Evidence map›Paper›PMID 41550505›Full record

ArticleBiochemistry and biophysics reports2026

Comparative spatial whole transcriptome analysis of matched frozen and formalin-fixed paraffin-embedded colorectal cancer tissues.

Kullanist Thanormjit, Thanawat Suwatthanarak, Tantip Arigul, Amphun Chaiboonchoe, Onchira Acharayothin, Piroon Jenjaroenpun, Vitoon Chinswangwatanakul, Pariyada Tanjak

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In one paragraph

Article in Biochemistry and biophysics reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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0cells of the map it votes in
1citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

8 authors.

Kullanist ThanormjitSiriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Thanawat SuwatthanarakSiriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Tantip ArigulDivision of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Amphun ChaiboonchoeSiriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Onchira AcharayothinDepartment of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Piroon JenjaroenpunDivision of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Vitoon ChinswangwatanakulSiriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
Pariyada TanjakSiriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Spatial transcriptomic technology enables resolving a tumor microenvironment heterogeneity of colorectal cancer (CRC) tissue samples. However, there is limited evidence regarding the relative strengths and weaknesses of different CRC sample types and preservation methods, including formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF) and snap frozen (SF). Here, we examine gene expression profiles in 36 tissue areas, FFPE, FF and SF samples, derived from a patient with stage IV CRC, using spatial analysis of the whole transcriptome. The tissue samples obtained from surgical resection of the cancer were subjected to a detailed histological evaluation and spatial transcriptomics analysis to compare the quality of the sample between different preservation methods. Spatial transcriptomic analysis demonstrated that FFPE tissue samples offered improved resolution of cellular morphology in the tumor microenvironment, facilitating greater detail of gene expression and cell types. In contrast, gene expression analysis of FF and SF tissues embedded in optimal cutting temperature compound revealed a high level of CRC gene expression. FFPE, FF and SF samples shared a significant overlap among the top 300 genes that were strongly associated with key biological processes in CRC. In summary, the spatial analysis of the whole transcriptome across FFPE, FF and SF CRC tissues revealed intratumoral heterogeneity and highlighted key transcriptomic signatures, suggesting the specific value of different tissue preservation methods in the profiling of CRC.

Indexed as

Colorectal cancerFormalin-fixed paraffin-embeddedFresh frozenSnap frozenSpatial whole transcriptomics

Identifiers

PMID41550505
PMCPMC12808533

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.