2. Academic Validation
  3. Proteomic Analysis of Paired FFPE Tissue and Extracellular Vesicles Reveals Proteins Associated with Recurrence in Stage II Colorectal Cancer

Proteomic Analysis of Paired FFPE Tissue and Extracellular Vesicles Reveals Proteins Associated with Recurrence in Stage II Colorectal Cancer

  • J Proteome Res. 2026 May 1;25(5):2385-2399. doi: 10.1021/acs.jproteome.5c01148.
Raquel Rejas-González 1 2,  María Jesús Fernández-Aceñero 3,  Pernilla Seidi Tirado-Zambrana 4,  Lara Sanz-Criado 5,  Jana Dziaková 6,  Rodrigo Sanz-López 6,  Carmen Poves 6,  Jaime Feliu 7 8,  Victoria Heredia-Soto 7 8,  Marta Mendiola 7 8,  Javier Martínez-Useros 9 5,  Alberto Peláez-García 7 10,  Ana Montero-Calle 1,  Rodrigo Barderas 1 11
Affiliations

Affiliations

  • 1 Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain.
  • 2 Escuela de Doctorado, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
  • 3 Department of Legal Medicine, Psychiatry and Surgical Pathology, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Clínico San Carlos (IdISCC); Surgical Pathology Department, Hospital Universitario Clínico San Carlos, E-28040 Madrid, Spain.
  • 4 Hospital Universitario Infanta Leonor, E-28031 Madrid, Spain.
  • 5 Translational Oncology Division, OncoHealth Institute, Health Research Institute-University Hospital Fundación Jiménez Díaz-Universidad Autónoma de Madrid, E-28040 Madrid, Spain.
  • 6 Hospital Universitario Clínico San Carlos, E-28040 Madrid, Spain.
  • 7 La Paz University Hospital (IdIPAZ), 28046 Madrid, Spain.
  • 8 CIBER of Oncology (CIBERONC), Instituto de Salud Carlos III, 28046 Madrid, Spain.
  • 9 Area of Physiology, Department of Basic Health Sciences, Faculty of Health Sciences, Rey Juan Carlos University, E-28922 Madrid, Spain.
  • 10 Proteomics Core, UCCTs, Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain.
  • 11 CIBER Frailty and Healthy Aging (CIBERFES), Madrid, E-28029 Madrid, Spain.
PMID: 41966223 DOI: 10.1021/acs.jproteome.5c01148
Abstract

Colorectal Cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Stage II CRC poses a clinical challenge due to its heterogeneous outcomes, with 15-20% of patients experiencing recurrence. Current prognostic models based on clinicopathologic features lack sufficient precision, highlighting the need for new molecular markers. In this study, we employed an integrative TMT-based proteomics strategy to identify biomarkers of recurrence in stage II CRC. We analyzed paired formalin-fixed paraffin-embedded (FFPE) tissues and small extracellular vesicles (sEVs) from stage II recurrent and nonrecurrent CRC patients. Validation of proteomics data was performed in silico and by WB, immunohistochemistry, ELISA, and in vitro functional cell-based assays. This multifaceted approach identified several dysregulated proteins associated with CRC recurrence, including MANF, TLN1, TALDO1, and CDCA2, among Others. CDCA2 knockdown altered the tumorigenic properties of CRC cells in vitro, correlating findings with its association with prognosis. Conversely, higher plasma levels of MANF were found in nonrecurrent CRC patients, aligning results with its favorable prognosis profile. Collectively, our findings support the value of combining paired FFPE tissue and sEVs proteomics analyses to uncover recurrence-associated biomarkers, offering the potential for risk stratification and management of stage II CRC patients.

Keywords

CDCA2; FFPE tissue; MANF; colorectal cancer; functional proteomics; small extracellular vesicles; stage II.

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