Dana Pe’er

Neoantigen-reactive CD8+ T cell engagement marks exceptional survivors of pancreatic cancer

The paper identifies TIE CD8+ T cell clonotypes associated with prolonged survival in pancreatic cancer patients and links resistance to stromal and immune barriers.

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

IL-1β/IL-6 signaling circuit in the tumor microenvironment drives prostate cancer development

This study identifies an IL-1β/IL-6 signaling circuit in the tumor microenvironment that drives prostate cancer progression from pre-invasive to invasive stages.

The basal cell state maintains pancreatic cancers by controlling an immunosuppressive circuit

This study identifies the basal cell state in pancreatic cancer as critical for maintaining tumors through an immunosuppressive circuit, showing its ablation leads to tumor collapse.

Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing

GIFT enables high-accuracy genotyping in single cells, revealing mutation-dependent hematopoietic responses in MPN patients.

Hierarchical classification of immune cell transcriptomes at population-scale

The paper introduces Suco and Compocyte to classify immune cells from 3,965 patients, identifying new macrophage and monocyte states and T cell memory erosion in metastases.

Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition

In mouse pancreatic cancer models, p53, CDKN2A and SMAD4 programs converge on a rare Kras-mutant progenitor-like state whose niche KRAS inhibition collapses and p53 loss expands.

POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancer

The paper identifies MDF, a repair scar linked to POLQ-driven error-prone repair, as a marker of immune-responsive HRD pancreatic cancer with increased neoantigens and favorable clinical outcomes.

Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer

The paper analyzes transcriptomic changes in metastatic pancreatic cancer using a patient's autopsy data to identify site-specific gene programs and clonal phylogeny.

Metastatic site influences driver gene function in pancreatic cancer

This study shows that metastatic site influences the function of driver genes like SMAD4 in pancreatic cancer, with organ-specific epigenetic states affecting tumor growth.

Joint representation and visualization of derailed cell states with Decipher

Decipher is a deep generative model that integrates single-cell RNA-seq data to visualize and characterize transitions between normal and perturbed cell states across different diseases.

Engineering mtDNA Deletions by Reconstituting End-Joining in Human Mitochondria

This paper develops a method to engineer specific mtDNA deletions in human cells using end-joining machinery and targeted endonucleases, revealing a 75% heteroplasmy threshold for mitochondrial dysfunction.

A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate

The paper creates a single-cell RNA sequencing atlas of gene expression during mouse cranial neural tube closure, identifying spatially regulated genes and SHH-regulated programs in different brain regions.

Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data

Segger improves cell segmentation in spatial transcriptomics by using a graph neural network, achieving high sensitivity and speed with minimal manual intervention.

The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1

This study identifies ASCL1 as a critical driver of neuroendocrine lineage transition in prostate cancer using an in vivo model and spatial transcriptomics.

Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference

The paper identifies artifacts in single-cell mtDNA variant calling that mislead phylogenetic inference and warns against using low-evidence variant workflows.

The covariance environment defines cellular niches for spatial inference

This paper introduces COVET and ENVI to model spatial niches and improve gene expression imputation and spatial context inference from single-cell data.

Microbial cancer immunotherapy reprograms hematopoietic stem cells to enhance anti-tumor immunity

This study shows that bladder BCG immunotherapy reprograms hematopoietic stem cells to enhance anti-tumor immunity in mice and humans.

Supervised discovery of interpretable gene programs from single-cell data

This paper introduces Spectra, an algorithm that identifies and refines gene programs from single-cell data, outperforming existing methods in tumor immune contexts by improving interpretability and capturing cell-state changes.

Unified fate mapping in multiview single-cell data

The paper introduces CellRank 2, a framework for analyzing multiview single-cell data to study cellular fate, showing it recovers terminal states and fate probabilities across modalities in hematopoiesis and endodermal development.

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities

The paper uses single-cell RNA and ATAC-seq to study bidirectional reprogramming between embryonic states, revealing differences in lineage plasticity.

SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data

SEACells identifies metacells from single-cell data, improving gene-peak associations and revealing chromatin dynamics in hematopoiesis and COVID-19.

CellRank for directed single-cell fate mapping

CellRank maps cell fates in single-cell RNA sequencing data by integrating RNA velocity and trajectory inference, revealing novel regeneration trajectories in lung injury.

Sparcle: assigning transcripts to cells in multiplexed images

Sparcle reassigns transcripts to cells in multiplexed images using gene covariation and spatial features, improving quantification and cell boundary delineation without requiring accurate segmentation.

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

The paper defines a shared differentiation trajectory of CD8 T cell dysfunction across cancer and infection using ATAC-seq and RNA-seq data from multiple studies.

A single-cell atlas of the human healthy airways

The paper constructs a single-cell atlas of the human healthy airways using RNA sequencing data from 77,969 cells across 35 locations, revealing cell-type-specific gene expression patterns and cellular heterogeneity.

Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions

The paper develops BayesPrism, a Bayesian method to infer cellular composition and gene expression from bulk RNA-seq using scRNA-seq as prior, revealing tumor-microenvironment interactions across multiple cancer types.

Palantir characterizes cell fate continuities in human hematopoiesis

Palantir models cell fate as a probabilistic process using entropy to analyze differentiation trajectories in human hematopoiesis, identifying key transcription factors and terminal states.

Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution

The paper maps the developmental trajectories of endoderm cells in the mouse embryo to reveal lineage relationships and spatial organization during gut formation.

MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data

MAGIC improves single-cell RNA-seq data by imputing missing values and revealing gene-gene interactions through a diffusion-based method.