# Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity

**Authors:** Dianshan Ke, Hanhao Dai, Yibin Su, Hongyi Zhu, Xiaofeng Liu, Xiaochun Bai, Changqing Zhang, Jie Xu, Jinshan Zhang

PMC · DOI: 10.1038/s12276-025-01619-6 · Experimental & Molecular Medicine · 2026-01-28

## TL;DR

The study reveals that natural killer cells contribute to ankylosing spondylitis severity through antigen presentation, offering new insights into immune mechanisms driving the disease.

## Contribution

The novel finding is the role of APC-NK cells in exogenous antigen presentation linked to AS severity and progression.

## Key findings

- APC-NK abundance and antigen presentation scores increase during AS aggravation but decrease during remission.
- HLA-DPB1/DPA1 in APC-NK mediates antigen presentation targeting CD4+ T cells, contributing to AS severity.
- NK cell exhaustion improves AS-like mouse phenotypes, suggesting a therapeutic potential.

## Abstract

Ankylosing spondylitis (AS) is an autoimmune disease that can cause severe deformities, and the immunological patterns associated with its onset and progression remain poorly understood. Here, after recruiting healthy donors and patients in different stages, we performed single-cell RNA sequencing for peripheral blood mononuclear cells to investigate the cytotaxonomic and immunological hallmarks associated with AS onset, aggravation and remission and explore the intrinsic laws causing AS lesions. The results showed that innate antibacterial defense functions were generally enhanced in most cell types at disease onset and were negatively associated with AS severity. The abundance and exogenous antigen presentation scores of the natural killer (NK) cell subset characterized as antigen-presenting cells (APC-NK) increased during disease aggravation but decreased during remission. Generally, APC-NK abundance and their presentation scores were negatively correlated with innate defense scores for multiple cell types. CD4+ effector T cell abundance and cytotoxicity, as well as the enhancement of CD4+ T cell responses by HLA-DRB1+ NK cells (similar to APC-NK), were associated with AS severity. The implantation of HLA-DRB1+ NK cells accelerated AS-like alterations in SKG modeling mice with curdlan induction; this was blocked with CD4+ T cell exhaustion. NK cell exhaustion improved the phenotypes of AS-like mice. HLA-DPB1/DPA1 in APC-NK participated in AS aggravation by mediating antigen presentation targeting CD4+ T cells. Overall, innate defense antigen presentation coupling drives AS lesions and different outcomes. Furthermore, the trade-off between innate defense and NK-dependent exogenous antigen presentation results in CD4+ T cell activation or inactivation, thereby contributing to AS aggravation or remission; this reveals that APC-NK is a crucial factor causing ankylosing deformities.

Ankylosing spondylitis (AS) is a chronic disease affecting the spine and joints, often leading to disability. Current treatments mainly focus on symptom relief, but understanding the disease’s underlying causes is crucial for better therapies. Researchers aimed to explore the immune processes involved in AS using advanced techniques such as single-cell RNA sequencing. The study involved 14 patients with AS and 3 healthy donors. Researchers collected blood samples and analyzed immune cells to understand their roles in AS. They found that certain immune cells, including T cells and natural killer cells, behave differently in patients with AS compared with healthy individuals. These differences are linked to the disease’s progression and severity. The study revealed that immune responses, particularly those involving NK cells, play a significant role in AS. These findings suggest that targeting specific immune pathways could improve treatment strategies.

This summary was initially drafted using artificial intelligence, then revised and fact-checked by the author.

