A. K. Shalek

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

This study uses spatial multi-omics to compare EBV-positive and EBV-negative cHL, identifying distinct TME features and immunological signatures linked to EBV.

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

This study introduces MicroCart, a framework for spatial multi-omics analysis of host-microbiome interactions in colitis, revealing tissue-level immune responses and microbial shifts.

Congenital T cell activation impairs transitional to follicular B cell maturation in humans

Congenital T cell activation in CTLA4-deficient patients impairs transitional to follicular B cell maturation and can be rescued by CTLA4 replacement therapy in vivo.

Glycan-costumed virus-like particles promote type 1 anti-tumor immunity

This study develops glycan-costumed virus-like particles that activate dendritic cells and induce type 1 anti-tumor immunity in a murine model.

CD4+ T cells are homeostatic regulators during Mtb reinfection

The paper shows that CD4+ T cells reduce inflammation and disease severity during Mtb reinfection by reprogramming CD8+ T cells and innate immune cells.

Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas

The paper identifies four immunomodulatory programs in glioma-associated myeloid cells using scRNA-seq and shows they are driven by microenvironmental cues and therapies, not cell type or mutation status.

B cell directed CAR-T cell therapy results in activation of CD8+ cytotoxic CAR-negative bystander T cells in both non-human primates and patients

The paper identifies a novel mechanism where CAR-T cell therapy activates CD8+ cytotoxic bystander T cells in non-human primates and patients, showing they can kill leukemic cells independently of TCR.

Protective intravenous BCG vaccination induces enhanced immune signaling in the airways

This study shows that high-dose IV BCG vaccination in rhesus macaques enhances airway immune signaling and cellular responses, improving protection against Mtb.

Early cellular and molecular signatures correlate with severity of West Nile Virus infection

The paper identifies cellular and molecular signatures associated with varying severities of West Nile Virus infection using multi-omics analysis of immune responses.

Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection

This study identifies pro-inflammatory feedback loops in immune responses to pathogenic lentivirus infection, showing that highly pathogenic variants induce delayed, sustained, and amplifying inflammatory circuits.

Tobacco smoke exposure results in recruitment of inflammatory airspace monocytes and accelerated growth of Mycobacterium tuberculosis

Tobacco smoke exposure recruits inflammatory monocytes to the lungs, which support faster Mycobacterium tuberculosis growth.

Cancer tissue of origin constrains the growth and metabolism of metastases

This study shows that cancer tissue-of-origin influences the metabolism and growth preferences of both primary and metastatic tumors.

Identification and characterization of the T cell receptor (TCR) repertoire of the Cynomolgus macaque (Macaca Fascicularis)

The paper characterizes the T cell receptor repertoire in Cynomolgus macaques using single-cell RNA sequencing and identifies similarities with human and Rhesus macaque TCR repertoires.

Comparative analysis of cell-cell communication at single-cell resolution

This paper introduces Scriabin, a framework for analyzing cell-cell communication at single-cell resolution, validating its findings through multiple experimental approaches and demonstrating its application in uncovering communication pathways in health and disease.

Single-cell Multiomics Reveals Clonal T-cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm

This study uses single-cell multiomics to analyze T-cell responses in BPDCN, finding upregulated IFNA and downregulated TNFA pathways, along with T-cell exhaustion and clonotype expansion.

Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity

The paper develops a workflow for collecting and analyzing liver immune cells via fine-needle aspirates and single-cell RNA sequencing to better understand tissue-specific immunity in chronic hepatitis B.

HIV-specific CD8+ T-cells in tonsils express exhaustive TRM-like signatures

The paper examines HIV-specific CD8+ T-cells in tonsils, finding they exhibit TRM-like exhaustion signatures compared to blood, with differences in natural HIV controllers.

Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform.

The paper introduces RM-scTCR-Seq, a method for tracking T cell clones in Rhesus Macaques, and applies it to study GVHD.

Enteric coronavirus infection and treatment modeled with an immunocompetent human intestine-on-a-chip

This paper uses an intestine-on-a-chip model to study NL63 coronavirus infection effects on the human intestine and tests antiviral treatments.

Gene signatures and host-parasite interactions revealed by dual single-cell profiling of Plasmodium vivax liver infection

This study uses single-cell profiling to analyze P. vivax liver infection, identifying host and parasite transcriptional signatures and revealing new insights into parasite dormancy and host responses.

Deciphering the tumor-specific immunopeptidome in vivo with genetically engineered mouse models

This paper uses genetically engineered mouse models to isolate and profile tumor-specific MHC-I peptides in vivo, revealing post-translational shaping of the immunopeptidome and novel tumor-associated antigens in lung adenocarcinoma.

Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure

The paper characterizes CD8+ T cell responses to SARS-CoV-2 across HLA alleles, showing HLA genotype influences pre-existing immunity and immune repertoire upon viral exposure.

Aggregated Mycobacterium tuberculosis enhances the inflammatory response

The paper investigates how aggregated Mycobacterium tuberculosis triggers a stronger inflammatory response in macrophages compared to single or multiple non-aggregated bacilli.

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

This study analyzes nasopharyngeal samples from COVID-19 patients and healthy controls to identify how SARS-CoV-2 infection affects respiratory epithelial cells and immune responses, finding impaired local intrinsic immunity in severe cases.

Single Cell and Spatial Transcriptomics Defines the Cellular Architecture of the Antimicrobial Response Network in Human Leprosy Granulomas

The paper uses single cell and spatial transcriptomics to map the cellular architecture of antimicrobial responses in leprosy granulomas, identifying gene expression differences and spatial organization in reversal reactions.

MR1-restricted MAIT cells from the human lung mucosal surface have distinct phenotypic, functional, and transcriptomic features that are preserved in HIV infection

This study identifies distinct phenotypic, functional, and transcriptomic features of MR1-restricted MAIT cells in the human lung mucosa, showing their preservation in HIV infection.

Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells

This study identifies cyclin D3 as essential for inertial cell cycling in dark zone germinal center B cells, enabling clonal expansion and linking it to potential lymphoproliferative disorders.

Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu

The paper uses single-cell RNA-sequencing to study leukocyte dynamics in a living patient after intracerebral hemorrhage, revealing rapid immune responses and adaptations to the hematoma microenvironment.

Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

This study uses single-cell RNA-sequencing to analyze prostate cancer tumor microenvironment, identifying heterogeneous epithelial cell states and tumor-associated club cells.

Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice

This study measures CTC kinetics and metastatic potential by exchanging blood between tumor-bearing and healthy mice, finding short CTC half-life and high shedding rates.