# Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers

**Authors:** Julian Frädrich, Carmen Mota Reyes, Michel Hendel, Vanessa Brunner, Batu Toledo, Damjan Manevski, Alexander Sommer, Daniel Häußler, Dominik Beck, Daniele Lucarelli, Jaime Martínez de Villareal, Lennard Halle, Raphael Kfuri-Rubens, Kaan Çifcibaşı, Anna Hirschberger, Rupert Öllinger, Percy A. Knolle, Katja Steiger, Roland Rad, Fabian J. Theis, Francisco X. Real, Stefanie Bärthel, Jan P. Böttcher, Dieter Saur, Ihsan Ekin Demir, Achim Krüger

PMC · DOI: 10.1016/j.xcrm.2025.102546 · Cell Reports Medicine · 2026-01-20

## TL;DR

The study identifies a secretory profile in pancreatic cancer that promotes tumor growth by suppressing immune cells, with TIMP-1 as a key driver and potential therapeutic target.

## Contribution

The study introduces a novel cancer-immunoinstructive secretory signature (CISS) dominated by TIMP-1, linking it to immunosuppression and therapeutic targeting in pancreatic cancer.

## Key findings

- CISS is a secretory profile linked to poor prognosis and immunosuppressive tumor environments across cancers.
- TIMP-1 is central to CISS in pancreatic cancer, suppressing natural killer cell activity and mTOR signaling.
- TIMP-1/CISS can be targeted in pre-clinical pancreatic cancer using approved drugs trametinib and nintedanib.

## Abstract

The immunosuppressive tumor microenvironment (TME) fosters cancer progression, yet overarching determinants of cancer-borne immunoinstruction remain ill-defined. By multimodal integration of single-nucleus and bulk transcriptomics, proteomics, functional approaches, and clinical parameters, we discover a cancer-immunoinstructive secretory signature (CISS) across multiple human cancers—a set of inflammatory proteins correlated with poor prognosis and pro-tumorigenic TMEs. In pancreatic cancer (PC), CISS arises in pre-malignant epithelium, intensifies along transformation toward most malignant basal-like PC, and particularly correlates with suppressed natural killer (NK) cell activity. The CISS is quantitatively dominated by tissue inhibitor of metalloproteinases (TIMP)-1, most prevalent in TIMP-1hi/CISShi basal-like PC, and causal for PC-cell-mediated NK cell suppression, reflected by impaired cytotoxicity, interleukin-2 (IL-2) responses, and mammalian target of rapamycin (mTOR) signaling. In pre-clinical PC, TIMP-1/CISS proves targetable through combined inhibition of upstream kinases with clinically approved drugs trametinib and nintedanib. Collectively, CISS represents a ubiquitous signature of pro-tumor immunoinstruction with actionable diagnostic and therapeutic potential across human cancers.

•A secretory profile (CISS) links malignant evolution to immunosuppression in cancer•In PDAC, CISS arises in pre-malignancy and culminates in TIMP-1hi basal-like cancer•PDAC-cell-mediated NK cell suppression is TIMP-1-dependent•TIMP1/CISS identify high-risk patients and prove targetable in pre-clinical PDAC

A secretory profile (CISS) links malignant evolution to immunosuppression in cancer

In PDAC, CISS arises in pre-malignancy and culminates in TIMP-1hi basal-like cancer

PDAC-cell-mediated NK cell suppression is TIMP-1-dependent

TIMP1/CISS identify high-risk patients and prove targetable in pre-clinical PDAC

By multiomic profiling across human cancers, Frädrich et al. discover a secretory profile linking malignant evolution to immunosuppression and poor patient survival. In pancreatic cancer, this profile is shaped by TIMP-1-dependent NK cell suppression and proves targetable through clinically approved kinase inhibitors, highlighting exploitable prognostic and therapeutic potential.

## Linked entities

- **Proteins:** TIMP1 (TIMP metallopeptidase inhibitor 1), IL2 (interleukin 15)
- **Chemicals:** trametinib (PubChem CID 11707110), nintedanib (PubChem CID 135423438)
- **Diseases:** pancreatic cancer (MONDO:0005192)

