{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T10:54:00Z","timestamp":1764068040328,"version":"3.45.0"},"reference-count":49,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016036","name":"Health Holland","doi-asserted-by":"publisher","award":["TKI2122"],"award-info":[{"award-number":["TKI2122"]}],"id":[{"id":"10.13039\/100016036","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Patients with pancreatic ductal adenocarcinoma (PDAC) face a very poor prognosis despite advancements in therapeutic strategies. Signal transduction pathways (STPs) that show altered activity in cancer cells may provide new therapeutic targets. Here, we used simultaneous transcriptome-based activation profiling (STAP)-STP technology to identify abnormal STP activity in PDAC. STAP-STP infers STP activity from messenger RNA expression of the target genes of each pathway-associated transcription factor, which is not possible with conventional bioinformatic analysis. We searched the Gene Expression Omnibus database for publicly available PDAC Affymetrix (GPL570) datasets and included six datasets: four datasets with samples from both normal pancreatic duct epithelial cells and PDAC tumor cells and two datasets with PDAC derived cell lines. The activity of the twelve most relevant STPs (androgen receptor, estrogen receptor, PI3K, MAPK, TGF\u03b2, Notch, Hedgehog, Wnt, NF\u03baB, STAT1\/2 type I interferon, STAT1\/2type II interferon and STAT3) was quantified. Increased activity of the MAPK, STAT3, Wnt, Hedgehog, Notch TGF\u03b2, and NF\u03baB pathways was found in at least two out of four datasets. In PDAC cell lines, MAPK, PI3K, and STAT3 STPs showed higher activity than in patient samples. Cell type deconvolution analysis showed a variable mixture of fibroblasts, immune cells, and tumor cells in the patient samples, which likely influenced the STP activity profile. This is the first time that STP activity has been quantified in PDAC. We conclude that PDAC is characterized by increased MAPK STP activity in combination with high Ki67 and increased activity of developmental pathways (Wnt, Hedgehog, Notch, TGF\u03b2). Drugs targeting specific STPs will be evaluated in PDAC model systems to develop new therapies for PDAC.<\/jats:p>","DOI":"10.3390\/ijms262311385","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T10:46:18Z","timestamp":1764067578000},"page":"11385","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Quantification of Signal Transduction Pathway Activity in Pancreatic Ductal Adenocarcinoma"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1530-8786","authenticated-orcid":false,"given":"L\u00e9on","family":"Raymakers","sequence":"first","affiliation":[{"name":"Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"},{"name":"Division of Imaging & Oncology, University Medical Center Utrecht Cancer Center, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9227-7178","authenticated-orcid":false,"given":"Lois A.","family":"Daamen","sequence":"additional","affiliation":[{"name":"Division of Imaging & Oncology, University Medical Center Utrecht Cancer Center, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"},{"name":"Department of Surgery, Regional Academic Cancer Center Utrecht, University Medical Center Utrecht Cancer Center & St. Antonius Hospital Nieuwegein, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5068-5517","authenticated-orcid":false,"given":"Martijn P. W.","family":"Intven","sequence":"additional","affiliation":[{"name":"Department of Radiotherapy, Division Imaging and Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4982-6914","authenticated-orcid":false,"given":"Jeanette H. W.","family":"Leusen","sequence":"additional","affiliation":[{"name":"Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6100-9290","authenticated-orcid":false,"given":"Patricia A.","family":"Olofsen","sequence":"additional","affiliation":[{"name":"Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5870-7004","authenticated-orcid":false,"given":"Anja","family":"van de Stolpe","sequence":"additional","affiliation":[{"name":"Drug Companion Diagnostics Company (DCDC-Tx), Eikenheuveldreef 16, 5263 EM Vught, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4352-4598","authenticated-orcid":false,"given":"Reinier A. P.","family":"Raymakers","sequence":"additional","affiliation":[{"name":"Drug Companion Diagnostics Company (DCDC-Tx), Eikenheuveldreef 16, 5263 EM Vught, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,25]]},"reference":[{"key":"ref_1","first-page":"10","article-title":"Cancer