# KLF2 overrides the resident memory CD8 T cell differentiation program, in opposition to KLF3

**Authors:** Taylor A. DePauw, Kexin Gai, Jian Shen, Nicholas J. Maurice, Ka Hyun Rhee, William J. Valente, Christine H. O’Connor, Weiguo Cui, Changwei Peng, Stephen C. Jameson

PMC · DOI: 10.1073/pnas.2533700123 · Proceedings of the National Academy of Sciences of the United States of America · 2026-03-23

## TL;DR

This study shows that KLF2 and KLF3 control how memory T cells become either tissue-resident or recirculating, with KLF2 preventing tissue-resident traits.

## Contribution

The study reveals that KLF2 and KLF3 act in opposition and cooperation to regulate CD8+ T cell differentiation and trafficking.

## Key findings

- Loss of KLF2 leads to premature acquisition of tissue-resident memory cell traits in CD8+ T cells.
- KLF3 opposes KLF2 in some T cell subsets but cooperates in others for differentiation.
- KLF2 and KLF3 are central to controlling T cell trafficking and memory differentiation.

## Abstract

Memory T cells, generated after an immune response, fall into two main groups, depending on whether they circulate between tissues and blood or are “resident” in tissues. Various phenotypic and functional properties characterize recirculating and resident memory cells, but the transcription factors (TFs) that control differentiation of each group are unclear. We show that the TF Kruppel-like factor 2 (KLF2) regulates differentiation of recirculating memory T cells: Loss of KLF2 leads to generation of cells with characteristics of tissue-resident cells, which retained functionality. The related TF KLF3 opposes KLF2 in differentiation of some memory T cell subsets, while KLF2 and KLF3 cooperate for differentiation of others. These studies identify key transcriptional networks that control memory T cell trafficking

Numerous transcriptional regulators have been associated with the differentiation pathways that lead to recirculating vs. tissue-resident memory T cells. However, it is unclear whether independent, coordinated expression of these regulators is required to determine residency vs. recirculation or whether there is a hierarchy, with some factors playing a dominant role in controlling T cell trafficking. We report that ablation of the gene encoding Kruppel-like factor 2 (KLF2) during CD8+ T cell activation leads to rapid transcriptional reprogramming, such that effector T cells fail to recirculate and prematurely acquire canonical phenotypic and transcriptional characteristics of resident memory cells (TRM). Klf2-deficient memory CD8+ T cells retained the capacity to undergo recall responses, including in vivo pathogen control. These data suggest that KLF2 diverts CD8+ T cells from the TRM differentiation program. In contrast, ablation of another member of the KLF family, KLF3, enhanced differentiation of some recirculating T cell subsets and limited production of TRM in lymphoid tissues. However, both KLF2 and KLF3 were required for differentiation of long-lived effector cells, suggesting cooperation between these factors in some situations. These findings indicate that KLFs occupy a central nexus in coordinating activated CD8+ T cell differentiation and trafficking.

## Linked entities

- **Genes:** KLF2 (KLF transcription factor 2) [NCBI Gene 10365], KLF3 (KLF transcription factor 3) [NCBI Gene 51274]

