Metastatic melanoma evolution was illustrated through research autopsy and extensive multiomic profiling and revealed the diverse routes to treatment resistance, including extensive copy-number alterations, mutations in key drivers, and extrachromosomal DNA.

Background: The vast majority of cancer deaths can be attributed to tumor metastases. Disseminated tumor cells (DTCs) are thought to act as a reservoir of tumor clones which can lie dormant before causing overt metastases. Their presence has been shown to be a poor prognostic indicator in several tumor types. Despite their importance, the timing and source of DTCs is unclear across most solid cancers and even less is known about them in late-stage disease. The Posthumous Evaluation of the Advanced Cancer Environment (PEACE) post-mortem study enables extensive sampling of malignant lesions but also normal tissues, thereby allowing study of DTCs in patients with advanced cancer. Methods: We performed research autopsy sampling of macroscopically normal bone, lung and liver in 3 patients with advanced clear cell renal cell carcinoma (RCC). In addition, we performed bone marrow aspiration at autopsy from vertebral bodies and the ilium using an anterior approach. Mechanical disaggregation followed by collagenase digestion was used to generate single cell suspensions. Detection of tumor cells was carried out using antibodies against known tumor or epithelial markers carbonic anhydrase IX (CAIX). Epithelial cell adhesion molecule (EpCAM) was also used for bone marrow samples as native bone marrow cells do not express this marker. These sub-populations were then isolated using fluorescence activated cell sorting and DNA was extracted and amplified from single cells. Results: We performed and optimised collagenase-based digestion on all solid tissues collected. The percentage of viable cells generated varied significantly between subjects and tissues with bone marrow samples more viable than lung and liver. Rare and distinct populations of CAIX+ and EpCAM+ cells were detected in normal tissues between 0.5-2%. DNA amplification was successful on single cells isolated from normal lung and liver but not from bone tissue. Pilot shallow coverage whole genome sequencing revealed genomically aberrant cells ranging from single chromosome arm losses to widespread copy number aberrations. Conclusion: We demonstrate feasibility of sequencing single cells from autopsy study subjects. Rare populations of single cells with markers of clear cell RCC were detected and isolated both in normal tissues of patients with advanced disease. Genomic analyses of these cells will lead to insights into their relationship to the primary tumor and overt metastatic lesions. Citation Format: Haixi Yan, Cristina Cotobal Martin, Christie English, Annelien Verfaillie, Jonas Demeulemeester, Andrew Rowan, Annika Fendler, Anne-Laure Cattin, Sucheta Mahapatra, Lewis Au, Scott Shepherd, Ben Shum, Charlotte Spencer, Zayd Tippu, Ula Mahadeva, Anna Green, Eleanor Carlyle, Cristina Naceur-Lombardelli, PEACE consortium, Mariam Jamal-Hanjani, Charles Swanton, Samra Turajlic, Peter Van Loo. Detection of disseminated tumor cells in advanced clear cell renal cell carcinoma through research autopsy [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A011.

Circulating cell-free DNA (ccfDNA) sequencing for low-burden cancer monitoring is limited by sparsity of circulating tumor DNA (ctDNA), the abundance of genomic material within a plasma sample, and pre-analytical error rates due to library preparation, and sequencing errors. Sequencing costs have historically favored the development of deep targeted sequencing approaches for overcoming sparsity in ctDNA detection, but these techniques are limited by the abundance of ccfDNA in samples, which imposes a ceiling on the maximal depth of coverage in targeted panels. Whole genome sequencing (WGS) is an orthogonal approach to ctDNA detection that can overcome the low abundance of ccfDNA by supplanting sequencing depth with breadth, integrating signal across the entire tumor mutation landscape. However, the higher cost of WGS limits the practical depth of coverage and hinders broad adoption. Lower sequencing costs may thus allow for enhanced ctDNA cancer monitoring via WGS. We therefore applied emerging lower-cost WGS (Ultima Genomics, 1USD/Gb) to plasma samples at ∼120x coverage. Copy number and single nucleotide variation profiles were comparable between matched Ultima and Illumina datasets, and the deeper WGS coverage enabled ctDNA detection at the parts per million range. We further harnessed these lower sequencing costs to implement duplex error-corrected sequencing at the scale of the entire genome, demonstrating a ∼1,500x decrease in errors in the plasma of patient-derived xenograft mouse models, and error rates of ∼10−7 in patient plasma samples. We leveraged this highly de-noised plasma WGS to undertake cancer monitoring in the more challenging context of resectable melanoma without matched tumor sequencing. In this context, duplex-corrected WGS allowed us to harness known mutational signature patterns for disease monitoring without matched tumors, paving the way for de novo cancer monitoring.

Squamous cell carcinoma (SCC) is the most common malignant tumour of the penis. The 2022 WHO classification reinforces the 2016 classification and subclassifies precursor lesions and tumours into human papillomavirus (HPV)‐associated and HPV‐independent types.

Introduction Systemic corticosteroids are the mainstay of treatment for immune checkpoint inhibitor induced (CPI) colitis but are associated with complications including life-threatening infection. The topically acting oral corticosteroid beclomethasone dipropionate (BD) is an effective treatment for mild to moderate flares of ulcerative colitis, and has fewer side effects than systemic corticosteroids. We hypothesized that BD would be an effective treatment for CPI-induced colitis. Methods We performed a retrospective analysis of all patients who started BD for CPI-induced colitis at three UK cancer centers between November 2017 and October 2020. All patients underwent endoscopic assessment and biopsy. The initial regimen of BD was 5 mg once daily for 28 days. Data were collected from electronic patient records. Clinical outcomes were assessed at 28 days after initiation of treatment. Results Twenty-two patients (14 male) with a median age of 64 (range 45–84) with CPI-induced colitis were treated with BD. At baseline, the median number of loose stools in a 24-hour period was six (common terminology criteria for adverse events, CTCAE grade diarrhea=2). Thirteen patients (59%) were dependent on systemic corticosteroids prior to starting BD. Baseline sigmoidoscopy showed moderate inflammation (Mayo Endoscopic Score (MES) = 2) in two patients (9%), mild inflammation (MES=1) in nine patients (41%) and normal findings (MES=0) in eleven patients (50%). Twenty patients (91%) had histopathological features of inflammation. All 22 patients (100%) had a clinical response to BD and 21 (95%) achieved clinical remission with a return to baseline stool frequency (CTCAE diarrhea=0). Ten patients (45%) had symptomatic relapse on cessation of BD, half within 7 days of stopping. All patients recaptured response on restarting BD. No adverse events were reported in patients treated with BD. Conclusions Topical BD represents an appealing alternative option to systemic immunosuppressive treatments to treat colonic inflammation. In this study, BD was effective and safe at inducing remission in CPI-induced colitis, which was refractory to systemic corticosteroids. Further randomized studies are needed to confirm these findings and determine the optimum dosing regimen.