statistics, 2025","volume":"75","author":"Siegel","year":"2025","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S1470-2045(13)70546-1","article-title":"Cancer survival in Europe 1999-2007 by country and age: Results of EUROCARE--5-a population-based study","volume":"15","author":"Sant","year":"2014","journal-title":"Lancet Oncol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2913","DOI":"10.1158\/0008-5472.CAN-14-0155","article-title":"Projecting cancer incidence and deaths to 2030: The unexpected burden of thyroid, liver, and pancreas cancers in the United States","volume":"74","author":"Rahib","year":"2014","journal-title":"Cancer Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ejca.2019.11.002","article-title":"Nationwide trends in incidence, treatment and survival of pancreatic ductal adenocarcinoma","volume":"125","author":"Latenstein","year":"2020","journal-title":"Eur. J. Cancer"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/s13014-019-1345-6","article-title":"Pancreatic ductal adenocarcinoma: Biological hallmarks, current status, and future perspectives of combined modality treatment approaches","volume":"14","author":"Orth","year":"2019","journal-title":"Radiat. Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1670","DOI":"10.1038\/s12276-022-00864-3","article-title":"Molecular targeted therapy for anticancer treatment","volume":"54","author":"Min","year":"2022","journal-title":"Exp. Mol. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"571","DOI":"10.4251\/wjgo.v15.i4.571","article-title":"Recent advances in targeted therapy for pancreatic adenocarcinoma","volume":"15","author":"Fang","year":"2023","journal-title":"World J. Gastrointest. Oncol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Javadrashid, D., Baghbanzadeh, A., Derakhshani, A., Leone, P., Silvestris, N., Racanelli, V., Solimando, A.G., and Baradaran, B. (2021). Pancreatic Cancer Signaling Pathways, Genetic Alterations, and Tumor Microenvironment: The Barriers Affecting the Method of Treatment. Biomedicines, 9.","DOI":"10.3390\/biomedicines9040373"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Van de Stolpe, A., Verhaegh, W., Blay, J.Y., Ma, C.X., Pauwels, P., Pegram, M., Prenen, H., De Ruysscher, D., Saba, N.F., and Slovin, S.F. (2020). RNA Based Approaches to Profile Oncogenic Pathways From Low Quantity Samples to Drive Precision Oncology Strategies. Front. Genet., 11.","DOI":"10.3389\/fgene.2020.598118"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Thorner, J., Hunter, T., Cantley, L.C., and Sever, R. (2014). Signal transduction: From the atomic age to the post-genomic era. Cold Spring Harb. Perspect. Biol., 6.","DOI":"10.1101\/cshperspect.a022913"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s41392-021-00659-4","article-title":"The molecular biology of pancreatic adenocarcinoma: Translational challenges and clinical perspectives","volume":"6","author":"Wang","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2936","DOI":"10.1158\/0008-5472.CAN-13-2515","article-title":"Selection of personalized patient therapy through the use of knowledge-based computational models that identify tumor-driving signal transduction pathways","volume":"74","author":"Verhaegh","year":"2014","journal-title":"Cancer Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1956","DOI":"10.1016\/j.ajpath.2018.05.020","article-title":"Assessment of Functional Phosphatidylinositol 3-Kinase Pathway Activity in Cancer Tissue Using Forkhead Box-O Target Gene Expression in a Knowledge-Based Computational Model","volume":"188","author":"Hornsveld","year":"2018","journal-title":"Am. J. Pathol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Van de Stolpe, A., Holtzer, L., van Ooijen, H., Inda, M.A., and Verhaegh, W. (2019). Enabling precision medicine by unravelling disease pathophysiology: Quantifying signal transduction pathway activity across cell and tissue types. Sci. Rep., 9, Correction in Sci. Rep. 2020, 10, 4376.","DOI":"10.1038\/s41598-020-60886-7"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Cante-Barrett, K., Holtzer, L., van Ooijen, H., Hagelaar, R., Cordo, V., Verhaegh, W., van de Stolpe, A., and Meijerink, J.P.P. (2020). A Molecular Test for Quantifying Functional Notch Signaling Pathway Activity in Human Cancer. Cancers, 12.","DOI":"10.3390\/cancers12113142"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"102748","DOI":"10.1016\/j.scr.2022.102748","article-title":"Measurement of activity of developmental signal transduction pathways to quantify stem cell pluripotency and phenotypically characterize differentiated cells","volume":"61","author":"Holtzer","year":"2022","journal-title":"Stem. Cell Res."