Evidence map›Paper›PMID 28073359›Full record

ArticleRespiratory research2017

Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples.

Andre Koper, Leo A H Zeef, Leena Joseph, Keith Kerr, John Gosney, Mark A Lindsay, Richard Booton

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

Article in Respiratory research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.3field-weighted citation impact, top 47% 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

4 citing papers in PubMed, 6 citations in OpenAlex.

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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

7 authors at 5 institutions in 2 countries.

Andre KoperQiagen GmbH, Hilden, 40724, Germany.
Leo A H ZeefFaculty of Life Science, University of Manchester, Manchester, England, M13 9PT, UK.
Leena JosephDepartment of Pathology, University Hospital of South Manchester, Manchester, England, M23 9LT, UK.
Keith KerrDepartment of Pathology, University of Aberdeen, Aberdeen, Scotland, AB25 2ZD, UK.
John GosneyDepartment of Pathology, Royal Liverpool University Hospital, Liverpool, England, L7 8XP, UK.
Mark A LindsayDepartment of Pharmacy and Pharmacology, University of Bath, Bath, England, BA 7AY, UK.
Richard BootonManchester Thoracic Oncology Centre, University Hospital of South Manchester, Manchester, England, M23 9LT, UK. richard.booton@uhsm.nhs.uk.
University of Manchester · GBQiagen (Germany) · DEUniversity of Aberdeen · GBUniversity of Bath · GBUniversity of Liverpool · GB

Funding

Wellcome Trust 097820/Z/11/B
6 · The paper itself

Abstract

backgroundPreinvasive squamous cell cancer (PSCC) are local transformations of bronchial epithelia that are frequently observed in current or former smokers. Their different grades and sizes suggest a continuum of dysplastic change with increasing severity, which may culminate in invasive squamous cell carcinoma (ISCC). As a consequence of the difficulty in isolating cancerous cells from biopsies, the molecular pathology that underlies their histological variability remains largely unknown.

methodTo address this issue, we have employed microdissection to isolate normal bronchial epithelia and cancerous cells from low- and high-grade PSCC and ISCC, from paraffin embedded (FFPE) biopsies and determined gene expression using Affymetric Human Exon 1.0 ST arrays. Tests for differential gene expression were performed using the Bioconductor package limma followed by functional analyses of differentially expressed genes in IPA.

resultsExamination of differential gene expression showed small differences between low- and high-grade PSCC but substantial changes between PSCC and ISCC samples (184 vs 1200 p-value <0.05, fc ±1.75). However, the majority of the differentially expressed PSCC genes (142 genes: 77%) were shared with those in ISCC samples. Pathway analysis showed that these shared genes are associated with DNA damage response, DNA/RNA metabolism and inflammation as major biological themes. Cluster analysis identified 12 distinct patterns of gene expression including progressive up or down-regulation across PSCC and ISCC. Pathway analysis of incrementally up-regulated genes revealed again significant enrichment of terms related to DNA damage response, DNA/RNA metabolism, inflammation, survival and proliferation. Altered expression of selected genes was confirmed using RT-PCR, as well as immunohistochemistry in an independent set of 45 ISCCs.

conclusionsGene expression profiles in PSCC and ISCC differ greatly in terms of numbers of genes with altered transcriptional activity. However, altered gene expression in PSCC affects canonical pathways and cellular and biological processes, such as inflammation and DNA damage response, which are highly consistent with hallmarks of cancer.

Indexed as

TranscriptomeAgedCarcinoma, Squamous CellCells, CulturedFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansLaser Capture MicrodissectionLung NeoplasmsMaleMiddle AgedNeoplasm InvasivenessNeoplasm ProteinsTranscription FactorsTumor Cells, CulturedNeoplasm ProteinsTranscription FactorsExon arraysGene expression profilingInvasive squamous cell cancerMicrodissectionPreinvasive squamous cell cancer

Identifiers

PMID28073359
PMCPMC5223343
OpenAlexW2571031112

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.