## Full-text entities

- **Genes:** MBTPS1 (membrane bound transcription factor peptidase, site 1) [NCBI Gene 8720] {aka CAOP, PCSK8, S1P, SEDKF, SKI-1}, Il2 (interleukin 2) [NCBI Gene 16183] {aka Il-2}, F2R (coagulation factor II thrombin receptor) [NCBI Gene 2149] {aka CF2R, HTR, PAR-1, PAR1, TR}, Tnf (tumor necrosis factor) [NCBI Gene 21926] {aka DIF, TNF-a, TNF-alpha, TNFSF2, TNFalpha, Tnfa}, CXCR6 (C-X-C motif chemokine receptor 6) [NCBI Gene 10663] {aka BONZO, CD186, CDw186, STRL33, TYMSTR}, Klrg1 (killer cell lectin-like receptor subfamily G, member 1) [NCBI Gene 50928] {aka 2F1-Ag, MAFA, MAFA-L}, Mki67 (antigen identified by monoclonal antibody Ki 67) [NCBI Gene 17345] {aka D630048A14Rik, Ki-67, Ki67}, Klf3 (Kruppel-like transcription factor 3 (basic)) [NCBI Gene 16599] {aka 9930027G08Rik, Bklf, Tef-2}, NR4A1 (nuclear receptor subfamily 4 group A member 1) [NCBI Gene 3164] {aka GFRP1, HMR, N10, NAK-1, NGFIB, NP10}, KLF1 (KLF transcription factor 1) [NCBI Gene 10661] {aka CDAN4A, CDAN4B, EKLF, EKLF/KLF1}, Pphln1 (periphilin 1) [NCBI Gene 223828] {aka CR, HSPC206, HSPC232}, KLF3 (KLF transcription factor 3) [NCBI Gene 51274] {aka BKLF}, BHLHE40 (basic helix-loop-helix family member e40) [NCBI Gene 8553] {aka BHLHB2, Clast5, DEC1, HLHB2, SHARP-2, SHARP2}, Tigit (T cell immunoreceptor with Ig and ITIM domains) [NCBI Gene 100043314] {aka Vstm3}, S1pr1 (sphingosine-1-phosphate receptor 1) [NCBI Gene 13609] {aka Edg1, Lpb1, S1p, S1p1}, Gzma (granzyme A) [NCBI Gene 14938] {aka Ctla-3, Ctla3, Hf, Hf1, SE1, TSP-1}, ITGA1 (integrin subunit alpha 1) [NCBI Gene 3672] {aka CD49a, VLA1}, KLRG1 (killer cell lectin like receptor G1) [NCBI Gene 10219] {aka 2F1, CLEC15A, MAFA, MAFA-2F1, MAFA-L, MAFA-LIKE}, EOMES (eomesodermin) [NCBI Gene 8320] {aka TBR2}, S1PR4 (sphingosine-1-phosphate receptor 4) [NCBI Gene 8698] {aka EDG6, LPC1, S1P4, SLP4}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, S1pr4 (sphingosine-1-phosphate receptor 4) [NCBI Gene 13611] {aka Edg6, Lpc1, S1p4}, RUNX3 (RUNX family transcription factor 3) [NCBI Gene 864] {aka AML2, CBFA3, PEBP2aC}, Cxcr6 (C-X-C motif chemokine receptor 6) [NCBI Gene 80901] {aka BONZO, STRL33}, Cd19 (CD19 antigen) [NCBI Gene 12478], RBPJ (recombination signal binding protein for immunoglobulin kappa J region) [NCBI Gene 3516] {aka AOS3, CBF-1, CBF1, IGKJRB, IGKJRB1, KBF2}, Ccr9 (C-C motif chemokine receptor 9) [NCBI Gene 12769] {aka A130091K22Rik, Cmkbr10, GPR-9-6}, Itgal (integrin alpha L) [NCBI Gene 16408] {aka (p180), Cd11a, LFA-1, LFA-1A, Ly-15, Ly-21}, Itga1 (integrin alpha 1) [NCBI Gene 109700] {aka CD49A, E130012M19Rik, Vla1}, trm (tremor) [NCBI Gene 22052], CCR7 (C-C motif chemokine receptor 7) [NCBI Gene 1236] {aka BLR2, CC-CKR-7, CCR-7, CD197, CDw197, CMKBR7}, P2RX7 (purinergic receptor P2X 7) [NCBI Gene 5027] {aka P2X7}, Casp1 (caspase 1) [NCBI Gene 12362] {aka ICE, Il1bc}, Ctla4 (cytotoxic T-lymphocyte-associated protein 4) [NCBI Gene 12477] {aka Cd152, Ctla-4, Ly-56}, XCL1 (X-C motif chemokine ligand 1) [NCBI Gene 6375] {aka ATAC, LPTN, LTN, SCM-1, SCM-1a, SCM1}, AHR (aryl hydrocarbon receptor) [NCBI Gene 196] {aka FVH3, RP85, bHLHe76}, Thy1 (thymus cell antigen 1, theta) [NCBI Gene 21838] {aka