Disertasi

Karakteristik dan Potensi Protein Sekretom Sel Punca Kanker dari Subtipe Tripel Negatif sebagai Biomarker untuk Pengembangan Deteksi Keganasan Kanker Payudara = Characteristics and Potential of Secretome Proteins from Triple-Negative Breast Cancer Stem Cells as Biomarkers for the Development of Malignancy Detection in Breast Cancer.

Latar Belakang: Kanker payudara masih menjadi salah satu penyebab utama kematian pada wanita di seluruh dunia, terutama akibat tingginya resistensi terapi, kekambuhan, dan metastasis. Salah satu faktor utamanya adalah keberadaan sel punca kanker (SPK) yang ditemukan pada semua subtipe kanker payudara, dengan subtipe tripel negatif sebagai yang paling agresif. SPK mempertahankan karakteristiknya melalui interaksi dengan lingkungan mikrotumor, terutama melalui protein sekretom yang dapat terdeteksi dalam cairan tubuh. Hal ini memungkinkan deteksi non-invasif SPK melalui biopsi cairan tubuh sebagai alternatif dari biopsi jaringan berbasis imunohistokimia (IHK). Penelitian ini mengintegrasikan analisis in silico, in vitro, dan plasma untuk mengidentifikasi panel biomarker protein sekretom dari SPK dalam mendeteksi keganasan kanker payudara. Metode: Penelitian dilakukan di Molecular Biology and Proteomics Facilities (MBPCF), Stem Cells and Tissue Engineering (SCTE), dan Laboratorium Bioinformatika Institute of Medical Education and Research in Indonesia (IMERI) Fakultas Kedokteran Universitas Indonesia, bekerja sama dengan Poli Bedah Rumah Sakit Dr. Cipto Mangunkusumo (RSCM). Sampel in vitro berupa conditioned medium (CM) dari populasi SPK dan non-SPK dari sel lestari MDAMB-231. Sampel plasma diperoleh dari 24 pasien kanker payudara dengan berbagai subtipe dan stadium I–IV (Juli–Oktober 2024), serta 12 kontrol sehat. Hasil: Analisis in silico terhadap dua dataset GEO (GSE7513 dan GSE7515) menghasilkan empat kandidat biomarker: FOXO1 dan FYN (teregulasi naik), serta OCLN dan TOP2A (teregulasi turun). Hasil divalidasi secara in vitro dan plasma. Konsentrasi FOXO1 tidak berbeda signifikan, FYN dan OCLN lebih rendah, TOP2A lebih tinggi pada SPK. Skoring multivariat berbasis plasma mengidentifikasi FOXO1 dan FYN sebagai pasangan biomarker potensial (AUC 74,3%, p = 0,019, uji Hosmer-Lemeshow p > 0,05). Kesimpulan: FOXO1 dan FYN berpotensi sebagai biomarker sekretom potensial dari SPK untuk deteksi keganasan kanker payudara.
Kata kunci: sel punca kanker payudara, deteksi keganasan, protein sekretom, biomarker, biopsi cairan tubuh


Introduction: Breast cancer remains one of the leading causes of mortality among women worldwide, primarily due to high rates of therapy resistance, recurrence, and metastasis. A key contributing factor is the presence of cancer stem cells (CSCs), which are found across all breast cancer subtypes, with triple-negative breast cancer (TNBC) being the most aggressive. CSCs maintain their properties through interactions with the tumor microenvironment, particularly via secretome proteins that are detectable in body fluids. This enables the non-invasive detection of CSCs through liquid biopsy, offering a promising alternative to conventional tissue biopsy based on immunohistochemistry (IHC). This study integrates in silico, in vitro, and plasma-based analyses to identify a panel of CSC-derived secretome protein biomarkers for the detection of breast cancer malignancy Method: The study was conducted at the Molecular Biology and Proteomics Facilities (MBPCF), Stem Cells and Tissue Engineering (SCTE), and the Bioinformatics Laboratory of the Institute of Medical Education and Research in Indonesia (IMERI), Faculty of Medicine, Universitas Indonesia, in collaboration with the Surgery Clinic of Dr. Cipto Mangunkusumo Hospital (RSCM). In vitro samples consisted of conditioned medium (CM) from CSC and non-CSC populations of the MDAMB-231 cell line. Plasma samples were collected from 24 breast cancer patients of various subtypes and stages I–IV (July–October 2024), as well as from 12 healthy controls. Results: In silico analysis of two GEO datasets (GSE7513 and GSE7515) identified four candidate biomarkers: FOXO1 and FYN (upregulated), and OCLN and TOP2A (downregulated). These findings were validated through in vitro and plasma-based analyses. FOXO1 concentrations showed no significant difference, while FYN and OCLN were lower, and TOP2A was higher in CSCs. Plasma-based multivariate scoring identified FOXO1 and FYN as a potential biomarker pair (AUC 74.3%, p = 0.019; Hosmer–Lemeshow test, p > 0.05). Conclusion: FOXO1 and FYN were identified as potential secretome-derived biomarkers from CSCs for the non-invasive detection of breast cancer malignancy.
Key words : breast cancer stem cells, malignancy detection, secretome proteins, biomarkers, liquid biopsy