## Linked entities

- **Genes:** HLA-DRB1 (major histocompatibility complex, class II, DR beta 1) [NCBI Gene 3123], HLA-DPB1 (major histocompatibility complex, class II, DP beta 1) [NCBI Gene 3115], HLA-DPA1 (major histocompatibility complex, class II, DP alpha 1) [NCBI Gene 3113]
- **Diseases:** ankylosing spondylitis (MONDO:0005306), AS (MONDO:0007113)
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** IL17A (interleukin 17A) [NCBI Gene 3605] {aka CTLA-8, CTLA8, IL-17, IL-17A, IL17, ILA17}, IFNA1 (interferon alpha 1) [NCBI Gene 3439] {aka IFL, IFN, IFN-ALPHA, IFN-alphaD, IFNA13, IFNA@}, HLA-B (major histocompatibility complex, class I, B) [NCBI Gene 3106] {aka AS, B-4901, HLAB}, Ncam1 (neural cell adhesion molecule 1) [NCBI Gene 17967] {aka CD56, E-NCAM, NCAM-1, Ncam}, HLA-DRB1 (major histocompatibility complex, class II, DR beta 1) [NCBI Gene 3123] {aka DRB1, HLA-DR1B, HLA-DRB, SS1}, CD28 (CD28 molecule) [NCBI Gene 940] {aka IMD123, Tp44}, Cd19 (CD19 antigen) [NCBI Gene 12478], THBD (thrombomodulin) [NCBI Gene 7056] {aka AHUS6, BDCA-3, BDCA3, CD141, THPH12, THRM}, CCL4 (C-C motif chemokine ligand 4) [NCBI Gene 6351] {aka ACT2, AT744.1, G-26, HC21, LAG-1, LAG1}, GZMB (granzyme B) [NCBI Gene 3002] {aka C11, CCPI, CGL-1, CGL1, CSP-B, CSPB}, MZB1 (marginal zone B and B1 cell specific protein) [NCBI Gene 51237] {aka MEDA-7, PACAP, pERp1}, IFNL3 (interferon lambda 3) [NCBI Gene 282617] {aka IFN-lambda-3, IFN-lambda-4, IL-28B, IL-28C, IL28B, IL28C}, KLRC2 (killer cell lectin like receptor C2) [NCBI Gene 3822] {aka CD159c, NKG2-C, NKG2C}, ALB (albumin) [NCBI Gene 213] {aka FDAHT, HSA, PRO0883, PRO0903, PRO1341}, ANAPC13 (anaphase promoting complex subunit 13) [NCBI Gene 25847] {aka APC13, SWM1}, PRF1 (perforin 1) [NCBI Gene 5551] {aka HPLH2, P1, PFP}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, Drb1 (dopamine receptor binding 1) [NCBI Gene 116749], CD14 (CD14 molecule) [NCBI Gene 929], IFNL2 (interferon lambda 2) [NCBI Gene 282616] {aka IFNL2a, IFNL3a, IL-28A, IL28A}, CD19 (CD19 molecule) [NCBI Gene 930] {aka B4, CVID3}, KLRF1 (killer cell lectin like receptor F1) [NCBI Gene 51348] {aka CLEC5C, NKp80}, CD1C (CD1c molecule) [NCBI Gene 911] {aka BDCA1, CD1, R7}, CRP (C-reactive protein) [NCBI Gene 1401] {aka PTX1}, Hbegf (heparin-binding EGF-like growth factor) [NCBI Gene 15200] {aka Dtr, Dts, Hegfl}, IFNL1 (interferon lambda 1) [NCBI Gene 282618] {aka IL-29, IL29}, JCHAIN (joining chain of multimeric IgA and IgM) [NCBI Gene 3512] {aka IGCJ, IGJ, JCH}, KLRC4 (killer cell lectin like receptor C4) [NCBI Gene 8302] {aka NKG2-F, NKG2F}, CAPG (capping actin protein, gelsolin like) [NCBI Gene 822] {aka AFCP, HEL-S-66, MCP}, PODXL2 (podocalyxin like 2) [NCBI Gene 50512] {aka EG, PODLX2}, KLRK1 (killer cell lectin like receptor K1) [NCBI Gene 22914] {aka CD314, D12S2489E, KLR, NKG2-D, NKG2D}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, Apc (APC, WNT signaling pathway regulator) [NCBI Gene 11789] {aka CC1, Min, mAPC}, FCER1G (Fc epsilon receptor Ig) [NCBI Gene 2207] {aka FCRG}, Gzmb (granzyme B) [NCBI Gene 14939] {aka CCP-1/C11, CCP1, Ctla-1, Ctla1, GZB}, CD3D (CD3 delta subunit of T-cell receptor