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Recovery of biological signals lost in single-cell batch integration with CellANOVA

A statistical framework quantifies single-cell batch variation and recovers meaningful biological signals.

Zhaojun Zhang
Divij Mathew
Nancy R. Zhang
Research26 Nov 2024
Nature Biotechnology

P: 1-17
Author Correction: Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation

Mohamed S. Abdel-Hakeem
Sasikanth Manne
E. John Wherry
Amendments and Corrections29 Sept 2021
Nature Immunology

Volume: 22, P: 1465
CD8⁺ T cells contribute to survival in patients with COVID-19 and hematologic cancer

A study of hospitalized patients infected with SARS-CoV-2 and who have liquid or solid cancer suggests that hematologic malignancy is an independent risk factor for mortality and that CD8⁺ T cells might limit infection in this setting irrespective of humoral immunity.

Erin M. Bange
Nicholas A. Han
Alexander C. Huang
Research20 May 2021
Nature Medicine

Volume: 27, P: 1280-1289
Automated cytometric gating with human-level performance using bivariate segmentation

High-throughput cytometry generates complex single-cell data with challenging manual gating process. Here, authors introduce UNITO, a framework that transforms cell classification into image segmentation, outperforming existing methods in identifying cytometric subpopulations across diverse datasets.

Jiong Chen
Matei Ionita
Li Shen
ResearchOpen Access12 Feb 2025
Nature Communications

Volume: 16, P: 1-15
Prior vaccination promotes early activation of memory T cells and enhances immune responses during SARS-CoV-2 breakthrough infection

Wherry and colleagues define the kinetics of vaccine-primed recall immune responses during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infection, highlighting rapid activation of memory T cells and broadly enhanced immune responses in previously vaccinated individuals.

Mark M. Painter
Timothy S. Johnston
E. John Wherry
Research21 Sept 2023
Nature Immunology

Volume: 24, P: 1711-1724
Shared and distinct biological circuits in effector, memory and exhausted CD8⁺ T cells revealed by temporal single-cell transcriptomics and epigenetics

Wherry and colleagues provide a comparative analysis of paired single-cell RNA-sequencing and single-cell assay for transposase-accessible chromatin sequencing profiles of CD8⁺ T cells in acute and chronic lymphocytic choriomeningitis virus infections, identifying new features about T_ex cell subsets and epigenetic differences from acutely infected precursors seen at early time points in infection.

Josephine R. Giles
Shin Foong Ngiow
E. John Wherry
Research21 Oct 2022
Nature Immunology

Volume: 23, P: 1600-1613
Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation

Wherry and colleagues examine whether exhausted T cells (T_EX) can differentiate into functional memory T cells (T_MEM) when chronic antigen is withdrawn. Using the chronic LCMV infection mouse model, they show that ‘recovering’ T_EX cells (REC-T_EX) only partially recover immunophenotypic and functional characteristics of T_MEM cells. The epigenomic status of REC-T_EX cells more closely resembles that of T_EX cells, and, upon rechallenge, the REC-T_EX cells were still compromised in their ability to respond to virus.

Mohamed S. Abdel-Hakeem
Sasikanth Manne
E. John Wherry
Research26 Jul 2021
Nature Immunology

Volume: 22, P: 1008-1019
Cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy

SARS-CoV-2-specific antibodies and memory B cells are significantly reduced, but CD4⁺ and CD8⁺ T cells are robustly activated, in patients with multiple sclerosis on anti-CD20 monotherapy versus healthy controls after BNT162b2 or mRNA-1273 mRNA vaccination.

Sokratis A. Apostolidis
Mihir Kakara
Amit Bar-Or
ResearchOpen Access14 Sept 2021
Nature Medicine

Volume: 27, P: 1990-2001

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