Abstract
Recent advancements in probe-based, full-transcriptome, high-resolution technologies for Formalin-Fixed Paraffin-Embedded (FFPE) tissues, such as Visium CytAssist, Chromium Flex (10X Genomics), and GeoMx DSP (Nanostring), have opened new opportunities for studying decades-old archival samples in biobanks, facilitating the generation of data from extensive cohorts. However, the experimental protocols can be labor-intensive and costly; therefore, it is thus essential for researchers to carefully evaluate the strengths and limitations of each technology in relation to their specific research objectives.
Here, we report the results of a comparative analysis of the three methods mentioned above on FFPE archival tumor samples from four non-small cell lung cancer, four breast cancer and six diffuse large B-cell lymphoma. We highlight some relative advantages and disadvantages of each method in the context of operational challenges, bioinformatic analysis and biological discovery. Our results show that: 1) all three methods yielded good-quality, highly reproducible transcriptomic data from serial sections of the same FFPE block; 2) GeoMx data contained mixtures of cell types, even when pre-selecting areas with cell type-specific markers; 3) high-throughput spot-level (Visium) or cell-level (Chromium) data enabled the identification of tumor heterogeneity within and between patients, which could be used to identify targeted therapies.
Our data support the use of Visium and Chromium for high-throughput and discovery-driven projects, while the GeoMx platform could be suited for addressing specialized questions on targeted regions. All data generated from this study, including GeoMx, Visium, Chromium, H&E, and expert annotations are publicly available.
Competing Interest Statement
R.G. has received consulting income from Takeda, Arcellx and Sanofi, and declares ownership in Ozette Technologies. S.P. has received educational grants, provided consultation, attended advisory boards, and/or delivered lectures for the following organizations, from which S.P. has received honoraria (all fees directed to their institution): AbbVie, Amgen, Arcus, AstraZeneca, Bayer, Beigene, BioNTech, BerGenBio, Bicycle Therapeutics, Biocartis, BioInvent, Blueprint Medicines, Boehringer Ingelheim, Bristol-Myers Squibb, Clovis, Daiichi Sankyo, Debiopharm, Eli Lilly, F-Star, Foundation Medicine, Genmab, Genzyme, Gilead, GSK, Hutchmed, Illumina, Incyte, Ipsen, iTeos, Janssen, Qlucore, Merck Sharp and Dohme, Merck Serono, Merrimack, Mirati, Nuvation Bio, Nykode Therapeutics, Novartis, Novocure, Pharma Mar, Promontory Therapeutics, Pfizer, Regeneron, Roche/Genentech, Sanofi, Seattle Genetics, Takeda, and Zymeworks. S.P. has spoken at company-organized public events for AstraZeneca, Boehringer Ingelheim, Bristol-Myers Squibb, Eli Lilly, Foundation Medicine, GSK, Illumina, Ipsen, Merck Sharp and Dohme, Mirati, Novartis, Pfizer, Roche/Genentech, Sanofi, Seattle Genetics, and Takeda. Additionally, S.P. has served as a principal investigator for trials sponsored by Amgen, Arcus, AstraZeneca, Beigene, Bristol-Myers Squibb, Eli Lilly, GSK, iTeos, Merck Sharp and Dohme, Mirati, Pharma Mar, Promontory Therapeutics, Roche/Genentech, and Seattle Genetics, with institutional financial support for these clinical trials. G.C. has received honoraria from Bristol-Myers Squibb. The Lausanne University Hospital (CHUV) has received honoraria for advisory services G.C. has provided to Iovance and EVIR. GC has received royalties from the University of Pennsylvania for CAR T cell therapy licensed to Novartis and Tmunity Therapeutics, and from the Ludwig Institute for Cancer Research, the University of Lausanne and the CHUV, for NeoTIL intellectual property previously licensed to Tigen Pharma. S.R.T is also affiliated with CHUV. C.H. is an Owkin Employee; Consultant for Nanobiotix. E.M., A.E.P., Q.B., S.C., E.Y.D., R.S., K.v.L., R.D., C.H., S.L.L., A.K., and V.S. are Owkin employees.
