Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models

Abstract

Purpose Patients with cancer who graciously consent for autopsy represent an invaluable resource for the study of cancer biology. To advance the study of tumor evolution, metastases, and resistance to treatment, we developed a next-generation rapid autopsy program integrated within a broader precision medicine clinical trial that interrogates pre- and postmortem tissue samples for patients of all ages and cancer types. Materials and Methods One hundred twenty-three (22%) of 554 patients who consented to the clinical trial also consented for rapid autopsy. This report comprises the first 15 autopsies, including patients with metastatic carcinoma (n = 10), melanoma (n = 1), and glioma (n = 4). Whole-exome sequencing (WES) was performed on frozen autopsy tumor samples from multiple anatomic sites and on non-neoplastic tissue. RNA sequencing (RNA-Seq) was performed on a subset of frozen samples. Tissue was also used for the development of preclinical models, including tumor organoids and patient-derived xenografts. Results Three hundred forty-six frozen samples were procured in total. WES was performed on 113 samples and RNA-Seq on 72 samples. Successful cell strain, tumor organoid, and/or patient-derived xenograft development was achieved in four samples, including an inoperable pediatric glioma. WES data were used to assess clonal evolution and molecular heterogeneity of tumors in individual patients. Mutational profiles of primary tumors and metastases yielded candidate mediators of metastatic spread and organotropism including CUL9 and PIGM in metastatic ependymoma and ANKRD52 in metastatic melanoma to the lung. RNA-Seq data identified novel gene fusion candidates. Conclusion A next-generation sequencing–based autopsy program in conjunction with a pre-mortem precision medicine pipeline for diverse tumors affords a valuable window into clonal evolution, metastasis, and alterations underlying treatment. Moreover, such an autopsy program yields robust preclinical models of disease.

Rapid research autopsy is a stealthy but growing contributor to cancer research

“…Currently, the number of rapid autopsy programs (RAPs) in the United States is relatively small, and a few Cancer September 1, 2019 additional programs have been established in Canada, Australia, and, very recently, Europe. Some of these programs are focused on just 1 tumor type (eg, prostate cancer 9 ), whereas others accept a greater variety of patients. These programs may be directed by pathologists (usually), oncologists (frequently), or other researchers (occasionally), although pathologist involvement is always important for a properly executed autopsy procedure and for the selection of the best quality tissue for sampling.…”

“…Finally, different and often unique tissue samples for multiple researchers/research projects may be collected during a single case. 9,10 Parallel specimens may be collected for the comparison of gross and microscopic pathology and for the molecular analysis of tumor clones. 11,12…”

Cytology techniques for minimally invasive molecular autopsies: An opportunity not to be missed

“…As a matter of fact, next‐generation sequencing studies have shown that molecular profiles of primary tumors differ from those of their metastases, with the acquisition and loss of mutations that may confer more aggressive behavior, and therefore these profiles may lead to the development of specific therapeutic strategies . Following this rationale, a recent study described successful results with whole‐exome sequencing of postmortem samples from multiple metastatic sites obtained from a series of 15 rapid autopsies, with a time from death to the collection of material of up to 18 hours . Tumor tissue collected from these autopsies was even found to be suitable for cell cultures and RNA sequencing, with the identification of novel candidate biomarkers involved in the progression of tumors such as melanomas and ependymomas …”

“…Following this rationale, a recent study described successful results with whole‐exome sequencing of postmortem samples from multiple metastatic sites obtained from a series of 15 rapid autopsies, with a time from death to the collection of material of up to 18 hours . Tumor tissue collected from these autopsies was even found to be suitable for cell cultures and RNA sequencing, with the identification of novel candidate biomarkers involved in the progression of tumors such as melanomas and ependymomas …”

“…Autolysis, nucleic acid degradation, and the production of bacterial DNases and RNases are undoubtedly associated with the time elapsed from death until the actual sampling of fluids/tissue . However, the implementation of rapid autopsy programs is not always straightforward because they are subjected to complex hospital networks and infrastructure . Other issues that might potentially hamper the wider implementation of molecular diagnosis using postmortem samples include the requirement for the validation of such novel technologies for autopsy material and factors already associated with the decreased rates of autopsies worldwide, such as the need for additional consent from the family for genetic testing and the potential to reveal conditions that might prompt medical litigation.…”