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Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma
Open accessAbstract
Pancreatic ductal adenocarcinoma (PDAC) remains a lethal disease with a 5-year survival rate of 4%. A key hallmark of PDAC is extensive stromal involvement, which makes capturing precise tumor-specific molecular information difficult. Here we have overcome this problem by applying blind source separation to a diverse collection of PDAC gene expression microarray data, including data from primary tumor, metastatic and normal samples. By digitally separating tumor, stromal and normal gene expression, we have identified and validated two tumor subtypes, including a 'basal-like' subtype that has worse outcome and is molecularly similar to basal tumors in bladder and breast cancers. Furthermore, we define 'normal' and 'activated' stromal subtypes, which are independently prognostic. Our results provide new insights into the molecular composition of PDAC, which may be used to tailor therapies or provide decision support in a clinical setting where the choice and timing of therapies are critical.
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“Moffit and colleagues devised a “virtual dissection strategy” to computationally subtract the transcriptional background imposed by stromal and immune cells from bulk-RNA sequencing signatures131. Using this approach, they identified two subtypes of PDAC tumors, termed “classical” and “basal-like”, in addition to two stromal subtypes termed “normal stroma” and “activated stroma”.”
From Pancreatic cancer: Advances and challenges (2023) · cites this paper as [131]
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“The dichotomous Moffitt classification schema of “basal-like” and “classical” subtypes was initially established using bulk RNA sequencing strategies applied to human tumor samples (Moffitt 2015)36.”
From Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution (2022) · cites this paper as Moffitt 2015
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“The dichotomous Moffitt classification schema of “basal-like” and “classical” subtypes was initially established using bulk RNA sequencing strategies applied to human tumor samples (Moffitt 2015)36.”
From Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution (2022) · cites this paper as [36]
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Metadata
- Authors
- Moffitt, R. A., Marayati, R., Flate, E. L., Volmar, K. E., Loeza, S. G. H., Hoadley, K. A., Rashid, N. U., Williams, L. A., Eaton, S. C., Chung, A. H., Smyla, J. K., Anderson, J. M., Kim, H. J., Bentrem, D. J., Talamonti, M. S., Iacobuzio-Donahue, C. A., Hollingsworth, M. A., & Yeh, J. J.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- University of Nebraska–Lincoln (US)
- Northwestern University (US)
- Corresponding author
- Yeh, Jen Jen
- ORCID
- Venue
- Nature Genetics
- Published
- 2015-09-07
- Volume
- 47
- Issue
- 10
- Pages
- 1168-1178
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4912058
- OpenAlex
- W1497915798
- Cited by
- 2,194
- References
- 63
- Citations by year
- 2026: 227 · 2025: 237 · 2024: 236 · 2023: 252 · 2022: 256 · 2021: 298 · 2020: 223 · 2019: 168 · 2018: 124 · 2017: 96 · 2016: 65 · 2015: 9
- FWCI
- 42.80
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (T32CA009156, R01CA140424, P30CA060553)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30-DK034897, P30DK034987)
- National Institute of Environmental Health Sciences (P30ES010126)
- Topics
- Health Sciences › Medicine › Oncology › Pancreatic and Hepatic Oncology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Breast Cancer Treatment Studies
- Keywords
- pancreatic ductal adenocarcinoma, tumor stroma, tumor subtypes, gene expression signatures, blind source separation, basal-like subtype, prognostic subtypes, metastatic pancreatic cancer, molecular classification
- MeSH terms
- Adenocarcinoma, Animals, Female, Humans, Male, Pancreatic Neoplasms, Gene Expression, Stromal Cells, Genetic Heterogeneity, Carcinoma, Pancreatic Ductal, Heterografts
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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