Single‐cell analysis reveals cytotoxic and memory CD8+ T cells associated with prolonged survival in relapsed/refractory leukaemia patients after haplo+cord haematopoietic stem cell transplantation

TL;DR

This study shows that a specific type of CD8+ T cell, with both cytotoxic and memory properties, is linked to better survival in leukemia patients after a combined stem cell transplant.

Contribution

The study identifies a novel CD8+ T cell subtype associated with improved survival in leukemia patients following haplo+cord HSCT.

Findings

CD8+ T cells with cytotoxic and memory properties are enriched in patients receiving haplo+cord HSCT and correlate with prolonged survival.

Single-cell multi-omics analysis reveals that cytotoxic-related genes in CD8+ T cells are regulated by cooperative enhancer networks.

Haplo+cord HSCT leads to superior survival outcomes compared to single cord HSCT in relapsed/refractory leukemia patients.

Abstract

Allogeneic haematopoietic stem cell transplantation (allo‐HSCT) is a curative treatment for haematological malignancies. Sequential transplantation of haploidentical stem cell and umbilical cord blood (haplo+cord HSCT) among recipients with relapsed/refractory (R/R) leukaemia exhibited superior survival outcomes compared with single cord HSCT. However, the underlying mechanisms remain unclear.

Here, we profiled and compared single‐cell gene expression and chromatin accessibility in bone marrow from 16 patients receiving haplo+cord or single cord HSCT.

We observed distinct compositions and functions of global immune landscapes, with haplo+cord HSCT exhibiting effective anti‐tumour and anti‐viral immunity mediated by type I interferon signalling. Analysis of T cells revealed specific CD8+ T cell subtype (CD8‐c1), enriched in recipients with haplo+cord HSCT, which was also confirmed by flow cytometry. Functionally, gene signature scoring suggests a dual effector and memory property of CD8‐c1 that potentially offers long‐term protection. Furthermore, single‐cell multi‐omics analysis delineated the expression of cytotoxic‐related genes up‐regulated in CD8‐c1 are cooperatively regulated by enhancer networks. Notably, a proportion‐based survival analysis indicated that high proportion of CD8‐c1 was associated with better survival.

Our results collectively demonstrate that a population of CD8+ T cells with effector and memory properties contributes to improved survival in patients with R/R leukaemia receiving haplo+cord HSCT.

1. Haplo+cord HSCT yields superior survival compared with single cord HSCT in patients with R/R leukaemia.

2. Single‐cell RNA‐seq revealed a functionally critical CD8⁺ T cell population, with cytotoxic and memory phenotypes, which expands after haplo+cord HSCT and tracks with prolonged survival.

3. Multi‐omics profiling at single‐cell resolution showed that the CD8⁺ T cell elevated cytotoxic‐related genes is orchestrated by a cooperative enhancer network.

Figures