Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response in nasopharyngeal carcinoma

Sep 21, 2026

Uploaded by Asher

Single-cell and spatial transcriptome profiling in nasopharyngeal carcinoma maps tertiary lymphoid structures (TLS) and clarifies their links to tumour progression and immunotherapy. Analyses of 343,829 cells from biopsy and blood samples and spatial data from 15 tumours identify key TLS populations, including CXCL13+ cancer-associated fibroblasts, CXCL13+ stem-like CD8+ T cells, and B/T follicular helper cells. Germinal centre maturation generates plasma cells that intersperse with tumour aggregates, promoting apoptosis of EBV-related malignant cells and enhancing immunotherapy response. CXCL13+ fibroblasts support B-cell adhesion and antibody production while triggering CXCL13+CD8+ T-cell activation that becomes exhausted within aggregates. TLS-related signatures correlate with prognosis and PD-1 blockade benefit, informing therapeutic strategies.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages22

Reading Time55 min

AccessFree to download

Introduction

Tumour microenvironment and TLS significance

Methods and Study Design

Single-cell and spatial transcriptome profiling in NPC

Key Findings

Essential TLS cell populations

Germinal centre maturation and plasma-cell function

CXCL13+ fibroblast, B-cell, and CD8+ T-cell interactions

Clinical correlations with prognosis and PD-1 blockade response

Background and Rationale

GC reaction and TLS composition in tumours

Unresolved questions in human tumour TLS dynamics

Article [https://doi.org/10.1038/s41467-024-52153-4](https://doi.org/10.1038/s41467-024-52153-4) Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response innasopharyngeal carcinoma Received: 13 July 2023 | Accepted: 22 August 2024 | | --- | | | | Check for updates | Yang Liu1,10, Shuang-Yan Ye2,10, Shuai He 1,10, Dong-Mei Chi 1,3,10, Xiu-Zhi Wang1,10, Yue-Feng Wen4, Dong Ma1, Run-Cong Nie1, Pu Xiang1, You Zhou1, Zhao-Hui Ruan1, Rou-Jun Peng1, Chun-Ling Luo 1, Pan-Pan Wei1, Guo-Wang Lin5, Jian Zheng 1, Qian Cui6, Mu-Yan Cai 1, Jing-Ping Yun 1, Junchao Dong7, Hai-Qiang Mai 1, Xiaojun Xia 1 & Jin-Xin Bei 1,8,9 Tertiary lymphoid structures are immune cell aggregates linked with cancer outcomes, but their interactions with tumour cell aggregates are unclear. Using nasopharyngeal carcinoma as a model, here we analyse single-cell transcriptomes of 343,829 cells from 77 biopsy and blood samples and spatially-resolved transcriptomes of 31,316 spots from 15 tumours to decipher their components and interactions with tumour cell aggregates. We identify essential cell populations in tertiary lymphoid structure, including CXCL13+ cancer-associated ﬁbroblasts, stem-like CXCL13+CD8+ T cells, and B and T follicular helper cells. Our study shows that germinal centre reaction matures plasma cells. These plasma cells intersperse with tumour cell aggregates, promoting apoptosis of EBV-related malignant cells and enhancing immunotherapy response. CXCL13+ cancer-associated ﬁbroblasts promote B cell adhesion and antibody production, activating CXCL13+CD8+ T cells that become exhausted in tumour cell aggregates. Tertiary lymphoid structurerelated cell signatures correlate with prognosis and PD-1 blockade response, offering insights for therapeutic strategies in cancers. Immune cell inﬁltration is a common pathological observation in cancer, where tumoral, immune, and stromal cells, as well as extracellular components, are assembled to form a tumour microenvironment (TME). The organisation of these components is essential to an effective immunity against tumour1. Tertiary lymphoid structure (TLS) represents such a well-organised ectopic compartment of immune cells that develops in inﬂamed, infected, or tumoral tissues2,3. Initially, both T and B cell zones are characterised in TLS using immunohistochemistry (IHC) assays4. Subsequently, several studies reveal that TLSs also contain antigen-presenting cells (APCs) as regulators andstromal cells as supportive infrastructures5, in addition toT follicular helper(Tfh)cells and follicular dendritic cells(FDC)closetoB cells6. Recently, single-cell RNA sequencing and spatial transcriptomics studies reveal speciﬁc cell populations of TLS in tumours, such as CXCL13+ T-helper cells in ovarian cancer7, SEMA4A+ germinal centre (GC) B cells in head and neck squamous cell carcinoma8, and CXCL12+ A full list of afﬁliations appears at the end of the paper. e-mail: [beijx@sysucc.org.cn](beijx@sysucc.org.cn) ﬁbroblasts in renal cell cancer9. These ﬁndings suggest a complicated and heterogeneous composition of TLS in tumours from different technological perspectives, which await further investigations with larger sample sizes and cutting-edge technologies under higher resolution. GC is a crucial feature of matured TLSs in tumours and is a wellknown compartment for the selective activation and ampliﬁcation of B cell clonesand the production oflong-lived plasma cells6. Although the coexistence of GC B cells and tumour-inﬁltrating B or plasma cells has been demonstrated in multiple tumours9–11, little is known about the dynamic features of GC reaction and developmental trajectories of B cells within the tumours, especially at TLSs. A recent study has demonstrated GC B cells characterised by a continuum of gene expression states spanning the dark-light zone axis12,13. Apart from GC reaction, multiple cellular components, in

FAQs

What is the main goal of the study in nasopharyngeal carcinoma?

To determine the cellular composition, formation, and function of tertiary lymphoid structures and relate them to tumour progression and immunotherapy response using single-cell and spatial transcriptomics.

Which key cell populations are identified as essential for TLS in this work?

The study highlights CXCL13+ cancer-associated fibroblasts, stem-like CXCL13+CD8+ T cells, and B and T follicular helper cells.

How do plasma cells and TLS activity affect tumour cells and treatment response?

Germinal-centre reactions mature plasma cells that intersperse with tumour aggregates, promote apoptosis of EBV-related malignant cells, and enhance immunotherapy response; TLS-related signatures correlate with prognosis and PD-1 blockade outcomes.

Sep 21, 2026

Uploaded by Asher