Title: Evolution of high-grade serous ovarian carcinoma: spatial and temporal aspects on tumour initiation and treatment effects.

Supervisors: 

Ingrid Hedenfalk, Srinivas Veerla, Jenny-Maria Jönsson, Anna Måsbäck, Päivi Kannisto

Reviewers: 

Kajsa Paulsson, Division of Clinical Genetics, Lund University

David Lindgren, Translational Cancer Research, Lund University

Abstract

Background

High-grade serous ovarian carcinoma (HGSOC) is the most common and aggressive form of epithelial ovarian cancer, with a poor prognosis after treatment and a low overall survival rate. TP53 signatures and serous tubal intraepithelial carcinomas in the fallopian tubes are likely the precursors of HGSOC^1,2,3, and gBRCA1/2 mutations confer an increased risk of up to 40%⁴. Current treatments include debulking surgery, chemotherapy and targeted therapy (VEGF and PARP inhibitors). Ovarian cancer-derived tumor DNA can be detected in routine liquid-based Pap tests^5,6,7,8, opening an opportunity for early detection and intervention. 

Research questions: 

1. Can copy number aberrations be detected in archival cervical samples from women with HGSOC? 
2. What is the spatial profile of fallopian tubes (FT) with gBRCA1/2 mutations?
3. Is AGR2 a prognostic marker in HGSOC?
4. What are the multi-cellular processes in HGSOC before and after treatments?

Preliminary results

I:  Shallow whole-genome sequencing (~1X) was performed on 204 samples from 18 HGSOC, four gBRCA1/2 and seven benign cases. Six cervical copy number signatures (CerCNsig) were generated, where Signatures 2 and 3 predominant in tumors were also found in diagnostic and pre-diagnostic cervical samples. To validate the CerCNsig, an additional 114 cervical samples (52 HGSOC, 18 gBRCA1/2 with/without HGSOC and 44 benign cases) were sequenced. Data analysis is ongoing.

II: Visium spatial transcriptomic analysis (OVisium) was performed on 18 FT tissues from 12 gBRCA1/2 cases who had risk-reducing salpingo-oophorectomy. Twelve transcriptome clusters were identified, and cluster 0 and 10 had gene enrichment in TNFα signaling via NF-kB while cluster 11 was enriched for immune populations. Moreover, AGR2 was upregulated in the fimbriated end and could be a diagnostic or prognostic biomarker in epithelial ovarian cancer^9,10. 

III: AGR2 expression level will be studied in relation to clinical variables. Tissue microarray immunohistochemistry will be performed on 130 HGSOC cases.

IV: Single cell RNA and ATAC sequencing will be used to characterize different cell populations and identify regulatory networks and new biomarkers related to e.g., platinum response and resistance on samples from HGSOC cases before and after treatments.

Significance

CerCNsig could identify early signs of HGSOC and OVisium expands knowledge of FT in a high-risk group. 

Manuscripts

1. Copy number signatures for early diagnosis of high-grade serous ovarian carcinoma.

Laura Martín de la Fuente, Minerva Li, Anna Måsbäck, Susanne Malander, Päivi Kannisto, Srinivas Veerla, Ingrid Hedenfalk

1. Spatial transcriptional landscapes of fallopian tubes from germline BRCA1/2 mutation carriers. 

Minerva Li, Anna Ebbesson, Sofia Westbom Fremer, Katja Harbst, Bengt Phung, Göran Jönsson, Srinivas Veerla, Ingrid Hedenfalk

References

1. Bell, D. et al. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
2. Labidi-Galy, S. I. et al. High grade serous ovarian carcinomas originate in the fallopian tube. Nat Commun 8, 1093 (2017).
3. Akahane, T. et al. TP53 variants in p53 signatures and the clonality of STICs in RRSO samples. J Gynecol Oncol 33, e50 (2022).
4. Kuchenbaecker, K. B. et al. “Risks of Breast, Ovarian, and Contralateral Breast Cancer for BRCA1 and BRCA2 Mutation Carriers.” JAMA 317, 23 (2017) 
5. Kinde, I. et al. Evaluation of DNA from the Papanicolaou Test to Detect Ovarian and Endometrial Cancers. Science Translational Medicine 5, 167 (2013).
6. Paracchini, L. et al. Detection of TP53 Clonal Variants in Papanicolaou Test Samples Collected up to 6 Years Prior to High-Grade Serous Epithelial Ovarian Cancer Diagnosis. JAMA Netw Open 3, e207566 (2020).
7. Arildsen, N. S. et al. Detecting TP53 mutations in diagnostic and archival liquid-based Pap samples from ovarian cancer patients using an ultra-sensitive ddPCR method. Sci Rep 9, 15506 (2019).
8. Paracchini, L. et al. Genomic Instability Analysis in DNA from Papanicolaou Test Provides Proof-of-Principle Early Diagnosis of High-Grade Serous Ovarian Cancer. Science Translational Medicine 15, 725 (2023).
9. Park, K. et al. AGR2, a mucinous ovarian cancer marker, promotes cell proliferation and migration. Exp Mol Med 43, 91–100 (2011).
10. Fessart, D. et al. The Anterior GRadient (AGR) family proteins in epithelial ovarian cancer. J Exp Clin Cancer Res 40, 271 (2021).