# Direct contact with natural killer cells reprograms monocyte-derived dendritic cells into a tolerogenic phenotype

**Authors:** Ammar J Alsheikh, Liang Chen, Daniel Korenfeld, Jason Tam, Suresh Patil, Hsi-Ju Wei, Jianing Li, Suju Zhong, Feng Dong, Terry Melim, Karin Orsi, Samuel Karsen, Yingli Yang, Susan Westmoreland, Aridaman Pandit, Kevin White, Timothy Radstake, Abel Suarez-Fueyo

PMC · DOI: 10.1093/immhor/vlag007 · ImmunoHorizons · 2026-03-26

## TL;DR

Contact with natural killer cells changes monocyte-derived dendritic cells into a form that reduces inflammation and promotes immune tolerance.

## Contribution

The study identifies a novel approach to reprogram dendritic cells into a tolerogenic phenotype using natural killer cell interactions and confirms key transcription factors involved.

## Key findings

- Dendritic cells exposed to natural killer cells show reduced T-cell activation and increased regulatory mediators like IL-10 and IDO1.
- CRISPR knockout experiments reveal that transcription factors IKZF1 and PU.1 are essential for the tolerogenic reprogramming of dendritic cells.
- The study confirms that tolerogenic dendritic cells have decreased levels of co-stimulatory markers such as CD11c, CD40, and CD44.

## Abstract

Tissue-infiltrating monocyte-derived dendritic cells (DCs) and macrophages are key antigen-presenting cells promoting inflammation and tissue damage by releasing proinflammatory cytokines and strongly activating T cells. These antigen-presenting cells are prominent in inflamed tissues, including in conditions such as inflammatory bowel disease. Modulating the number or function of these cells presents an opportunity to mitigate inflammation and promote immune tolerance in inflammatory disorders. In this study, we comprehensively evaluate a novel approach to modulate these cell populations. First, we employ an antibody-mediated approach to selectively deplete inflammatory DCs while simultaneously reprogramming surviving cells toward a tolerogenic phenotype. Second, we utilize a natural killer–DC co-culture system to dissect molecular mechanisms of DC tolerance induction through integrated transcriptomic and epigenomic analysis, complemented by functional assays. We confirm that the generated DCs exhibit tolerogenic properties, marked by a reduced ability to induce allogenic T-cell activation, increased expression of regulatory mediators including IL-10 and IDO1, and decreased levels of co-stimulatory and activation markers such as CD11c, CD40, and CD44. Finally, using CRISPR knockout, we confirm the essential role of transcription factors IKZF1 and PU.1 in this process. Our findings advance the understanding of how epigenetic remodeling and transcription factor activity govern DC tolerance, and highlight promising therapeutic avenues for DC-targeted therapeutic approaches in inflammatory disorders.

## Linked entities

- **Genes:** IL10 (interleukin 10) [NCBI Gene 3586], IDO1 (indoleamine 2,3-dioxygenase 1) [NCBI Gene 3620], ITGAX (integrin subunit alpha X) [NCBI Gene 3687], CD40 (CD40 molecule) [NCBI Gene 958], CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960], IKZF1 (IKAROS family zinc finger 1) [NCBI Gene 10320], SPI1 (Spi-1 proto-oncogene) [NCBI Gene 6688]
- **Diseases:** inflammatory bowel disease (MONDO:0005265)