CD90, T25, Thy-1, Thy-1.2, Thy1.1, Thy1.2}, Cd160 (CD160 antigen) [NCBI Gene 54215] {aka By55}, Ptcra (pre T cell antigen receptor alpha) [NCBI Gene 19208] {aka gp33, pT-alpha, pT-alpha-TCR, pT[a], pTa, pTalpha}, CD69 (CD69 molecule) [NCBI Gene 969] {aka AIM, BL-AC/P26, CLEC2C, EA1, GP32/28, MLR-3}, P2rx7 (purinergic receptor P2X, ligand-gated ion channel, 7) [NCBI Gene 18439] {aka P2X(7), P2X7R}, DARS1 (aspartyl-tRNA synthetase 1) [NCBI Gene 1615] {aka DARS, HBSL, aspRS}, ZEB2 (zinc finger E-box binding homeobox 2) [NCBI Gene 9839] {aka HSPC082, SIP-1, SIP1, SMADIP1, ZFHX1B}, CX3CR1 (C-X3-C motif chemokine receptor 1) [NCBI Gene 1524] {aka CCRL1, CMKBRL1, CMKDR1, GPR13, GPRV28, V28}, S1PR5 (sphingosine-1-phosphate receptor 5) [NCBI Gene 53637] {aka EDG8, Edg-8, S1P5, SPPR-1, SPPR-2}, Cx3cr1 (C-X3-C motif chemokine receptor 1) [NCBI Gene 13051] {aka mCX3CR1}, Trav6-3 (T cell receptor alpha variable 6-3) [NCBI Gene 328483] {aka Gm13948, Gm193, Gm4, TCR}, Tbx21 (T-box 21) [NCBI Gene 57765] {aka TBT1, Tbet, Tblym}, Cd69 (CD69 antigen) [NCBI Gene 12515] {aka 5830438K24Rik, AIM, VEA}, Pdcd1 (programmed cell death 1) [NCBI Gene 18566] {aka Ly101, PD-1, Pdc1}, Ptprc (protein tyrosine phosphatase receptor type C) [NCBI Gene 19264] {aka B220, CD45R, Cd45, L-CA, Ly-5, Lyt-4}, Itgae (integrin alpha E, epithelial-associated) [NCBI Gene 16407] {aka A530055J10, CD103, aM290, alpha-E1, alpha-M290}, TRBV20OR9-2 (T cell receptor beta variable 20/OR9-2 (non-functional)) [NCBI Gene 6962] {aka CDR3, TCRBV20S2, TCRBV2O, TCRBV2S2O}, Il6ra (interleukin 6 receptor, alpha) [NCBI Gene 16194] {aka CD126, IL-6R, IL-6R-alpha, IL-6RA, Il6r}, Xcl1 (chemokine (C motif) ligand 1) [NCBI Gene 16963] {aka ATAC, LTN, Lptn, SCM-1, SCM-1a, Scyc1}, S1PR1 (sphingosine-1-phosphate receptor 1) [NCBI Gene 1901] {aka CD363, CHEDG1, D1S3362, ECGF1, EDG-1, EDG1}, Rap1a (Rap1a member of RAS oncogene family) [NCBI Gene 109905] {aka G-22K, Krev-1, Rap1}, Tox (thymocyte selection-associated high mobility group box) [NCBI Gene 252838] {aka 1700007F02Rik}, S1pr5 (sphingosine-1-phosphate receptor 5) [NCBI Gene 94226] {aka Edg8, S1P5, lpB4}, Zfp683 (zinc finger protein 683) [NCBI Gene 100503878] {aka Gm13060, Hobit}
- **Diseases:** tumors (MESH:D009369), NLTs (MESH:D017695), infection (MESH:D007239), acute infection (MESH:D000208), SLO (MESH:D019082)
- **Chemicals:** PNAS (MESH:D020135), Cr (MESH:D002857), FTY720 (MESH:D000068876), Armstrong (-), Cy5.5 (MESH:C098793)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], LCMV [taxon 11623], Listeria monocytogenes (species) [taxon 1639], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** P14, P14 T
- **Cell lines:** Cr — Mus musculus (Mouse), Hybridoma (CVCL_A0AJ), SI-IEL — Sus scrofa (Pig), Spontaneously immortalized cell line (CVCL_6A79), /6 — Homo sapiens (Human), Tongue squamous cell carcinoma, Cancer cell line (CVCL_5985), Klf2-Cr — Mus musculus (Mouse), Transformed cell line (CVCL_C0NG)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13037849/full.md

## References

68 references — full list in the complete paper: https://tomesphere.com/paper/PMC13037849/full.md

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Source: https://tomesphere.com/paper/PMC13037849