GoKawiilHuman subjects
All human samples included in this study were collected with informed consent for research use and received approval from the Institutional Review Boards of Yale University School of Medicine and Washington University School of Medicine, in accordance with the principles of the Declaration of Helsinki (2013). These samples, obtained from a total of 123 human subjects, were divided into four cohorts.
Cohort 1
Intact and dissociated tumour samples were collected from seven patients (four with colon cancer and three with melanoma) at the time of surgery. Each sample underwent bulk RNA sequencing and the dissociated tumour samples also underwent scRNA-seq.
Cohort 2
Matched tumour and plasma cfDNA samples were collected from 23 patients with metastatic melanoma, with matched PBMCs also collected for seven. Tumour samples for each patient were profiled by ST and/or whole-genome EM-seq, depending on availability (Visium, Visium HD and/or EM-seq). A further 23 plasma cfDNA samples were collected from healthy individuals. All PBMC and plasma cfDNA samples were profiled by whole-genome EM-seq. Matched melanoma samples are graphically depicted in Fig. 4d and a full inventory is provided in Supplementary Table 17.
Cohort 3
Plasma samples were collected from 78 patients with melanoma treated at Yale Cancer Center, including seven from cohort 2, who received ICI monotherapy (30 received anti-PD-1 and five received anti-CTLA-4) or combination therapy (43 received anti-PD-1 and anti-CTLA-4). Samples were collected before treatment initiation (before or on the first day of ICI cycle 1) and underwent whole-genome EM-seq. ICI response was classified as either durable clinical benefit or no durable benefit by a board-certified medical oncologist, reflecting each patient’s disease response six months after ICI initiation. Progression-free survival was determined from the start of ICI treatment.
Cohort 4
Plasma samples were collected from ten patients with melanoma treated at Siteman Cancer Center, including eight from cohort 2, who received immune checkpoint inhibitor (ICI) monotherapy (seven received anti-PD-1) or combination therapy (three received anti-PD-1 and anti-CTLA-4). Samples were collected before or during treatment and underwent whole-genome EM-seq. ICI response was classified as described for cohort 3.
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