M. Haniffa

Single cell transcriptomics reveals chondrocyte differentiation dynamics in vivo and in vitro

This study uses single-cell transcriptomics to compare in vitro and in vivo chondrocyte differentiation, identifies off-target differentiation, and improves in vitro protocols by inhibiting FOXO1.

Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

This study identifies oncofetal reprogramming in juvenile myelomonocytic leukemia, linking RAS-pathway activation to fetal gene expression and revealing CD52 as a therapeutic target.

Multi-scale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma

The paper creates a multi-scale spatial atlas of healthy human skin and basal cell carcinoma using various omics and imaging techniques, revealing cell population localization and origins.

Early human lung immune cell development and its role in epithelial cell fate

The paper profiles lung immune cells during development using scRNAseq and identifies IL-1β's role in driving epithelial progenitor differentiation.

Transcriptional signals of dedifferentiation in human cancer

This study examines dedifferentiation in cancer using single-cell atlases, finding that adult cancers do not revert to an embryonic state but retain foetal signals, while childhood cancers show universal foetal state features.

Dandelion utilizes single cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

Dandelion improves V(D)J analysis in scVDJ-seq data, enabling better lineage commitment predictions and insights into lymphocyte development.

Mapping the developing human immune system across organs

This study maps the developing human immune system across organs using single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics, revealing cross-gestation and cross-organ variability and identifying prenatal B1 cells and unconventional T cell origins.

Obesity associated with attenuated tissue immune cell responses in COVID-19

The paper finds that obesity is associated with reduced immune and inflammatory responses in COVID-19 patients, including lower expression of IFN and IFNγ response genes in lung and blood cells.

Conjunctival epithelial cells resist productive SARS-CoV-2 infection

The paper investigates whether conjunctival epithelial cells can be infected by SARS-CoV-2 and finds that while genome expression occurs, productive infection does not.

Epigenetic regulator genes direct lineage switching in MLL-AF4 leukaemia

This study shows that lineage switching in MLL-AF4 leukaemia is driven by dysregulation of epigenetic regulators like NuRD, leading to reprogramming of gene regulatory networks from B lymphoid to myeloid.

Delayed induction of type I and III interferons mediates nasal epithelial cell permissiveness to SARS-CoV-2

This study shows that delayed type I and III interferon responses in nasal epithelial cells allow SARS-CoV-2 replication, but pre-infection IFN treatment restricts virus and preserves barrier integrity.

Tumor to normal single cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

The paper compares tumor and normal single-cell mRNA data to show neuroblastoma cells resemble fetal sympathoblasts across diverse samples.

Cellular mRNA signals in human kidney tumors

This study analyzes mRNA signals in 1,300 kidney tumors to determine their differentiation state and origin, finding that childhood tumors show fetal signals while most adult tumors do not, with exceptions in certain cancer types.

A cell atlas of human thymic development defines T cell repertoire formation

This study creates a cell atlas of the human thymus using scRNA-seq, revealing new cell populations and insights into T-cell development and TCR recombination.

Donor monocyte-derived macrophages promote human acute graft versus host disease

The paper identifies donor monocyte-derived macrophages as key players in human acute graft versus host disease, showing their enhanced activation of T cells and secretion of inflammatory cytokines.

Single cell transcriptomics of regulatory T cells reveals trajectories of tissue adaptation

The paper uses single-cell RNA-seq to study Treg and Tmem cells in mouse tissues, revealing a lymphoid-to-tissue adaptation trajectory and conserved molecular signals across species.