N. Hacohen

Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics

This study uses single-cell image-based CRISPR screens to identify host factors regulating Ebola virus infection, revealing new therapeutic targets like UQCRB and STRAP.

Intrarenal myeloid subsets associated with kidney injury are comparable in mice and patients with lupus nephritis

This study identifies conserved myeloid subsets and disease-associated gene expression changes in kidney injury across lupus mouse models and human patients with lupus nephritis.

The HLA-II immunopeptidome of SARS-CoV-2

The paper identifies SARS-CoV-2 peptides presented by HLA-II complexes, showing their association with CD4+ T cell epitopes and distinct targeting of viral proteins compared to HLA-I.

Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response

The paper identifies immune hubs in lung cancer that are associated with better responses to PD-1-blockade immunotherapy and contain stem-like CD8 T cells.

Cytotoxic CD4+ T cells eliminate senescent cells by targeting cytomegalovirus antigen

The paper shows that cytotoxic CD4+ T cells eliminate senescent fibroblasts by targeting HCMV-gB antigen expressed on these cells, reducing their accumulation in old skin.

Proximity-dependent labeling identifies dendritic cells that drive the tumor-specific CD4+ T cell response

The paper identifies dendritic cells that present antigens to CD4+ T cells in tumor-draining lymph nodes and the tumor microenvironment using LIPSTIC-based single-cell transcriptomics.

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics

The paper combines single cell and spatial transcriptomics to map spatial organization and functional interactions in colorectal cancer across species.

Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients

This study identifies distinct neutrophil phenotypes linked to disease severity in hospitalized COVID-19 patients using longitudinal data and multi-omics analyses.

ESCRT-dependent STING degradation curtails steady-state and cGAMP-induced signaling

The paper identifies an ESCRT complex that degrades STING to suppress its signaling, showing its role in maintaining immune homeostasis.

Plasma proteomic biomarkers identify non-responders and reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade

The paper identifies plasma proteomic biomarkers that predict non-response to PD1 blockade in melanoma patients and links them to tumor microenvironment biology.

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.

Spatially regulated protease activity in lymph nodes renders B cell follicles a sanctuary for retention of intact antigens

The paper shows that spatially restricted protease activity in lymph node follicles preserves antigen integrity, leading to stronger GC responses when antigens are targeted to follicular dendritic cells.

Altered interactions between circulating and tissue-resident CD8 T cells with the colonic mucosa define colitis associated with immune checkpoint inhibitors

This study identifies altered interactions between circulating and tissue-resident CD8 T cells with the colonic mucosa in immune checkpoint inhibitor-associated colitis using single-cell RNA sequencing and other multi-omics approaches.

Optimized liquid and gas phase fractionation increase HLA-peptidome coverage for primary cell and tissue samples

The paper improves HLA-peptidome coverage using optimized liquid and gas phase fractionation methods, enabling detection of more peptides from limited clinical tissue samples.

Early cross-coronavirus reactive signatures of protective humoral immunity against COVID-19

The paper profiles early humoral immune responses in COVID-19 patients, finding that survivors show rapid SARS-CoV-2-specific immunity linked to pre-existing OC43 immunity, while non-survivors have delayed and blunted responses.

Differentiation of exhausted CD8 T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory

The paper shows that exhausted CD8 T cells do not fully recover functional memory after antigen removal in chronic HCV infection.

An efficient lentiviral CRISPRi approach to silence genes in primary human monocytes

This paper develops a lentiviral CRISPRi system to silence genes in primary human monocytes and demonstrates its use in studying gene function.

A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

This paper introduces CeVICA, a cell-free platform for generating SARS-CoV-2 neutralizing antibodies, identifying over 800 binder families and 6 effective inhibitors.

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs

The paper identifies HLA-I peptides from SARS-CoV-2 in infected cells, revealing epitopes from both canonical and out-of-frame ORFs, which could inform vaccine development.

Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19

The paper identifies a regulatory myeloid program, MS1, associated with sepsis mortality and up-regulated in severe COVID-19, showing its immunosuppressive role and cytokine-dependent induction.

Alternative splicing of SLAMF6 in human T cells creates a co-stimulatory isoform that counteracts the inhibitory effect of the full-length receptor

This study identifies an alternative splicing event in SLAMF6 that generates a co-stimulatory isoform, which enhances T cell cytotoxicity and is associated with improved anti-tumor responses in melanoma.

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

The paper identifies thousands of novel unannotated proteins in cancer that contribute to the MHC I immunopeptidome, expanding potential targets for immunotherapy.

SLAMF6 deficiency augments tumor killing and skews towards an effector phenotype revealing it as a new T cell checkpoint

This study shows that SLAMF6 deficiency enhances T cell tumor-killing ability and shifts T cells toward an effector phenotype, suggesting SLAMF6 as a new immune checkpoint.

The immune cell landscape in kidneys of lupus nephritis patients

This study uses single-cell RNA-seq to analyze immune cell subsets in lupus nephritis kidneys, identifying pro-inflammatory and resolving responses and potential therapeutic targets.

Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry

The paper identifies key inflammatory cell states in RA synovial tissues using integrated single-cell and mass cytometry data from patient samples.

High dimensional analyses of cells dissociated from cryopreserved synovial tissue

This paper establishes a protocol for dissociating cryopreserved synovial tissue to obtain viable cells with preserved transcriptomes and surface markers, enabling high-dimensional analysis of rheumatoid arthritis pathology.

Multiplexed enrichment and genomic profiling of peripheral immune cell subsets on a microfluidic chip

This paper presents a microfluidic system for sorting and profiling immune cell subsets using RNA-seq, demonstrating its utility in identifying cell-specific disease signatures in lupus patients.

Targeting individual cells by barcode in pooled sequence libraries

The paper introduces a method combining molecular enrichment with FACS to efficiently sample rare dendritic cell populations in single-cell RNA-Seq libraries.

Single Cell Transcriptomics And Flow Cytometry Reveal Disease-Associated Fibroblast Subsets In Rheumatoid Arthritis

The paper identifies disease-associated fibroblast subsets in rheumatoid arthritis using single-cell transcriptomics and flow cytometry, revealing subset-specific markers and functional differences.