Dan Landau

PATH (phylogenetic analysis of trait heritability) is out @NatureGenet! Excited about tackling the fundamentals of somatic evolution: *measuring cell state heritability *a quantitative definition for cell plasticity (1-heritability) *cell-state transition dynamics 👀🧵👇

Now out in @NatureBiotech ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones. nature.com/articles/s4158…

To close out the week, here’s a favorite poem by Naomi Shihab Nye!

@CarlosC24501217 @HebrewU @LautenbergI @WeizmannScience @bitonm congrats!!! youtube.com/watch?v=Grn7v2…

Proud of being around colleagues like this! Amazing science! @HebrewU @LautenbergI @WeizmannScience wis-wander.weizmann.ac.il/life-sciences/…

before long / you, too, shall rest Goethe

Our recent @CellCellPress study with @ChrisAWalsh1 lab on somatic mutations in microglia of AD brains highlighted in @NatureAging nature.com/articles/s4358…

Our scalable, cost-effective, and optics-free spatial genomic technique, IRISeq, is out in Nature Neuroscience today! Congrats to incredible @Abdul_Squared and @Weirong_Jiang from our lab at @RockefellerUniv

First of many great collaborations with @AbdelWahablab and our lab's first foray into spatial transcriptomics: "Ecological determinants of disease and immunity in myelodysplastic syndromes". We wanted to get into this area for a long time but were drawn to this unique ecological niche by @dewolf_susan: lnkd.in/ew4eGEvM The bone marrow is both difficult to derive samples from and challenging to analyze due to its lack of organized architecture compared to solid tissue. With key technological advancements and heroic effort Susan, Rob Stanley MD PhD and Kimon Argyropoulos addressed the first challenge with Ronan Chaligné. To tackle the second, Beatrice Zhang, a brilliant PhD student I am fortunate to co-mentor with Omar, under the guidance of @stephen_martis (the first fellow in @MSKCancerCenter 's Theory Group) developed a suite of analytical methods. Stephen's background in theoretical ecology was essential to our approach. They developed a paired set of methods called SAND-DUNE. SAND (Spatial Adjacency Network Detection) allowed for profiling of unique cell aggregates with awareness of immune cell specific features, while DUNE (Discovery by Unsupervised Niche Enrichment), allowed for sample to sample comparison of niche enrichment. Using these tools, we identified how hematopoetic niche enrichment stratified disease stages. If that was not enough, we paired our analysis with customized TCR and cancer cell specific probes to uncover the spatial distribution and phenotype of cancer cells and abundant T cell clones, revealing both that early immune activation, possibly against the shared neoantigens observed by Omar's lab, may indicate favorable response, and a specific mechanism by which cancer cells can modulate immune cells to facilitate escape. This unique team science approach led by first authors Beatrice, Rob and Kimon led to a rich analytical characterization of the hard to see microenvironment. The overarching view shows how such an approach may be able to yield clinically actionable strategies with an interpretable backbone of ecological principles based on richly characterized hard data.

Spatial genomics has existed for many years, but it has often been limited by complex imaging systems, specialized equipment, and $$$. With IRISeq, we wanted to simplify this to a simple PCR rxn. nature.com/articles/s4159…

When do cells shift from benign to malignant? In @CellCellPress, Endeavor Awardees @LoweLabMSKCC, @dana_peer & @DrPaulRomesser use spatial mapping to identify a "progenitor" state that could be targeted to intercept pancreatic cancer before it spreads. cell.com/cell/fulltext/…

Interested in single cell and spatial genomics? Check out the agenda for our 10th Single Cell Genomics Day on Friday 6/12. Speakers: Aviv Regev @anshulkundaje @junyue_cao @xinjin + many more! All talks are free and live-streamed at satijalab.org/scgd

Excited to present the first pre-print from our group, an investigation the human bone marrow microenvironments in patients with myelodysplastic syndromes (MDS) and normal age-matched subjects using Xenium genotype-informed spatial transcriptomics: biorxiv.org/content/10.648…

Science takes you places....

First visit to Seoul.... what an incredible city!

Seamus Heaney, with Ireland's best-loved poem from the past century

"Everyone forgets that Icarus also flew" - Jack Gilbert

Alu repeat-containing RNAs spatially organize actively transcribed genomic regions around nuclear speckles dlvr.it/TSRVyd

—Anne Carson

Excited to share a new preprint from the lab led by @LukeKoblan and @WilliamNColgan in which we describe our efforts to define a quantitative cell fate map of mouse embryogenesis! biorxiv.org/content/10.648…

Jack Gilbert

Through the Mark Foundation-@AACR-@lustgartenfdn-@TinasWish Early Detection Award for Ovarian Cancer, @landau_lab, @ronny_drapkin, @adamjwidman, and Paul Mischel are searching for early signs of ovarian cancer that can be detected in a blood test.🩸