complex) [NCBI Gene 915] {aka CD3-DELTA, CD3DELTA, IMD19, T3D}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, CCR7 (C-C motif chemokine receptor 7) [NCBI Gene 1236] {aka BLR2, CC-CKR-7, CCR-7, CD197, CDw197, CMKBR7}, Klrk1 (killer cell lectin-like receptor subfamily K, member 1) [NCBI Gene 27007] {aka D6H12S2489E, NKG2-D, Nkg2d}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, Ifng (interferon gamma) [NCBI Gene 15978] {aka IFN-g, If2f, Ifg}, Cd4 (CD4 antigen) [NCBI Gene 12504] {aka L3T4, Ly-4}, LCP1 (lymphocyte cytosolic protein 1) [NCBI Gene 3936] {aka CP64, HEL-S-37, L-PLASTIN, LC64P, PLS2}, FCGR3A (Fc gamma receptor IIIa) [NCBI Gene 2214] {aka CD16-II, CD16A, FCG3, FCGR3, FCRIIIA, FcGRIIIA}, XCL1 (X-C motif chemokine ligand 1) [NCBI Gene 6375] {aka ATAC, LPTN, LTN, SCM-1, SCM-1a, SCM1}, Cd3e (CD3 antigen, epsilon polypeptide) [NCBI Gene 12501] {aka CD3, CD3epsilon, T3e}, HLA-DPA1 (major histocompatibility complex, class II, DP alpha 1) [NCBI Gene 3113] {aka DP(W3), DP(W4), DPA1, HLA-DP1A, HLA-DPA, HLADP}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, HLA-DPB1 (major histocompatibility complex, class II, DP beta 1) [NCBI Gene 3115] {aka DPB1, HLA-DP, HLA-DP1B, HLA-DPB}, CALCA (calcitonin related polypeptide alpha) [NCBI Gene 796] {aka CALC1, CGRP, CGRP-I, CGRP-alpha, CGRP1, CT}, MSN (moesin) [NCBI Gene 4478] {aka HEL70, IMD50}
- **Diseases:** FG (MESH:C537923), graft-versus-host disease (MESH:D006086), infection (MESH:D007239), rash (MESH:D005076), autoimmune disease (MESH:D001327), bacterial infection (MESH:D001424), spinal deformities or joint destruction (MESH:D008105), deformities (MESH:D009140), spinal deformity (MESH:D013122), spinal degeneration (MESH:D009410), NK (MESH:D000077428), ankylosing deformities (MESH:D000844), UMAP (MESH:C567162), cytotoxic (MESH:D064420), ankle-joint destruction (MESH:D016512), structural damage in hip joints (MESH:D025981), spinal ossification (MESH:C562735), swelling (MESH:D004487), Orthopaedic Trauma (MESH:D014947), arthritis (MESH:D001168), RM (MESH:D012075), autoimmune inflammation (MESH:D007249), LD (MESH:D000067562), diarrhea (MESH:D003967), pneumonia (MESH:D011014), HDs (MESH:D000067329), rheumatic disease (MESH:D012216), AS (MESH:D013167), anorexia (MESH:D000855), ADCC (MESH:D007153)
- **Chemicals:** lipid (MESH:D008055), TRIzol (MESH:C411644), Fast Green FCF (MESH:C007704), polybrene (MESH:D006583), 4',6-diamidino-2-phenylindole (MESH:C007293), Epizyme (-), Fast Green (MESH:C035906), leflunomide (MESH:D000077339), puromycin (MESH:D011691), curdlan (MESH:C038459), beta-glucan (MESH:D047071), citrate (MESH:D019343), paraformaldehyde (MESH:C003043), Triton X-100 (MESH:D017830), EDTA (MESH:D004492), propidium iodide (MESH:D011419), fluorescein (MESH:D019793), eosin (MESH:D004801), sulfasalazine (MESH:D012460), PVDF (MESH:C024865), H&amp;E (MESH:D006371), paraffin (MESH:D010232), CO2 (MESH:D002245), hematoxylin (MESH:D006416), methotrexate (MESH:D008727), water (MESH:D014867), Safranin O. (MESH:C009195)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

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Source: https://tomesphere.com/paper/PMC12868835