Ignas Masilionis

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.

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.

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.

Complementary modes of resistance to EGFR TKI in lung adenocarcinoma through MAPK activation and cellular plasticity

This study identifies MAPK activation and cellular plasticity as complementary resistance mechanisms to EGFR TKI in lung adenocarcinoma using single-nuclei RNA sequencing and clinical data.

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.

Single Cell Analysis of Treatment-Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies

The paper uses single-cell analysis to study how cell surface antigen expression changes in treatment-resistant prostate cancer, revealing transcriptional heterogeneity and shared gene regulatory networks between NEPC and SCLC.

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.