## Full-text entities

- **Genes:** CCL2 (C-C motif chemokine ligand 2) [NCBI Gene 6347] {aka GDCF-2, HC11, HSMCR30, MCAF, MCP-1, MCP1}, CD83 (CD83 molecule) [NCBI Gene 9308] {aka BL11, HB15}, SPI1 (Spi-1 proto-oncogene) [NCBI Gene 6688] {aka AGM10, OF, PU.1, SFPI1, SPI-1, SPI-A}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, CD40LG (CD40 ligand) [NCBI Gene 959] {aka CD154, CD40L, HIGM1, IGM, IMD3, T-BAM}, CD274 (CD274 molecule) [NCBI Gene 29126] {aka ADMIO5, B7-H, B7H1, PD-L1, PDCD1L1, PDCD1LG1}, CD38 (CD38 molecule) [NCBI Gene 952] {aka ADPRC 1, ADPRC1, cADPR1}, IRF5 (interferon regulatory factor 5) [NCBI Gene 3663] {aka SLEB10}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, MAF (MAF bZIP transcription factor) [NCBI Gene 4094] {aka AYGRP, CCA4, CTRCT21, c-MAF}, Cd14 (CD14 antigen) [NCBI Gene 12475], Cd83 (CD83 antigen) [NCBI Gene 12522], CAT (catalase) [NCBI Gene 847], MYD88 (MYD88 innate immune signal transduction adaptor) [NCBI Gene 4615] {aka IMD68, MYD88D, WM1}, CD209 (CD209 molecule) [NCBI Gene 30835] {aka CDSIGN, CLEC4L, DC-SIGN, DC-SIGN1, hDC-SIGN}, ITGAX (integrin subunit alpha X) [NCBI Gene 3687] {aka CD11C, SLEB6}, CXCL13 (C-X-C motif chemokine ligand 13) [NCBI Gene 10563] {aka ANGIE, ANGIE2, BCA-1, BCA1, BLC, BLR1L}, IL1A (interleukin 1 alpha) [NCBI Gene 3552] {aka IL-1 alpha, IL-1A, IL1, IL1-ALPHA, IL1F1}, ITGAM (integrin subunit alpha M) [NCBI Gene 3684] {aka CD11B, CR3A, HNA-4, MAC-1, MAC1A, MO1A}, CXCL12 (C-X-C motif chemokine ligand 12) [NCBI Gene 6387] {aka IRH, PBSF, SCYB12, SDF1, TLSF, TPAR1}, CCL22 (C-C motif chemokine ligand 22) [NCBI Gene 6367] {aka A-152E5.1, ABCD-1, DC/B-CK, MDC, SCYA22, STCP-1}, IL10 (interleukin 10) [NCBI Gene 3586] {aka CSIF, GVHDS, IL-10, IL10A, TGIF}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, CD69 (CD69 molecule) [NCBI Gene 969] {aka AIM, BL-AC/P26, CLEC2C, EA1, GP32/28, MLR-3}, Il10 (interleukin 10) [NCBI Gene 16153] {aka CSIF, If2a, Il-10}, SNAR-F (small NF90 (ILF3) associated RNA F) [NCBI Gene 100126781], CXCL10 (C-X-C motif chemokine ligand 10) [NCBI Gene 3627] {aka C7, IFI10, INP10, IP-10, SCYB10, crg-2}, IL2 (interleukin 2) [NCBI Gene 3558] {aka IL-2, TCGF, lymphokine}, TRAF6 (TNF receptor associated factor 6) [NCBI Gene 7189] {aka MGC:3310, RNF85}, IL2RA (interleukin 2 receptor subunit alpha) [NCBI Gene 3559] {aka CD25, IDDM10, IL2R, IMD41, TCGFR, p55}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, Il23a (interleukin 23, alpha subunit p19) [NCBI Gene 83430] {aka IL-23, p19}, CASP1 (caspase 1) [NCBI Gene 834] {aka ICE, IL1BC, P45}, IL15 (interleukin 15) [NCBI Gene 3600] {aka IL-15}, IRF1 (interferon regulatory factor 1) [NCBI Gene 3659] {aka IMD117, IRF-1, MAR}, NCAM1 (neural cell adhesion molecule 1) [NCBI Gene 4684] {aka CD56, MSK39, NCAM}, CASP4 (caspase 4) [NCBI Gene 837] {aka CASP-4, ICE(rel)II, ICEREL-II, ICH-2, Mih1, Mih1/TX}, IL13 (interleukin 13) [NCBI Gene 3596] {aka IL-13, P600}, IL23A (interleukin 23 subunit alpha) [NCBI Gene 51561] {aka IL-23, IL-23A, IL23P19, P19, SGRF}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, Cd38 (CD38 antigen) [NCBI Gene 12494] {aka ADPRC 1, Cd38-rs1, I-19}, IL4 (interleukin 4) [NCBI Gene 3565] {aka BCGF-1, BCGF1, BSF-1, BSF1, IL-4}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, HLA-E (major histocompatibility complex, class I, E) [NCBI Gene 3133] {aka HLA-6.2, QA1}, KLRK1 (killer cell lectin like receptor K1) [NCBI Gene 22914] {aka