## Full-text entities

- **Genes:** IL7R (interleukin 7 receptor) [NCBI Gene 3575] {aka CD127, CDW127, IL-7R-alpha, IL-7Ralpha, IL7RA, IL7Ralpha}, Kras (Kras proto-oncogene, GTPase) [NCBI Gene 16653] {aka K-Ras, K-Ras 2, K-ras, Ki-ras, Kras-2, Kras2}, CP (ceruloplasmin) [NCBI Gene 1356] {aka AB073614, CP-2}, FXYD3 (FXYD domain containing ion transport regulator 3) [NCBI Gene 5349] {aka MAT8, PLML}, Tgfb1 (transforming growth factor, beta 1) [NCBI Gene 21803] {aka TGF-beta1, TGFbeta1, Tgfb, Tgfb-1}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, VIM (vimentin) [NCBI Gene 7431], HSPG2 (heparan sulfate proteoglycan 2) [NCBI Gene 3339] {aka HSPG, PLC, PRCAN, SJA, SJS, SJS1}, SLC4A4 (solute carrier family 4 member 4) [NCBI Gene 8671] {aka HNBC1, KNBC, NBC1, NBC2, NBCe1, NBCe1-A}, CFTR (CF transmembrane conductance regulator) [NCBI Gene 1080] {aka ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-CFTR}, ANXA5 (annexin A5) [NCBI Gene 308] {aka ANX5, CPB-I, ENX2, HEL-S-7, PP4, RPRGL3}, KRT8 (keratin 8) [NCBI Gene 3856] {aka CARD2, CK-8, CK8, CYK8, K2C8, K8}, CDK1 (cyclin dependent kinase 1) [NCBI Gene 983] {aka CDC2, CDC28A, P34CDC2}, MUC1 (mucin 1, cell surface associated) [NCBI Gene 4582] {aka ADMCKD, ADMCKD1, ADTKD2, CA 15-3, CD227, Ca15-3}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, Trp53 (transformation related protein 53) [NCBI Gene 22059] {aka Tp53, bbl, bfy, bhy, p44, p53}, VN1R17P (vomeronasal 1 receptor 17 pseudogene) [NCBI Gene 441931] {aka GPCR}, Fn1 (fibronectin 1) [NCBI Gene 14268] {aka E330027I09, Fn, Fn-1}, COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277] {aka CAFYD, EDSARTH1, EDSC, OI1, OI2, OI3}, FCGR3A (Fc gamma receptor IIIa) [NCBI Gene 2214] {aka CD16-II, CD16A, FCG3, FCGR3, FCRIIIA, FcGRIIIA}, S100A4 (S100 calcium binding protein A4) [NCBI Gene 6275] {aka 18A2, 42A, CAPL, FSP1, MTS1, P9KA}, GLIS3 (GLIS family zinc finger 3) [NCBI Gene 169792] {aka NDH, ZNF515}, TCF7 (transcription factor 7) [NCBI Gene 6932] {aka TCF-1}, CD74 (CD74 molecule) [NCBI Gene 972] {aka CLIP, DHLAG, HLADG, II, Ia-GAMMA, p33}, Fbln2 (fibulin 2) [NCBI Gene 14115] {aka 5730577E14Rik, FIBL-2}, MAPK3 (mitogen-activated protein kinase 3) [NCBI Gene 5595] {aka ERK-1, ERK1, ERT2, HS44KDAP, HUMKER1A, P44ERK1}, MUC6 (mucin 6, oligomeric mucus/gel-forming (gene/pseudogene)) [NCBI Gene 4588] {aka MUC-6}, COL3A1 (collagen type III alpha 1 chain) [NCBI Gene 1281] {aka EDS4A, EDSVASC, PMGEDSV}, TIMP1 (TIMP metallopeptidase inhibitor 1) [NCBI Gene 7076] {aka CLGI, EPA, EPO, HCI, TIMP, TIMP-1}, COL4A1 (collagen type IV alpha 1 chain) [NCBI Gene 1282] {aka BSVD, BSVD1, COL4A1s, PADMAL, RATOR}, Pdx1 (pancreatic and duodenal homeobox 1) [NCBI Gene 18609] {aka IDX-1, IPF-1, Ipf1, Mody4, STF-1, pdx-1}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, AMY2B (amylase alpha 2B) [NCBI Gene 280] {aka AMY2, AMY3, HXA}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, HMGA2 (high mobility group AT-hook 2) [NCBI Gene 8091] {aka BABL, HMGI-C, HMGIC, LIPO, SRS5, STQTL9}, PTK2B (protein tyrosine kinase 2 beta) [NCBI Gene 2185] {aka CADTK, CAKB, FADK2, FAK2, PKB, PTK}, CCR7 (C-C motif chemokine receptor 7) [NCBI Gene 1236] {aka BLR2, CC-CKR-7, CCR-7, CD197, CDw197, CMKBR7}, VCAN (versican) [NCBI Gene 1462] {aka CSPG2, ERVR, GHAP, PG-M, WGN, WGN1}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, Anxa2 (annexin A2) [NCBI Gene 12306] {aka Cal1h, PAP-IV, p36}, CIT (citron rho-interacting serine/threonine kinase) [NCBI Gene 11113] {aka CITK, CRIK, MCPH17, STK21}, MT1E (metallothionein 1E) [NCBI Gene 4493] {aka MT-1E, MT-IE, MT1, MTD}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, ZEB1 (zinc finger E-box binding homeobox 1) [NCBI Gene 6935] {aka AREB6, BZP, DELTAEF1, FECD6, NIL2A, PPCD3}, MAP2K7 (mitogen-activated protein kinase kinase 7) [NCBI Gene 5609] {aka JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7}, MT2A (metallothionein 2A) [NCBI Gene 4502] {aka MT-2, MT-II, MT2}, SYTL2 (synaptotagmin like 2) [NCBI Gene 54843] {aka CHR11SYT, EXO4, PPP1R151, SGA72M, SLP2, SLP2A}, Timp1 (tissue inhibitor of metalloproteinase 1) [NCBI Gene 21857] {aka Clgi, EPA, TIMP-1, TPA-S1, Timp}, SNAI2 (snail family transcriptional repressor 2) [NCBI Gene 6591] {aka SLUG, SLUGH, SLUGH1, SNAIL2, WS2D}, BAG6 (BAG cochaperone 6) [NCBI Gene 7917] {aka BAG-6, BAT3, D6S52E, G3}, Ptf1a (pancreas specific transcription factor, 1a) [NCBI Gene 19213] {aka PTF1-p48, PTF1p48, bHLHa29}, CCNG1 (cyclin G1) [NCBI Gene 900] {aka CCNG}, BICC1 (BicC family RNA binding protein 1) [NCBI Gene 80114] {aka BICC}, CELA3A (chymotrypsin like elastase 3A) [NCBI Gene 10136] {aka ELA3, ELA3A}, COL1A2 (collagen type I alpha 2 chain) [NCBI Gene 1278] {aka EDSARTH2, EDSCV, OI4}, CPA2 (carboxypeptidase A2) [NCBI Gene 1358], STAT5A (signal transducer and activator of transcription 5A) [NCBI Gene 6776] {aka MGF, STAT5}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, IL2 (interleukin 2) [NCBI Gene 3558] {aka IL-2, TCGF, lymphokine}, ADM (adrenomedullin) [NCBI Gene 133] {aka AM, PAMP}
- **Diseases:** c2 (OMIM:217000), Inflammation (MESH:D007249), BRCA (MESH:D001943), tumorigenesis (MESH:D063646), basal (MESH:D002280), LUAD (MESH:D000077192), PDAC (MESH:D021441), colorectal, kidney, and breast (MESH:D061325), pancreatic, colorectal, kidney, and brain cancer (MESH:D015179), chronic pancreatitis (MESH:D050500), death (MESH:D003643), pancreatitis (MESH:D010195), invasive cancer (MESH:D009362), Ductal (MESH:D044584), PRAD (MESH:D000230), BLCA (MESH:D001749), STES (MESH:D013274), cytotoxicity (MESH:D064420), LIHC (MESH:D006528), Tumor (MESH:D009369), melanoma (MESH:D008545), epithelial (MESH:D009375), GBM (MESH:D005909), PanIN (MESH:D002578), kidney cancer (MESH:D007680), HNSC (MESH:D000077195), PAAD (MESH:D010190), THCA (MESH:D013964), solid (MESH:D018250), colorectal adenocarcinoma (MESH:D003110), SKCM (MESH:C562393)
- **Chemicals:** Nintedanib (MESH:C530716), water (MESH:D014867), trypan blue (MESH:D014343), CO2 (MESH:D002245), zirconium (MESH:D015040), Trametinib (MESH:C560077), milatuzumab (MESH:C540932), DMSO (MESH:D004121), Batimastat (MESH:C080985), P/S (MESH:D010758), AlexaFluor Plus 405 (-), cerulein (MESH:D002108), Methanol (MESH:D000432), Brefeldin A (MESH:D020126), Lipid (MESH:D008055), 7-AAD (MESH:C025942), Alexa Fluor 488 (MESH:C000711379)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** S4F, S6D, g.64C>T, S6, 6C, 4S, G12D, R172H
- **Cell lines:** CRL-1420 — Homo sapiens (Human), Finite cell line (CVCL_JD99), LSL — Homo sapiens (Human), Hemophilia A, Induced pluripotent stem cell (CVCL_A4EK), C57BL/6 — Mus musculus (Mouse), Transformed cell line (CVCL_C0MU), K562 — Homo sapiens (Human), Blast phase chronic myelogenous leukemia, BCR-ABL1 positive, Cancer cell line (CVCL_0004), MIA PaCa-2 — Homo sapiens (Human), Pancreatic undifferentiated carcinoma, Cancer cell line (CVCL_0428), VSMC — Homo sapiens (Human), Finite cell line (CVCL_4009)

## Full text

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## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12866174/full.md

## References

109 references — full list in the complete paper: https://tomesphere.com/paper/PMC12866174/full.md

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Source: https://tomesphere.com/paper/PMC12866174