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Bouwman, W., Verhaegh, W., Holtzer, L., and van de Stolpe, A. (2020). Measurement of Cellular Immune Response to Viral Infection and Vaccination. Front. Immunol., 11.","DOI":"10.3389\/fimmu.2020.575074"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: The next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"ref_19","first-page":"2016","article-title":"Combined gene expression analysis of whole-tissue and microdissected pancreatic ductal adenocarcinoma identifies genes specifically overexpressed in tumor epithelia","volume":"55","author":"Badea","year":"2008","journal-title":"Hepatogastroenterology"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/j.ccr.2009.07.016","article-title":"FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt","volume":"16","author":"Pei","year":"2009","journal-title":"Cancer Cell"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1158\/1078-0432.CCR-11-1539","article-title":"Integrative survival-based molecular profiling of human pancreatic cancer","volume":"18","author":"Donahue","year":"2012","journal-title":"Clin. Cancer Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"53165","DOI":"10.18632\/oncotarget.10242","article-title":"Globally increased ultraconserved noncoding RNA expression in pancreatic adenocarcinoma","volume":"7","author":"Jiang","year":"2016","journal-title":"Oncotarget"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bye, B.A., Jack, J., Pierce, A., Walsh, R.M., Eades, A., Chalise, P., Olou, A., and VanSaun, M.N. (2023). Combined PI3K and MAPK inhibition synergizes to suppress PDAC. bioRxiv, 17.","DOI":"10.1101\/2023.08.15.553438"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1038\/s41467-024-46811-w","article-title":"Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer","volume":"15","author":"Bulle","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"101510","DOI":"10.1016\/j.tranon.2022.101510","article-title":"Key signal transduction pathways and crosstalk in cancer: Biological and therapeutic opportunities","volume":"26","author":"Fu","year":"2022","journal-title":"Transl. Oncol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/s41392-025-02142-w","article-title":"Wnt signaling pathways in biology and disease: Mechanisms and therapeutic advances","volume":"10","author":"Xue","year":"2025","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1038\/s41420-025-02327-w","article-title":"Mechanisms and therapeutic potential of the hedgehog signaling pathway in cancer","volume":"11","author":"Cong","year":"2025","journal-title":"Cell Death Discov."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Chapnick, D.A., Warner, L., Bernet, J., Rao, T., and Liu, X. (2011). Partners in crime: The TGFbeta and MAPK pathways in cancer progression. Cell Biosci., 1.","DOI":"10.1186\/2045-3701-1-42"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41698-018-0049-y","article-title":"Interaction between Wnt\/beta-catenin and RAS-ERK pathways and an anti-cancer strategy via degradations of beta-catenin and RAS by targeting the Wnt\/beta-catenin pathway","volume":"2","author":"Jeong","year":"2018","journal-title":"NPJ Precis. Oncol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1476-4598-8-128","article-title":"Cooperation of Notch and Ras\/MAPK signaling pathways in human breast carcinogenesis","volume":"8","author":"Mittal","year":"2009","journal-title":"Mol. Cancer"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.semcancer.2015.08.003","article-title":"Mitogen-activated protein kinases and Hedgehog-GLI signaling in cancer: A crosstalk providing therapeutic opportunities?","volume":"35","author":"Rovida","year":"2015","journal-title":"Semin. Cancer Biol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Raymakers, L., Passchier, E.M., Verdonschot, M.E.L., Evers, M., Chan, C., Kuijpers, K.C., Raicu, G.M., Molenaar, I.Q., van Santvoort, H.C., and Strijbis, K. (2025). The Efficacy of Targeted Monoclonal IgA Antibodies Against Pancreatic Ductal Adenocarcinoma. Cells, 14.","DOI":"10.3390\/cells14090632"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1002\/ijc.35079","article-title":"High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment","volume":"155","author":"Wei","year":"2024","journal-title":"Int. J. Cancer"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/nm.2344","article-title":"Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy","volume":"17","author":"Collisson","year":"2011","journal-title":"Nat. Med."