Travis Fleming
@tjflemin.bsky.social
Harvard Medical School PhD '25 @bloodgenes.bsky.social lab
Functional genomics, CRISPR screens, Acute Myeloid Leukemia, Drug discovery, targeted protein degradation
@danafarber.bsky.social
@bostonchildrens.bsky.social
@broadinstitute.org
Functional genomics, CRISPR screens, Acute Myeloid Leukemia, Drug discovery, targeted protein degradation
@danafarber.bsky.social
@bostonchildrens.bsky.social
@broadinstitute.org
Amazing work @hemagene.bsky.social! He's a rising star for sure!
April 4, 2025 at 8:19 PM
Amazing work @hemagene.bsky.social! He's a rising star for sure!
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
January 7, 2025 at 10:23 PM
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...
www.biorxiv.org/content/10.1...
Thanks so much @dpastoors.bsky.social! Excited to see two great stories converging on the same biology :)
January 3, 2025 at 4:30 PM
Thanks so much @dpastoors.bsky.social! Excited to see two great stories converging on the same biology :)
Thank you so much! @ernstlaboratory.bsky.social
January 3, 2025 at 4:19 PM
Thank you so much! @ernstlaboratory.bsky.social
Definitely! Adapted from this paper: pubmed.ncbi.nlm.nih.gov/35618837/
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...
pubmed.ncbi.nlm.nih.gov
January 3, 2025 at 4:18 PM
Definitely! Adapted from this paper: pubmed.ncbi.nlm.nih.gov/35618837/
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.
January 2, 2025 at 2:47 PM
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...
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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!
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.
January 2, 2025 at 2:47 PM
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.