Transcriptomic analysis-guided assessment of precision-cut tumor slices (PCTS) as an ex-vivo tool in cancer research

Our plain-English summary of Transcriptomic analysis-guided assessment of precision-cut tumor slices (PCTS) as an ex-vivo tool in cancer research, by S. Trivedi, C. Tilsed, M. Liousia, et al (Scientific Reports, 2024).

The study

• Authors: S. Trivedi, C. Tilsed, M. Liousia, R.M. Brody, K. Rajasekaran, S. Singhal, S.M. Albelda, A. Klampatsa
• Journal: Scientific Reports
• Published: 2024;14(1):11006
• Cited by: 10 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

With cancer immunotherapy and precision medicine dynamically evolving, there is greater need for pre-clinical models that can better replicate the intact tumor and its complex tumor microenvironment (TME). Precision-cut tumor slices (PCTS) have recently emerged as an ex vivo human tumor model, offering the opportunity to study individual patient responses to targeted therapies, including immunotherapies. However, little is known about the physiologic status of PCTS and how culture conditions alter gene expression. In this study, we generated PCTS from head and neck cancers (HNC) and mesothelioma tumors (Meso) and undertook transcriptomic analyses to understand the changes that occur in the timeframe between PCTS generation and up to 72 h (hrs) in culture. Our findings showed major changes occurring during the first 24 h culture period of PCTS, involving genes related to wound healing, extracellular matrix, hypoxia, and IFNγ-dependent pathways in both tumor types, as well as tumor-specific changes. Collectively, our data provides an insight into PCTS physiology, which should be taken into consideration when designing PCTS studies, especially in the context of immunology and immunotherapy.

© 2024. The Author(s).

In plain English

This laboratory study looked at precision-cut tumor slices, which are thin slices cut from fresh human tumors removed at surgery and kept alive in culture. The authors made slices from three head and neck cancers and three mesotheliomas. They measured gene activity in slices fixed straight away and in slices kept 24 hours in culture, and in some tumors also at 48 and 72 hours. The study did not examine asbestos or any cause of disease. Under the microscope, the slices kept their structure for 72 hours with no visible necrosis. Even so, hundreds of genes changed in the first 24 hours, with more going down than up. Genes linked to hypoxia (low oxygen), myeloid-attracting chemokines, IL-6 and IL-11 rose. Genes for T cell-attracting chemokines, HLA Class II molecules and endothelial cells fell. In the mesothelioma slices, most tumor-related genes fell. The largest changes came in the first 24 hours, after which levels tended to plateau. The authors noted that the study used few tumors and two tumor types. They concluded that these baseline changes need careful consideration when designing such experiments.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory (ex vivo) study: gene-expression (transcriptomic) analysis of tumor slices, comparing freshly fixed slices with slices from the same tumor after culture
• Who was studied: Surplus surgically removed tumor tissue from 3 head and neck cancer (HNC) patients and 3 mesothelioma (Meso) patients, collected under University of Pennsylvania (Penn) IRB protocols. Later time points (48 and 72 h) were available for 4 tumors (3 Meso, 1 HNC). Dates are not given.
• Exposure: No asbestos or other fiber exposure was studied. The condition examined was slicing (300 μm slices) and culture in DMEM/F12 medium with 10% FBS and 1% penicillin/streptomycin for up to 72 hours. About 19,398 genes were measured.
• Main results:
  • In both HNC and Meso slices, tumor structure was preserved through 72 hours of culture without visible necrosis.
  • Between fresh and 24-hour slices, hundreds of genes changed, with more genes going down than up.
  • In the 24-hour slices, all myeloid cell-attracting chemokine genes examined were higher, among the largest increases seen. The fold increases were higher in Meso than HNC slices.
  • The lymphocyte-attracting chemokine genes CXCL9, CXCL10 and CCL5 showed large, statistically significant decreases at 24 hours. The decreases were greater in HNC than Meso slices.
  • The cytokine genes IL-6 and IL-11 showed large and significant increases at 24 hours. IL-1A, IL-1B and IL-33 increased, but the increases did not reach statistical significance.
  • HLA Class II genes and the transcription factors that regulate them were consistently and strongly downregulated, more so in HNC than Meso slices. HLA Class I genes showed no significant changes.
  • Hypoxia-related genes showed large and mostly significant increases at 24 hours, apart from NFE2L2. The response was generally greater in Meso slices.
  • Most endothelial cell genes went down in the 24-hour slices, with changes that were significant or near significant.
  • In the Meso slices, most tumor-related genes went down at 24 hours, which the authors interpreted as suggesting some loss of tumor cells. In HNC slices, the tumor genes changed little.
  • Some changes went in opposite directions in the two tumor types. For example, COL7A1 decreased significantly in HNC but increased significantly in Meso.
  • In the 4 tumors with later time points, the largest changes occurred between fresh and 24-hour slices. Levels then tended to plateau, and were most stable between 24 and 48 hours.
• The authors' conclusion: The authors concluded that tumor slices undergo multiple gene-expression changes after slicing and during early culture, and that these changes can differ by tumor type and by patient. They wrote that these baseline changes need careful consideration, and suggested that experiments might best be studied 24 hours after slicing.
• Limitations the authors state:
  • Only two tumor types were studied, and each showed its own specific changes.
  • Data came from a small number of tumors, without multiple biological replicates at all time points, which gave the study relatively low statistical power.
  • Only gene expression (mRNA) was measured. The findings were not checked at the protein level, and mRNA and protein levels may not correlate.

Topics

Medical terms in this study, explained in our Lexicon: Immunotherapy, Tumor Microenvironment, Mesothelioma, Hypoxia.

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