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Maupin, K.A., Sinha, A., Eugster, E., Miller, J., Ross, J., Paulino, V., Keshamouni, V.G., Tran, N., Berens, M., and Webb, C. (2010). Glycogene expression alterations associated with pancreatic cancer epithelial-mesenchymal transition in complementary model systems. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0013002"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2023","DOI":"10.1158\/1078-0432.CCR-20-3715","article-title":"Inhibition of Hedgehog Signaling Alters Fibroblast Composition in Pancreatic Cancer","volume":"27","author":"Steele","year":"2021","journal-title":"Clin. Cancer Res."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Dardare, J., Witz, A., Merlin, J.L., Gilson, P., and Harle, A. (2020). SMAD4 and the TGFbeta Pathway in Patients with Pancreatic Ductal Adenocarcinoma. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21103534"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Stanciu, S., Ionita-Radu, F., Stefani, C., Miricescu, D., Stanescu, S., Greabu, M., Ripszky Totan, A., and Jinga, M. (2022). Targeting PI3K\/AKT\/mTOR Signaling Pathway in Pancreatic Cancer: From Molecular to Clinical Aspects. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms231710132"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Mehra, S., Deshpande, N., and Nagathihalli, N. (2021). Targeting PI3K Pathway in Pancreatic Ductal Adenocarcinoma: Rationale and Progress. Cancers, 13.","DOI":"10.3390\/cancers13174434"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Principe, D.R., Timbers, K.E., Atia, L.G., Koch, R.M., and Rana, A. (2021). TGFbeta Signaling in the Pancreatic Tumor Microenvironment. Cancers, 13.","DOI":"10.3390\/cancers13205086"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Silke, J., and O\u2019Reilly, L.A. (2021). NF-kappaB and Pancreatic Cancer; Chapter and Verse. Cancers, 13.","DOI":"10.3390\/cancers13184510"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/j.soc.2021.06.003","article-title":"Pathology and Molecular Characteristics of Pancreatic Cancer","volume":"30","author":"Kearney","year":"2021","journal-title":"Surg. Oncol. Clin. N. Am."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1586\/erm.11.62","article-title":"Critical role of laser microdissection for genetic, epigenetic and proteomic analyses in pancreatic cancer","volume":"11","author":"Funel","year":"2011","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Robinson, M.D., and Speed, T.P. (2007). A comparison of Affymetrix gene expression arrays. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-449"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nrc.2017.103","article-title":"Differentiation therapy revisited","volume":"18","year":"2018","journal-title":"Nat. Rev. Cancer"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Sergeant, G., van Eijsden, R., Roskams, T., Van Duppen, V., and Topal, B. (2012). Pancreatic cancer circulating tumour cells express a cell motility gene signature that predicts survival after surgery. BMC Cancer, 12.","DOI":"10.1186\/1471-2407-12-527"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1158\/1940-6207.CAPR-10-0025","article-title":"A migration signature and plasma biomarker panel for pancreatic adenocarcinoma","volume":"4","author":"Balasenthil","year":"2011","journal-title":"Cancer Prev. Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","article-title":"Affy--analysis of Affymetrix GeneChip data at the probe level","volume":"20","author":"Gautier","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/d41586-019-00857-9","article-title":"Scientists rise up against statistical significance","volume":"567","author":"Amrhein","year":"2019","journal-title":"Nature"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/23\/11385\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T10:50:08Z","timestamp":1764067808000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/23\/11385"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,25]]},"references-count":49,"journal-issue":{"issue":"23","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["ijms262311385"],"URL":"https:\/\/doi.org\/10.3390\/ijms262311385","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2025,11,25]]}}}