Reposted by Alexis CaulierScience Magazine @science.org · 08/05/2026Rather than being the product of a churning, molten core, Ganymede’s dynamo may be powered by a core that is still forming, researchers report. Learn more: scim.ag/4etP0rF 0539
Alexis Caulier @hemagene.bsky.social · 04/05/2026I am happy to share that Perturb-Multiome ATAC fragment files (www.science.org/doi/10.1126/...) are now available on our GEO repository. 🧬👩💻 👉 (www.ncbi.nlm.nih.gov/geo/query/ac...) #SankaranLab #Multiome #Perturbationscreenncbi.nlm.nih.gov GEO Accession viewer NCBI's Gene Expression Omnibus (GEO) is a public archive and resource for gene expression data. 020
Alexis Caulier @hemagene.bsky.social · 01/05/2026What a beautiful work from my friend Peng Lyu in #SankaranLab, demonstrating how non-coding transcribed genetic information can rewire HSCs and modulate the risk to develop blood malignancies! www.sciencedirect.com/science/arti...sciencedirect.comGenetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cellsThe HOXA gene locus coordinates body patterning, hematopoiesis, and differentiation. While studying blood phenotype-associated variation within the HO… 040
Reposted by Alexis CaulierWaggoner Lab @labwaggoner.bsky.social · 18/04/2025Systemic inflammation impairs myelopoiesis and interferon type I responses in humans www.nature.com/articles/s41... @natimmunol.bsky.social 0226
Reposted by Alexis CaulierScience Magazine @science.org · 18/04/2025There’s an arms race going on between a disease-causing fungus and its host, and it’s not the one portrayed in HBO’s postapocalyptic series The Last of Us. #ScienceMagArchives scim.ag/42QS3Unscim.agArms race between ants and fungi has echoes of The Last of UsInsects are fighting off fungal invaders, but the fungi have some tricks up their sleeve 05913
Reposted by Alexis CaulierScience Magazine @science.org · 18/04/2025The Science Visuals team has been honored with three @commarts.com Awards of Excellence. These prestigious awards recognize creative excellence and outstanding execution in visual storytelling. (THREAD 🧵) scim.ag/4jDJ6TYscim.agScience Visuals honored with three Communication Arts AwardsThe prestigious awards recognize creative excellence and outstanding execution in visual storytelling. 18413
Alexis Caulier @hemagene.bsky.social · 16/04/2025A great ressource from the Khoriaty lab at University of Michigan to understand deeper the molecular regulation of erythropoiesis, this week in @natcomms.nature.com www.nature.com/articles/s41...nature.comA genome-wide screen identifies genes required for erythroid differentiation - Nature CommunicationsUsing a genome-wide CRISPR knock-out screen, the authors defined the repertoire of genes that are required for proerythroblast survival and for terminal erythroid differentiation. 020
Reposted by Alexis CaulierNature Biotechnology @natbiotech.nature.com · 03/04/2025Scalable spatial transcriptomics through computational array reconstruction - @broadinstitute.org go.nature.com/3QYfSDdgo.nature.comScalable spatial transcriptomics through computational array reconstruction - Nature BiotechnologyAn imaging-free spatial transcriptomics method facilitates high-throughput barcode array generation up to centimeter scale. 1349
Alexis Caulier @hemagene.bsky.social · 03/04/2025Our work nicely complements recently released papers from @thenormanlab www.cell.com/cell-systems... and @satijalab www.nature.com/articles/s41... that describe the value of multimodal perturb-seq using CRISPRi in cell lines to decipher gene regulatory networks ! 🧬 🧫 000
Alexis Caulier @hemagene.bsky.social · 03/04/2025We are also grateful to the @broadinstitute.org and the @GRO_Broad for their support, and to our editor and reviewers at @science.org! (end) 010
Alexis Caulier @hemagene.bsky.social · 03/04/2025I want to sincerely thank all our amazing co-authors and, in particular, my wonderful co-first author Jorge Martin-Rufino (@jmartinrufino), as well as my mentors @bloodgenes.bsky.social and @eric_lander. (12/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025Our findings reveal that heritable variation is predominantly enriched in specific gene regulatory networks controlled by master TFs, offering novel insights into the genetic architecture of complex traits. Protocols and much more can be found in our manuscript! (11/n) 120
Alexis Caulier @hemagene.bsky.social · 03/04/2025Most strikingly, we discovered that TF-sensitive regions comprise <0.3% of the genome but are enriched ~100-fold for SNPs associated with certain blood-cell phenotypes, which is remarkably higher than that of any other chromatin elements active throughout hematopoiesis. (10/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025…such as a GATA1-dependent regulatory network comprising the CPEB4 gene and an enhancer harboring variants with multiple associations to blood cell traits, exemplifying how Perturb-multiome can help systematically pinpoint associations between phenotypes and GWAS variants. (9/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025For example, we faithfully identified various well-characterized gene regulatory mechanisms in hematopoiesis, such as the BCL11A-mediated fetal-to-adult hemoglobin switch. Importantly, it also uncovered thousands of previously uncharacterized regulatory interactions… (8/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025As such, Perturb-multiome allowed us to reconstruct transcription factor-dependent gene regulatory networks throughout hematopoietic differentiation, capturing the complexity of the differentiation continuum and enabling a detailed understanding of regulatory mechanisms. (7/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025Perturb-multiome is highly effective in disease-relevant primary cells, such as hematopoietic stem and progenitor cells (which give rise to all blood cells) by overcoming challenges in perturbation efficiency and identification. (6/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025With Perturb-multiome we can now generate high-resolution analyses of gene regulatory networks in single cells, which enables genome-wide variant-to-function inferences. (5/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025To achieve this, we developed Perturb-multiome, which recovers from each cell: (1) the identity of the genetic perturbation (sgRNA), (2) the effect on chromatin accessibility at cis-regulatory elements (scATAC-seq), and (3) the effect on expression of genes (scRNA-seq). (4/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025Rather than recreating each variant, which is hard to scale, given the enrichment of noncoding causal variants in regulatory regions bound by transcription factors (TFs), we reasoned that systematic perturbation of TF networks in single cells could provide new insights (3/n) 110
Alexis Caulier @hemagene.bsky.social · 03/04/2025While GWAS have been successful in identifying a large number of genetic variants associated with complex traits, biological insights gained have been limited. This is largely due to the lack of systematic methods for linking these variants to their functional impacts. (2/n) 120
Alexis Caulier @hemagene.bsky.social · 03/04/2025Out 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/3YhBMoObit.lyTranscription factor networks disproportionately enrich for heritability of blood cell phenotypesMost 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... 45117
Reposted by Alexis CaulierDana-Farber News @danafarbernews.bsky.social · 06/03/2025Congratulations to @danafarber.bsky.social’s Lara Wahlster, MD, PhD, and Nina Weichert-Leahey, MD, for receiving the American Society for Clinical Investigation Emerging-Generation Awards. Read about Dr. Wahlster at bit.ly/4haxdTW and Dr. Weichert-Leahey at bit.ly/4h6BYxL. 042