CD314, D12S2489E, KLR, NKG2-D, NKG2D}, IL10RA (interleukin 10 receptor subunit alpha) [NCBI Gene 3587] {aka CD210, CD210a, CDW210A, HIL-10R, IL-10R1, IL10R}, IL12B (interleukin 12B) [NCBI Gene 3593] {aka CLMF, CLMF2, IL-12B, IMD28, IMD29, NKSF}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, CD19 (CD19 molecule) [NCBI Gene 930] {aka B4, CVID3}, PYCARD (PYD and CARD domain containing) [NCBI Gene 29108] {aka ASC, CARD5, TMS, TMS-1, TMS1}, CXCL16 (C-X-C motif chemokine ligand 16) [NCBI Gene 58191] {aka CXCLG16, SR-PSOX, SRPSOX}, IKZF1 (IKAROS family zinc finger 1) [NCBI Gene 10320] {aka CVID13, Hs.54452, IK1, IKAROS, LYF1, LyF-1}, Hbegf (heparin-binding EGF-like growth factor) [NCBI Gene 15200] {aka Dtr, Dts, Hegfl}, CLEC4A (C-type lectin domain family 4 member A) [NCBI Gene 50856] {aka CD367, CLECSF6, DCIR, DDB27, HDCGC13P, LLIR}, KLRD1 (killer cell lectin like receptor D1) [NCBI Gene 3824] {aka CD94}, FOXP3 (forkhead box P3) [NCBI Gene 50943] {aka AIID, DIETER, IPEX, JM2, PIDX, XPID}, PDCD1LG2 (programmed cell death 1 ligand 2) [NCBI Gene 80380] {aka B7DC, Btdc, CD273, PD-L2, PDCD1L2, PDL2}, KLRC1 (killer cell lectin like receptor C1) [NCBI Gene 3821] {aka CD159A, NKG2, NKG2A}, AHR (aryl hydrocarbon receptor) [NCBI Gene 196] {aka FVH3, RP85, bHLHe76}, IL18 (interleukin 18) [NCBI Gene 3606] {aka IGIF, IL-18, IL-1g, IL1F4}
- **Diseases:** colon carcinoma (MESH:D003110), immune dysregulation (OMIM:614878), graft-versus-host disease (MESH:D006086), dependent cellular cytotoxicity (MESH:D019966), arthritis (MESH:D001168), CD colon (MESH:D003108), ADCC (MESH:D007153), proinflammatory cytokines (MESH:D000080424), autoimmune and inflammatory disorders (MESH:D007249), rheumatoid arthritis (MESH:D001172), IBD (MESH:D015212), infection (MESH:D007239), systemic lupus erythematosus (MESH:D008180), autoimmune and inflammatory disease (MESH:D001327), atopic dermatitis (MESH:D003876), HS (MESH:D017497), CD (MESH:D003424), bacterial infection (MESH:D001424), UC (MESH:D003093), collagen (MESH:D003095)
- **Chemicals:** pyruvate (MESH:D019289), GlutaMAX (MESH:C054122), daratumumab (MESH:C556306), LPS (MESH:D008070), dexamethasone (MESH:D003907), Alexa Fluor 647 (MESH:C569686), tryptophan (MESH:D014364), HEPES (MESH:D006531), indoximod (MESH:C525396), CellTracker Green (MESH:C069306), formalin (MESH:D005557), streptomycin (MESH:D013307), vitamin D3 (MESH:D002762), 2-mercaptoethanol (MESH:D008623), CpG (MESH:C015772), paraffin (MESH:D010232), 5E11 (-), Lenalidomide (MESH:D000077269), H&amp;E (MESH:D006371), penicillin (MESH:D010406), CpG ODN2006 (MESH:C513533), PBS (MESH:D007854), amino acids (MESH:D000596)
- **Species:** Listeria monocytogenes (species) [taxon 1639], Homo sapiens (human, species) [taxon 9606], Yersinia pestis (species) [taxon 632], Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116]
- **Cell lines:** SCP1884 — Ovis aries (Sheep), Finite cell line (CVCL_4298), Expi293 — Homo sapiens (Human), Transformed cell line (CVCL_D615), HEK293 — Homo sapiens (Human), Transformed cell line (CVCL_0045), Pan T — Homo sapiens (Human), Pancreatic ductal adenocarcinoma, Cancer cell line (CVCL_A1II)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13020354/full.md

## References

84 references — full list in the complete paper: https://tomesphere.com/paper/PMC13020354/full.md

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Source: https://tomesphere.com/paper/PMC13020354