CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy

www.nature.com/npjsba ARTICLE OPEN CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy 1234567890():,; Marisol Salgado-Albarrán1,2, Julian Späth3, Rodrigo González-Barrios4, Jan Baumbach 3,5,6 ✉ and Ernesto Soto-Reyes1,6 ✉ High-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment, and chemoresistance. Improving the diagnosis and the development of targeted therapies is still needed. The molecular pathomechanisms driving HGSC progression are not fully understood though crucial for effective diagnosis and identification of novel targeted therapy options. The oncogene CTCFL (BORIS), the paralog of CTCF, is a transcriptional factor highly expressed in ovarian cancer (but in rarely any other tissue in females) with cancer-specific characteristics and therapeutic potential. In this work, we seek to understand the regulatory functions of CTCFL to unravel new target genes with clinical relevance. We used in vitro models to evaluate the transcriptional changes due to the presence of CTCFL, followed by a selection of gene candidates using de novo network enrichment analysis. The resulting mechanistic candidates were further assessed regarding their prognostic potential and druggability. We show that CTCFL-driven genes are involved in cytoplasmic membrane functions; in particular, the PI3K-Akt initiators EGFR1 and VEGFA, as well as ITGB3 and ITGB6 are potential drug targets. Finally, we identified the CTCFL targets ACTBL2, MALT1 and PCDH7 as mechanistic biomarkers to predict survival in HGSC. Finally, we elucidated the value of CTCFL in combination with its targets as a prognostic marker profile for HGSC progression and as putative drug targets. npj Systems Biology and Applications (2022)8:5 ; https://doi.org/10.1038/s41540-022-00214-z INTRODUCTION High-grade serous carcinoma (HGSC) is the most common type of ovarian cancer (OC) and the most lethal gynecologic malignancy1. The main reasons for the high mortality is the late diagnosis due to the lack of reliable biomarkers (60% of the tumors are detected once they have metastasized)2 and lack of effective treatment; i.e., current treatment involves surgical resection and standard chemotherapy, which has several side effects and tumors usually become resistant to it3. Thus, improving the diagnosis and the development of novel targeted therapies for HGSC is an ongoing research task since few previously proposed targeted therapies have been tested4. Furthermore, OC is a highly heterogeneous disease and the molecular mechanisms that drive OC progression and chemoresistance are not fully understood. Therefore, the identification of molecular pathway activity aberration in OC is a crucial first step in the development of effective diagnosis and novel targeted therapy options. Recent genome-wide studies show that, at the genetic level, the most frequent alterations in HGSC are in the P53 pathway, including mutations in the TP53 gene5. At the transcriptional level, Immuno, hormone-related, and MAPK signaling pathways are deregulated in specific clusters of HGSC patients6. Furthermore, integrative omic analyses of OC tumors indicate that the protein CTCFL is a relevant molecular driver of OC7,8. CTCFL (BORIS) is the paralog of the CTCF gene, which encodes a ubiquitous well-known transcription factor (TF) with an 11-zincfinger DNA-binding domain that recognizes binding sites (BSs) in the genome and participates in the establishment of chromatin organization and transcriptional regulation9,10. Likewise, CTCFL is a transcriptional regulator that competes for the same BSs with CTCF11. CTCFL has gained interest because omics data show that it is a cancer-specific protein: it is highly expressed in OC but absent in healthy normal tissue in women, except in testis (www. proteinatlas.org/ENSG00000124092-CTCFL)9,12,13. Due to its particular tissue specificity, CTCFL is classified as a cancer-testis antigen (CTA), a family of proteins with therapeutic importance in cancer14,15. Notably, CTCFL is considered an oncogene16 and appears to be a master TF that maintains a stemness state in cancer17 through the transcriptional regulation of several wellcharacterized oncogenes and also other CTAs in several cancer types18–21. Integrative OC-specific omic analyses have found that CTCFL is a molecular marker of HGSC in three different levels: DNAmethylation, gene expression, and DNA copy number22. Also, CTCFL plays an important role in the progression of HGSC; for instance, Hillman et al. demonstrated that CTCFL expression could be a key factor of initiation8 and additional studies indicate that CTCFL can contribute to OC progression through different mechanisms; such as androgen receptor-associated pathway7, dysregulation of hTERT telomerase23 and it is associated with poor prognosis and advanced stage24. Together, the above makes CTCFL an exciting and promising unique target for OC treatment or biomarker development25,26. Despite the notable improvements in the study of CTCFL in cancer, a detailed examination of the transcriptional effects of CTCFL expression in OC remains to be fully characterized, as well as the extent to which it influences other cancer-related processes and their potential application for the development of mechanistic therapies for OC. 1 Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico. 2Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany. 3Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany. 4Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Mexico City, Mexico. 5Computational BioMedicine lab, Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. 6These authors contributed equally: Jan Baumbach, Ernesto Soto-Reyes. ✉email: ; Published in partnership with the Systems Biology Institute M. Salgado-Albarrán et al. 2 1234567890():,; In this work, we study the regulatory functions of CTCFL in OC at the transcriptional level to identify mechanistic targets with clinical relevance in OC. We used in vitro models to evaluate the transcriptional changes due to knockdown and overexpression of CTCFL; followed by a selection of gene candidates, the identification of CTCFL-DNA-binding sites and de novo pathway enrichment analysis for the identification of potential OC driver mechanisms controlled by CTCFL. Finally, the expression level of candidate genes were utilized as endophenotypic marker profiles to assess their prognostic power as molecular signature and their druggability potential. RESULTS CTCFL-regulated genes participate in cell motility, membrane transport, and extracellular matrix-related processes In this study, we aim to identify genes regulated by CTCFL that are of cl (...truncated)