Perturb - Shalek Lab

The disordered adapter protein linker for activation of T cells (LAT) propagates T cell receptor signaling. To interrogate how LAT coordinates multiple downstream pathways, we developed a single-cell screening approach, identifying widespread functional segments including protein interaction motifs and blocks of negative charge. Regardless of their position in LAT, individual segments generally conferred defects across all downstream signaling pathways. To understand the underlying mechanism, we used molecular biology, computational modeling, and imaging to demonstrate that disruption of LAT interaction with a single partner protein indirectly disrupts other partner interactions, likely […]

Disordered protein LAT encodes relative levels of signaling pathways in T cell activation

Phenotypic drug screening remains constrained by the vastness of chemical space and technical challenges scaling experimental workflows. To overcome these barriers, computational methods have been developed to prioritize compounds, but they rely on either single-task models lacking generalizability or heuristic-based genomic proxies that resist optimization. We designed an active deep-learning framework that leverages omics to enable scalable, optimizable identification of compounds that induce complex phenotypes. Our generalizable algorithm outperformed state-of-the-art models on classical recall, translating to a 13-17x increase in phenotypic hit-rate across two hematological discovery campaigns. Combining this algorithm […]

Active learning framework workflow diagram

High-throughput phenotypic screens using biochemical perturbationsand high-content readouts are constrained by limitations of scale. Toaddress this, we establish a method of pooling exogenous perturbationsfollowed by computational deconvolution to reduce required sample size,labor and cost. We demonstrate the increased efficiency of compressedexperimental designs compared to conventional approaches throughbenchmarking with a bioactive small-molecule library and a high-contentimaging readout. We then apply compressed screening in two biologicaldiscovery campaigns. In the first, we use early-passage pancreatic cancerorganoids to map transcriptional responses to a library of recombinanttumor microenvironment protein ligands, uncovering reproduciblephenotypic shifts induced by […]

Compressed phenotypic screening scalability figure

Efforts to cure BCR::ABL1 B cell acute lymphoblastic leukemia (Ph+ ALL) solely through inhibition of ABL1 kinase activity have thus far been insufficient despite the availability of tyrosine kinase inhibitors (TKIs) with broad activity against resistance mutants. The mechanisms that drive persistence within minimal residual disease (MRD) remain poorly understood and therefore untargeted. Utilizing 13 patient-derived xenograft (PDX) models and clinical trial specimens of Ph+ ALL, we examined how genetic and transcriptional features co-evolve to drive progression during prolonged TKI response. Our work reveals a landscape of cooperative mutational and […]

Ph+ ALL leukemia mutation and treatment study figure

The cellular composition of barrier epithelia is essential to organismal homoeostasis. In particular, within the small intestine, adult stem cells establish tissue cellularity, and may provide a means to control the abundance and quality of specialized epithelial cells. Yet, methods for the identification of biological targets regulating epithelial composition and function, and of small molecules modulating them, are lacking. Here we show that druggable biological targets and small-molecule regulators of intestinal stem cell differentiation can be identified via multiplexed phenotypic screening using thousands of miniaturized organoid models of intestinal stem […]

Paneth cell organoid drug screening platform

Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding […]

Pancreatic cancer organoid scRNA-seq graphical abstract

Background Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. Results To overcome the potentially confounding effects of donor-to-donor variability, we present a generally applicable computational framework for identifying reproducible patterns in gene expression across donors who share a unifying classification. Applying it, we discover a […]

HIV controller gene expression correlation heatmaps

We are inventing & applying scalable perturbation strategies to discover effective interventions.

Highlights

Disordered protein LAT encodes relative levels of signaling pathways in T cell activation

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes

Scalable, compressed phenotypic screening using pooled perturbations

Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers