Evidence map›Paper›PMID 36266629›Full record

ArticleClinical proteomics2022

Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma.

Qing Kay Li, Yingwei Hu, Lijun Chen, Michael Schnaubelt, Daniel Cui Zhou, Yize Li, Rita Jui-Hsien Lu, Mathangi Thiagarajan, Galen Hostetter, Chelsea J Newton and 10 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical proteomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 40% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors at 11 institutions in 2 countries.

Qing Kay LiDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA. qli23@jhmi.edu.
Yingwei HuDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA.
Lijun ChenDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA.
Michael SchnaubeltDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA.
Daniel Cui ZhouDepartment of Oncology, Washington University at Saint Louis, St Louis, MO, USA.
Yize LiDepartment of Oncology, Washington University at Saint Louis, St Louis, MO, USA.
Rita Jui-Hsien LuDepartment of Oncology, Washington University at Saint Louis, St Louis, MO, USA.
Mathangi ThiagarajanLeidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Galen HostetterVan Andel Research Institute, Grand Rapids, MI, USA.
Chelsea J NewtonVan Andel Research Institute, Grand Rapids, MI, USA.
Scott D JewellVan Andel Research Institute, Grand Rapids, MI, USA.
Gil OmennDepartment of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Ana I RoblesOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD, USA.
Mehdi MesriOffice of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD, USA.
Oliver F BatheDepartment of Surgery and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
Bing ZhangLester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Li DingDepartment of Oncology, Washington University at Saint Louis, St Louis, MO, USA.
Ralph H HrubanDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA.
Daniel W ChanDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA.
Hui ZhangDepartment of Pathology, the Johns Hopkins University, 400 N Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21231, USA. huizhang@jhu.edu.
Johns Hopkins University · USWashington University in St. Louis · USVan Andel Institute · USSidney Kimmel Cancer Center · USBaylor College of Medicine · USCancer Clinic · USLeidos (United States) · USNational Cancer Institute · USSidney Kimmel Comprehensive Cancer Center · USUniversity of Calgary · CAUniversity of Michigan–Ann Arbor · US

Funding

The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic TargetsU24CA210985 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2016 to 2020
$5.3M
NCI NIH HHS U24 CA210985NCI NIH HHS U24CA210985
6 · The paper itself

Abstract

backgroundThe identification of differentially expressed tumor-associated proteins and genomic alterations driving neoplasia is critical in the development of clinical assays to detect cancers and forms the foundation for understanding cancer biology. One of the challenges in the analysis of pancreatic ductal adenocarcinoma (PDAC) is the low neoplastic cellularity and heterogeneous composition of bulk tumors. To enrich neoplastic cells from bulk tumor tissue, coring, and laser microdissection (LMD) sampling techniques have been employed. In this study, we assessed the protein and KRAS mutation changes associated with samples obtained by these enrichment techniques and evaluated the fraction of neoplastic cells in PDAC for proteomic and genomic analyses.

methodsThree fresh frozen PDAC tumors and their tumor-matched normal adjacent tissues (NATs) were obtained from three sampling techniques using bulk, coring, and LMD; and analyzed by TMT-based quantitative proteomics. The protein profiles and characterizations of differentially expressed proteins in three sampling groups were determined. These three PDACs and samples of five additional PDACs obtained by the same three sampling techniques were also subjected to genomic analysis to characterize KRAS mutations.

resultsThe neoplastic cellularity of eight PDACs ranged from less than 10% to over 80% based on morphological review. Distinctive proteomic patterns and abundances of certain tumor-associated proteins were revealed when comparing the tumors and NATs by different sampling techniques. Coring and bulk tissues had comparable proteome profiles, while LMD samples had the most distinct proteome composition compared to bulk tissues. Further genomic analysis of bulk, cored, or LMD samples demonstrated that KRAS mutations were significantly enriched in LMD samples while coring was less effective in enriching for KRAS mutations when bulk tissues contained a relatively low neoplastic cellularity.

conclusionsIn addition to bulk tissues, samples from LMD and coring techniques can be used for proteogenomic studies. The greatest enrichment of neoplastic cellularity is obtained with the LMD technique.

Indexed as

Bulk tissueClinical Proteomic Tumor Analysis Consortium (CPTAC)Laser microdissection (LMD)Liquid chromatography–mass spectrometryTissue coringTissue sampling techniquesTMT-labeling

Identifiers

PMID36266629
PMCPMC9583468
OpenAlexW4306874557

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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.