Morphological characterization of colorectal cancers in The Cancer Genome Atlas reveals distinct morphology–molecular associations: clinical and biological implications
Open accessAbstract
The Cancer Genome Atlas data on colorectal carcinoma have provided a comprehensive view of the tumor's genomic alterations and their tumorigenic roles. Tumor morphology, however, has not been fully integrated into the analysis. The aim of this study was to explore relevant associations between tumor morphology and the newly characterized genomic alterations in colorectal carcinoma. Two hundred and seven colorectal carcinomas that had undergone whole-exome sequencing as part of The Cancer Genome Atlas project and had adequate virtual images in the cBioPortal for Cancer Genomics constituted our study population. Upon analysis, a tight association between 'microsatellite instability-high histology' and microsatellite instability-high (P<0.001) was readily detected and helped validate our image-based histology evaluation. Further, we showed, (1) among all histologies, the not otherwise specified type had the lowest overall mutation count (P<0.001 for entire cohort, P<0.03 for the microsatellite-instable group), and among the microsatellite-instable tumors, this type also correlated with fewer frameshift mutations in coding mononucleotide repeats of a defined set of relevant genes (P<0.01); (2) cytosine phosphate guanine island methylator phenotype-high colorectal cancers with or without microsatellite instability tended to have different histological patterns: the former more often mucinous and the latter more often not otherwise specified; (3) mucinous histology was associated with more frequent alterations in BRAF, PIK3CA, and the transforming growth factor-β pathway when compared with non-mucinous histologies (P<0.001, P=0.01, and P<0.001, respectively); and (4) few colorectal cancers (<9%) exhibited upregulation of immune-inhibitory genes including major immune checkpoints; these tumors were primarily microsatellite-instable (up to 43%, vs <3% in microsatellite-stable group) and had distinctly non-mucinous histologies with a solid growth. These morphology-molecular associations are interesting and propose important clinical implications. The morphological patterns associated with alterations of immune checkpoint genes bear the potential to guide patient selection for clinical trials that target immune checkpoints in colorectal cancer, and provide directions for future studies.
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Such a histopathological pattern is frequently observed in MSI tumors.
“Such a histopathological pattern is frequently observed in MSI tumors50.”
From Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer (2025) · cites this paper as [50]
Mucinous tumor tissue has been linked to KRAS mutational burden.
“which has also been linked to KRAS mutational burden50,56.”
From Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer (2025) · cites this paper as [50]
In many cases, highly scoring patches had a histological phenotype known to be associated with BRAF mutational status or MSI/dMMR, such as mucinous histology and/or poor differentiation.
“Qualitatively, we found that in many cases there was a histological phenotype known to be associated with either BRAF mutational status or MSI/ dMMR, such as mucinous histology and/or poor differentiation 30,31 .”
From Swarm learning for decentralized artificial intelligence in cancer histopathology (2022) · cites this paper as [30]
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- Authors
- Shia, J., Schultz, N., Kuk, D., Vakiani, E., Middha, S., Segal, N. H., Hechtman, J. F., Berger, M. F., Stadler, Z. K., Weiser, M. R., Wolchok, J. D., Boland, C. R., Gönen, M., & Klimstra, D. S.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Baylor University Medical Center (US)
- Corresponding author
- Shia, Jinru
- ORCID
- Venue
- Modern Pathology
- Publisher
- Elsevier BV
- Published
- 2017-04
- Volume
- 30
- Issue
- 4
- Pages
- 599-609
- ISSN
- 0893-3952 (ISSN-L)
- PMC
- PMC5380525
- OpenAlex
- W2565789802
- Cited by
- 105
- References
- 33
- Citations by year
- 2026: 4 · 2025: 11 · 2024: 15 · 2023: 11 · 2022: 16 · 2021: 12 · 2020: 17 · 2019: 6 · 2018: 10 · 2017: 3
- FWCI
- 5.76
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Modern Pathology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (P30CA008748)
- Topics
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Oncology › Colorectal Cancer Treatments and Studies
- Keywords
- colorectal cancer, tumor morphology, histology, microsatellite instability, CpG island methylator phenotype, mucinous histology, frameshift mutation, BRAF, PIK3CA, TGF-beta signaling, immune checkpoint genes, tumor immune microenvironment, TCGA
- MeSH terms
- Carcinoma, Humans, Colorectal Neoplasms, Transforming Growth Factor beta, DNA Methylation, Proto-Oncogene Proteins B-raf, Microsatellite Instability, Class I Phosphatidylinositol 3-Kinases
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