Excited to share our fun journey through time with the amazing team @D_Birschenkaum @FlorianIngelfi1 Yonathan @kathleenabadie @AssafWeiner from the @IdoAmitLab, measuring the temporal dynamics of immune cells in the GBM!

🧬 #ScienceSaturday ❓ Why does immunotherapy work so well for some cancers, but often fail in #glioblastoma, one of the most aggressive brain cancers? ➡️ A new study in @NatureCancer suggests the answer may depend less on how many DNA mutations a tumor has, and more on the tumor’s “cell state,” or what the cancer cells are actively doing. ➡️ Researchers studied 181 glioblastoma samples from patients treated with immune checkpoint blockade, a type of immunotherapy designed to help T cells recognize and attack cancer. ➡️ They found that glioblastomas in a mesenchymal, or MES, state were linked to better survival after immunotherapy. These tumors appeared more “immune-visible,” with higher levels of HLA class I, a signal that helps T cells recognize abnormal cells, and more T cell infiltration. ➡️ Surprisingly, #tumor mutational burden, a marker often used to predict immunotherapy response in other cancers, did not predict better outcomes in this glioblastoma group. ➡️ The study also revealed a possible escape route: after #immunotherapy, some tumors shifted away from the MES state toward non-MES states, which may make them less recognizable to the immune system and more resistant to treatment. 🧠 Why this matters: Glioblastoma has been extremely difficult to treat, and checkpoint immunotherapy has mostly been disappointing in this disease. This study suggests that future trials may need to look at a tumor’s RNA “activity pattern,” not just its #DNA mutations, to identify patients who may be more likely to benefit. ✨ Big takeaway: In glioblastoma, the tumor’s current “state of mind” may help predict whether immunotherapy can see it, attack it, and make a difference. Read more here: nature.com/articles/s43018-0… @Nature @DanaFarber @Harvard @harvardmed @MassGenBrigham @broadinstitute @IBMResearch @DanaFarberNews @EAChiocca @JackYGhannam

Very nice resource paper in @Cancer_Cell that enables correlation of cell type specific expression data with survival in #PancreaticCancer. cell.com/cancer-cell/fulltex… Takes TCGA type datasets based on bulk RNA to the next level. Interactive web tool (ctPANDA) allows facile queries.

very happy to share our lab's latest work, published today in @Cancer_Cell : sciencedirect.com/science/ar…. We show that we can decompose pathology images of cancer tissue into their constituent parts, measure tissue patterns with AI, and that these tissue patterns (1/n)

SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types cell.com/molecular-cell/full…

Charting human cellular senescence in aging and disease cell.com/cell/fulltext/S0092…

Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale log. Move on. Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/

Check out our newest paper using generative modeling of microscopy to study protein localization! Cellular deep fakes... 👀

Excited to share the first pre-print from our lab!! Check it out here! biorxiv.org/content/10.64898… We found that many RNA-binding proteins understood to regulate RNA processing can also function like transcription factors and cofactors to directly regulate transcription.

hello world. Excited to launch the Ingelfinger Lab account! We’re a young lab in Germany’s Black Forest tackling key questions in immunology with innovative single-cell technologies. Follow us for updates on systems immunology, machine learning & translational oncology. fi

Thrilled to share our new work in @Nature highlighting how GPR15-guided CD8 T cells control intestinal inflammation in humans. Great collaboration with Dr. Michael Lenardo. doi.org/10.1038/s41586-026-1…

We are thrilled to share the newest publication from our lab! In this work, @RoiBalaban & @OriMoskowitz investigated the effect of #efferocytosis on #macrophage state and function in the #TME. science.org/doi/10.1126/scii…

We present Effero-seq, a novel approach combining #scRNA-seq with lysosomal acidification tracking by using pHrodo - a pH-sensitive fluorescent marker. This method allowed us to track gradual changes in macrophage gene expression driven by efferocytosis of apoptotic cells (ACs).

Online Now: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma dlvr.it/TStQvf

A holy grail for our lab has been tracking myeloid cells in human tumors in the same way that we track T and B cells with TCR/BCR. @vincentzliu and @CalebLareau solved it! We developed Mitotrek using scATAC-seq mitochondrial DNA to do exactly this. Using Mitotrek, we find that new myeloid cells clones constantly infiltrate the tumor via circulating monocytes — and that their macrophage or dendritic cell fate is epigenetically programmed before tumor entry. @10xGenomics @parkerici @CancerResearch @TheMarkFdn cell.com/cancer-cell/fulltex…

Now online! Single-cell mapping of regulatory DNA-protein interactions dlvr.it/TStPv1

cell.com/issue/S0896-6273(25… On the cover: In this issue of Neuron, Du et al. @DuSiling show that repeated microglial depletion enables peripheral monocytes from both the blood and skull bone marrow to infiltrate the brain and engraft as monocyte-derived macrophages with distinct identities. Inspired by a passage from the Zuo Zhuan (“The first beat of the drum rouses the soldiers’ spirits; the second weakens their resolve; by the third, they are exhausted”), the artwork depicts three rounds of microglial depletion gradually exhausting the endogenous microglial niche. The two advancing armies represent distinct peripheral sources of invading cells: one arriving from the blood, illustrated by the army bearing the red flag, and the other emerging from the skull bone marrow, portrayed as descending from the mountains. Artist credit: Ying Xu.

📣 new preprint multimodal atlas. Imaging scRNA, 57M cells. 🧬🔬 Cells are complex dynamical systems — but most ways we measure them destroy them. We asked: how does live imaging compare to scRNA-seq, the field’s gold std? The answer surprised us 🧵 biorxiv.org/content/10.64898…

🚀 We are introducing PerturbPair (with @TakaKud0) — a platform that combines parallel Perturb-seq and optical pooled screening (OPS/PerturbView) in primary cells to systematically map at massive scale how genetic perturbations reshape cellular states across modalities. With wonderful collaborators @TakaKud0, @AnaMeireles, @AntRios, @jchuetter, @MinOta, @ORozenblattRosen, @LeviAGarraway, @KGeiger, @avtarsingh, @jkpritch, and Aviv Regev. Paper link: biorxiv.org/content/10.64898…

MoCAVI / PERCISTRA: Massively multiplex multimodal chemical screens at single-cell resolution biorxiv.org/content/10.64898…

In the latest issue! Unbiased niche labeling maps immune-excluded niche in bone metastasis dlvr.it/TSpHQr