Evidence map›Paper›PMID 34900135›Full record

ArticleComputational and structural biotechnology journal2021

Analysis of the immune landscape in virus-induced cancers using a novel integrative mechanism discovery approach.

Lindsay M Wong, Wei Tse Li, Neil Shende, Joseph C Tsai, Jiayan Ma, Jaideep Chakladar, Aditi Gnanasekar, Yuanhao Qu, Kypros Dereschuk, Jessica Wang-Rodriguez and 1 more

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

Article in Computational and structural biotechnology journal, 2021. 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
0.2field-weighted citation impact, top 46% 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, 3 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

11 authors at 1 institution in 1 country.

Lindsay M WongDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Wei Tse LiDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Neil ShendeDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Joseph C TsaiDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Jiayan MaDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Jaideep ChakladarDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Aditi GnanasekarDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Yuanhao QuDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Kypros DereschukDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
Jessica Wang-RodriguezDepartment of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
Weg M OngkekoDepartment of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA.
University of California San Diego · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe mechanisms of carcinogenesis from viral infections are extraordinarily complex and not well understood. Traditional methods of analyzing RNA-sequencing data may not be sufficient for unraveling complicated interactions between viruses and host cells. Using RNA and DNA-sequencing data from The Cancer Genome Atlas (TCGA), we aim to explore whether virus-induced tumors exhibit similar immune-associated (IA) dysregulations using a new algorithm we developed that focuses on the most important biological mechanisms involved in virus-induced cancers. Differential expression, survival correlation, and clinical variable correlations were used to identify the most clinically relevant IA genes dysregulated in 5 virus-induced cancers (HPV-induced head and neck squamous cell carcinoma, HPV-induced cervical cancer, EBV-induced stomach cancer, HBV-induced liver cancer, and HCV-induced liver cancer) after which a mechanistic approach was adopted to identify pathways implicated in IA gene dysregulation.

resultsOur results revealed that IA dysregulations vary with the cancer type and the virus type, but cytokine signaling pathways are dysregulated in all virus-induced cancers. Furthermore, we also found that important similarities exist between all 5 virus-induced cancers in dysregulated clinically relevant oncogenic signatures and IA pathways. Finally, we also discovered potential mechanisms for genomic alterations to induce IA gene dysregulations using our algorithm.

conclusionsOur study offers a new approach to mechanism identification through integrating functional annotations and large-scale sequencing data, which may be invaluable to the discovery of new immunotherapy targets for virus-induced cancers.

Indexed as

AlgorithmC2, Canonical pathwayC6, Oncogenic signatureC7, Immunological signatureCA, Cancer-associatedCervical squamous cell carcinoma and endocervical adenocarcinomaCESC, Cervical Squamous Cell Carcinoma and Endocervical AdenocarcinomaCNA, Copy number alterationEBV, Epstein-Barr virusEpstein-Barr virusFDR, False discovery rateGSEA, Gene set enrichment analysisHBV, Hepatitis B virusHCV, Hepatitis C virusHead and neck squamous cell carcinomaHepatitis BHepatitis CHNSCC, Head and Neck Squamous Cell CarcinomaHPV, Human papillomavirusHuman papillomavirusIA, Immune-associatedLIHC, Liver Hepatocellular CarcinomaLiver hepatocellular carcinomaMSigDB, Molecular Signature DatabaseSTAD, Stomach AdenocarcinomaStomach adenocarcinomaTCGATCGA, The Cancer Genome Atlas

Identifiers

PMID34900135
PMCPMC8636736
OpenAlexW3215600888

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.