.social

A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia - PubMed The treatment landscape of acute myeloid leukemia (AML) is evolving, with promising therapies entering clinical translation, yet patient responses remain heterogeneous, and biomarkers for tailoring tr...

Definitely! Adapted from this paper: pubmed.ncbi.nlm.nih.gov/35618837/

Wonderful to have this work led by @tjflemin.bsky.social along with other colleagues in our laboratory, as well as great collaborators, out on @biorxivpreprint.bsky.social! Stay tuned for exciting complementary work from @dpastoors.bsky.social, Ruud Delwel, and co coming soon!

Joao Paulo, Steven Gygi, @camimoso.bsky.social, Karen Adelman, Jennifer Perry, Yana Pikman, Kimberly Stegmaier, @nubama.bsky.social, @kmachlus.bsky.social, @hovestadt.bsky.social, Andrea Arruda, Mark Minden, and Richard Voit.

Just as important, none of this work could have been possible without immense help and mentorship from my good friends, collaborators and co-authors: @mantoszewski.bsky.social, Sander Lambo, Michael Gundry, Riccardo Piussi, Lara Wahlster, Sanjana Shah, Fiona Reed, Kevin Dong...

This work is the culmination of my PhD thesis in @bloodgenes.bsky.socials’ lab. I am incredibly grateful for the amazing support and mentorship Vijay has provided me over the years, allowing me to freely pursue my scientific interests.

I’m incredibly optimistic that these approaches can be extended across other leukemias and solid tumors, enabling therapeutic differentiation of malignant cells by rewiring dysregulated transcriptional activity.

In summary, we demonstrate how synergistic use of targeted protein degradation, functional genomic perturbations, and high-throughput screens can distill the functional significance of a complex oncogenic signaling network into a single, pivotal gene regulatory node.

Strikingly, activating this cisRE significantly impaired the engraftment ability of primary AML cells, highlighting the therapeutic potential of reactivating myeloid differentiation programs to disrupt the fitness of stem cell-like leukemia cells.

Finally, we transplanted these cells into immunodeficient mice to assess how CEBPA cisRE activation impacted leukemia burden and engraftment of modified cells.

The approach yielded a modest increase in CEBPA expression itself. However, this transient and subtle activation was sufficient to induce significant differentiation phenotypes during ex vivo culture.

We next assessed if activation of this cisRE alone was sufficient to induce differentiation of these primary AMLs. Here, we delivered CRISPRa mRNA and the same guide RNAs targeting this cisRE.

Remarkably, across a panel of patient samples, MECOM KO induced significant loss of stem cell-like leukemia cells, while inactivation of the CEBPA cisRE could almost completely rescue this phenotype and maintain cells in more stem cell-like states.

Nonetheless, we wanted to determine if the functional link between MECOM and this CEBPA cisRE was conserved in primary AML samples. To do so, we knocked out MECOM and co-inactivated this cisRE, hypothesizing that cisRE inactivation should rescue MECOM-KO-induced differentiation.

These functional screens and validation suggested a previously unappreciated and surprisingly simple regulatory logic underlying MECOM’s role in promoting stem cell-like states in AML through repression of a single critical cis-regulatory element.

We then performed an orthogonal screen using CRISPRa, asking if in the absence of MECOM perturbation, could activation of any single cisRE be sufficient to induce myeloid differentiation? Surprisingly, the only hit from this screen was the same cisRE linked to CEBPA!

We first leveraged a CRISPRi screen to determine if repressing any single cisRE is sufficient to maintain cells in a CD34+ stem cell-like state, even after MECOM degradation. The most significant hit from this screen was a cisRE 42 kb away from the myeloid TF CEBPA.

But which parts of these MECOM-regulated networks are functionally important? This motivated us to perform functional genomic screens to identify MECOM controlled cisREs that are essential in facilitating MECOM’s ability to block differentiation in stem cell-like leukemia cells.

We hypothesized that if our gene and cisRE networks are repressed in primary AML, MECOM-driven stem cell-like states would be anti-correlated with their activity. Indeed, analyses of single cell genomics data of a large AML patient cohort confirmed this hypothesis.

We defined conserved networks of genes and cis-regulatory elements (cisREs) under the direct repression of MECOM. However, we ultimately wanted to determine whether these MECOM-repressed gene and cisRE networks were relevant in primary AMLs.

We then profiled the direct molecular changes that occur upon MECOM loss. Interestingly, we observed significant increases in gene expression and chromatin accessibility hours after degradation, suggesting MECOM functions predominantly as a transcriptional repressor in AML.

Notably, MECOM degradation resulted in striking myeloid differentiation phenotypes and eventually cell death, presumably due to the loss of stem-like, self-renewal capabilities.

To characterize MECOM’s direct function, in the absence of confounding cell-state alterations, we engineered a suite of AML cell lines with an endogenous MECOM-FKBP12F36V degron. These models enable rapid and specific degradation of all MECOM protein in AML cells within minutes!

As shown by Ruud Delwel and co, HSC gene expression programs in AML are frequently driven by increased expression of MECOM, a TF that plays a key role in normal HSC maintenance. However, the mechanisms by which MECOM drives stem cell-like, high-risk features remained unclear.