Alexis J. Combes

RasGRP1 promotes efficient intestinal tuft cell differentiation

This study identifies RasGRP1 as a regulator of tuft cell differentiation in the intestine, showing it restricts progenitor proliferation and enhances IL-13-driven responses.

Single-Nuclei Analysis of the Unfolded Protein Response (SNUPR): A Novel Method revealing bortezomib resistance mechanisms in Multiple Myeloma

SNUPR enables single-cell UPR profiling and reveals the role of IRE-1 axis in predicting bortezomib resistance in multiple myeloma.

Spatial Orchestration of Skin Fibrosis by a CD8+ T cell-Myofibroblast Axis

The paper identifies CD8+ T cells as key drivers of fibrosis in morphea-spectrum diseases through fibroblast IFN-γ signaling using spatial transcriptomics.

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

This study develops an iSCST framework for FFPE biopsies, identifying colitis-associated cell networks and VDZ response signatures in IBD patients.

Differential Assembly of Mouse and Human Tumor Microenvironments

The paper compares mouse and human tumor microenvironments, identifying conserved and species-specific features in immune composition and gene expression programs.

Temporal AI model predicts drivers of cell state trajectories across human aging

The paper introduces a temporal AI model, MaxToki, trained on extensive gene data to predict cell state changes across human aging and identifies age-modulating targets.

Tumor Heterogeneity Induces Pro- and Anti-metastatic Myeloid Cell Phenotypes in Breast Cancer Lung Metastasis

The paper profiles myeloid cells in breast cancer primary tumors and metastases to show how tumor heterogeneity drives shifts in myeloid cell phenotypes from anti- to pro-metastatic.

Discovery of a Linked Constellation of Gene Expression Revealed by Local Editing of Fibroblasts in Tumors

The paper uses local gene editing in mouse tumor models to discover a novel fibroblast state and its impact on the tumor microenvironment.

Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states

The paper identifies coordinated variation between immune systems and microbiomes in healthy humans, linking it to tonic interferon states.

CD38 expression by neonatal human naïve CD4+ T cells shapes their distinct metabolic state and high tolerogenic potential

This study shows neonatal human naive CD4+ T cells have higher CD38 expression, linking it to glycolytic metabolism and tolerogenic function compared to adult cells.

Spatial Transcriptomics Reveals CXCL12+ Fibroblasts as Central Immune Organizers through CXCR4 Signaling in Abdominal Aortic Aneurysm

This study uses spatial transcriptomics to identify CXCL12+ fibroblasts as central immune organizers in AAA through CXCR4 signaling, revealing stromal-immune interactions that drive disease progression.

Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

The paper shows congenital CMV infection leads to oligoclonal expansion of cytotoxic γδ T cells with fetal-like TCR features in neonates.

TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity

STING activation reshapes the tumor microenvironment leading to tumor regression in osteosarcoma

This study shows that activating the STING pathway in osteosarcoma leads to tumor regression and immune memory, suggesting it as a therapeutic target.

Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses

The paper identifies shared mechanisms of HBsAg seroclearance using a mouse model and longitudinal PBMCs from CHB patients, showing CD4+ T cell activation is essential for clinical cure.

Anticlustering for Sample Allocation To Minimize Batch Effects

The paper introduces anticlustering to balance batches and minimize batch effects in high-throughput sequencing, showing improved balance compared to existing methods.

Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.

The paper uses single-cell proteomics and metabolomics to study how Ras pathway mutations affect hematopoiesis, finding distinct impacts on HSC compartments and metabolism.

Single-Cell Profiling Reveals Altered Endometrial Cellular Features Across the Menstrual Cycle in Endometriosis Patients

The paper uses single-cell transcriptomics to analyze endometrial cells from endometriosis patients, revealing altered cellular features and immune communication networks across the menstrual cycle.

Transient Dietary Changes Modulate Inflammatory Disease Trajectory in the Lean State

This study shows that a short-term high-fat diet during the onset of psoriasis worsens disease severity through immune system changes, even after returning to a normal diet.

Identification of a conserved subset of cold tumors responsive to immune checkpoint blockade

This study identifies a biomarker, {beta}Alt, that predicts immune checkpoint blockade response in cold tumors by integrating TGF{beta} signaling, DNA repair, and immune context signatures.

Single-cell RNA sequencing of peripheral blood defines two immunological subtypes of Sjögren's disease

The paper identifies two immunological subtypes of Sjögren's disease using single-cell RNA sequencing, highlighting distinct IFN-I signatures and transitional B cell characteristics.

A Multiomics, Spatiotemporal, and Single Cell Atlas for Mapping Cell-Type-Specific Dysregulation at the Maternal-Fetal Interface

This study creates a comprehensive single-cell atlas of the maternal-fetal interface, identifying cell-type-specific dysregulation in pregnancy complications.

Space-Time Mapping Identifies Concerted Multicellular Patterns and Gene Programs in Healing Wounds and their Conservation in Cancers

The paper identifies space-time gene expression patterns in healing wounds and finds their conservation in tumors, revealing multicellular coordination and gene program activation.

Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus

This study identifies ethnicity-specific transcriptomic subgroups in SLE patients using RNA-seq data and correlates them with disease activity.