Rapid autopsies to enhance metastatic research: the UPTIDER post-mortem tissue donation program

Research on metastatic cancer has been hampered by limited sample availability. Here we present the breast cancer post-mortem tissue donation program UPTIDER and show how it enabled sampling of a median of 31 (range: 5-90) metastases and 5-8 liquids per patient from its first 20 patients. In a dedicated experiment, we show the mild impact of increasing time after death on RNA quality, transcriptional profiles and immunohistochemical staining in tumor tissue samples. We show that this impact can be counteracted by organ cooling. We successfully generated ex vivo models from tissue and liquid biopsies from distinct histological subtypes of breast cancer. We anticipate these and future findings of UPTIDER to elucidate mechanisms of disease progression and treatment resistance and to provide tools for the exploration of precision medicine strategies in the metastatic setting.

Abstract P5-05-06: ctDNA detection in seven different types of body liquids in patients with metastatic breast cancer

Background. Liquid biopsies represent a less invasive alternative to tissue biopsy to characterize and possibly monitor the disease in patients with metastatic breast cancer. So far, blood remains the most frequently investigated body liquid in this context and the investigations mainly focus on the detection, quantification and characterization of the circulating tumor DNA (ctDNA). However, since blood might not capture the full disease profile, other sources of body liquids may have the potential to complement the information obtained from blood. The aims of the present study are therefore to assess whether: (i) ctDNA can be detected in different types of body liquids, and, (ii) the levels of ctDNA in a given liquid are associated with metastases in specific organs.

Patients and methods. Twelve patients from the post-mortem tissue donation program UPTIDER (NCT04531696) were included in this study. The receptor status of their primary tumor was: estrogen receptor negative, HER2 non-amplified (ER+/HER2-) (n=9), ER-/HER2- (n=2) and ER+/HER2+ (n=1). Median time between inclusion and death of the patient was 1.6 months (Interquartile range: [0.4-3.4]). Seven types of liquids were collected: blood, saliva, ascites, pleural fluid (PFL), cerebrospinal fluid (CSF), pericardial fluid and urine. Fluids were collected at study inclusion (blood, as well as saliva, urine, and ascites whenever possible) and at autopsy (except for saliva). In total, 108 liquid samples were collected and immediately centrifuged according to standard protocols. Cell free DNA (cfDNA) was extracted from the supernatant. All extracted cfDNA as well as germline DNA extracted from the 12 matched buffy coat samples underwent shallow whole genome sequencing. Log2 ratios were computed with CNVkit, and co-segmented per patient using the copynumber R package. Purity and ploidy were assessed by ABSOLUTE. Associations between organ involvement and ctDNA yield were assessed by Wilcoxon rank-sum tests. Samples at study inclusion and at autopsy were considered together unless otherwise specified.

Results. At the sample level, ctDNA could be identified in 54% of the samples. At the patient level, the proportion of liquid types in which ctDNA was detected was highly variable (median: 58%, IQR: 34-77%, Table 1). CtDNA was detected in ascites of all patients when investigated, in 78% of PFL, 73% of CSF, 67% of blood and 37% of pericardial fluid. Only for one patient with invasive lobular carcinoma, ctDNA was detected in saliva and urine, the latter most likely explained by invasion of the bladder. Of note, in 4/12 patients ctDNA could not be identified in blood but was detected in at least one of the other fluids for 3 of these patients. At autopsy, ctDNA levels tended to be higher in PFL, ascites, and CSF in case of pleural, peritoneal, and central nervous system (CNS) metastases respectively, reaching statistical significance only for PFL. In CSF, two patients have CSF ctDNA detected with no documented involvement of the CNS. No brain autopsy was however performed for these patients.

Conclusion. We have shown that ctDNA can be detected in all 7 different body liquids that were investigated in this study. The ctDNA levels in a given liquid can be associated with the presence of metastases in specific organs. Since ctDNA was not detected in 4 of our patients in blood but detectable for 3 of them in other liquids, the evaluation of additional sources of body fluids should be further investigated in patients with metastatic breast cancer. These results therefore open new avenues for the clinical monitoring and characterization of the disease.

Table 1. Summary of ctDNA detection per liquid type at the patient level based on the 108 evaluated samples. Histo.= Histological, ILC= Invasive lobular carcinoma, NA= not available, nr= number, NST= non-special type

Citation Format: François Richard, Tatjana Geukens, Maxim De Schepper, Amena Mahdami, Karen Van Baelen, Marion Maetens, Ha-Linh Nguyen, Anirudh Pabba, Sophia Leduc, Edoardo Isnaldi, Maysam Hajipirloo, Emily Vanden Berghe, Imane Bachir, Sigrid Hatse, Peter Vermeulen, Evy Vanderheyden, Bram Boeckx, Diether Lambrechts, Ann Smeets, Ines Nevelsteen, Kevin Punie, Patrick Neven, Hans Wildiers, Wouter Van Den Bogaert, Elia Biganzoli, Giuseppe Floris, Christine Desmedt. ctDNA detection in seven different types of body liquids in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-05-06.

Molecular Subtyping Combined with Biological Pathway Analyses to Study Regorafenib Response in Clinically Relevant Mouse Models of Colorectal Cancer

PURPOSE

Regorafenib (REG) is approved for the treatment of metastatic colorectal cancer, but has modest survival benefit and associated toxicities. Robust predictive/early response biomarkers to aid patient stratification are outstanding. We have exploited biological pathway analyses in a patient-derived xenograft (PDX) trial to study REG response mechanisms and elucidate putative biomarkers.

EXPERIMENTAL DESIGN

Molecularly subtyped PDXs were annotated for REG response. Subtyping was based on gene expression (CMS, consensus molecular subtype) and copy-number alteration (CNA). Baseline tumor vascularization, apoptosis, and proliferation signatures were studied to identify predictive biomarkers within subtypes. Phospho-proteomic analysis was used to identify novel classifiers. Supervised RNA sequencing analysis was performed on PDXs that progressed, or did not progress, following REG treatment.

RESULTS

Improved REG response was observed in CMS4, although intra-subtype response was variable. Tumor vascularity did not correlate with outcome. In CMS4 tumors, reduced proliferation and higher sensitivity to apoptosis at baseline correlated with response. Reverse phase protein array (RPPA) analysis revealed 4 phospho-proteomic clusters, one of which was enriched with non-progressor models. A classification decision tree trained on RPPA- and CMS-based assignments discriminated non-progressors from progressors with 92% overall accuracy (97% sensitivity, 67% specificity). Supervised RNA sequencing revealed that higher basal EPHA2 expression is associated with REG resistance.

CONCLUSIONS

Subtype classification systems represent canonical "termini a quo" (starting points) to support REG biomarker identification, and provide a platform to identify resistance mechanisms and novel contexts of vulnerability. Incorporating functional characterization of biological systems may optimize the biomarker identification process for multitargeted kinase inhibitors.