Evidence map›Paper›PMID 38773080›Full record

ArticleNature communications2024

Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci.

Christos Miliotis, Yuling Ma, Xanthi-Lida Katopodi, Dimitra Karagkouni, Eleni Kanata, Kaia Mattioli, Nikolas Kalavros, Yered H Pita-Juárez, Felipe Batalini, Varune R Ramnarine and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2024. 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
–field-weighted citation impact
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.

  1. Review
  2. Article
  3. Article
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

13 authors.

Christos MiliotisHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Yuling MaHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Xanthi-Lida KatopodiHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-8555-777X
Dimitra KaragkouniHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Eleni KanataHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0009-2828-2226
Kaia MattioliHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Nikolas KalavrosHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-5503-9808
Yered H Pita-JuárezHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6992-252X
Felipe BataliniHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3354-308X
Varune R RamnarineHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-6948-2744
Shivani NandaHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6358-2392
Frank J SlackHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. fslack@bidmc.harvard.edu.ORCID http://orcid.org/0000-0001-8263-0409
Ioannis S VlachosHarvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. ivlachos@bidmc.harvard.edu.ORCID http://orcid.org/0000-0002-8849-808X

Funding

Precision microRNA medicine in cancerR35CA232105 · NCI · BETH ISRAEL DEACONESS MEDICAL CENTER · PI SLACK, FRANK J. · 2019 to 2025
$7.2M
Pan-Cancer characterization of 3’UTR somatic mutations controlling tumor immune evasionR01CA258776 · NCI · BETH ISRAEL DEACONESS MEDICAL CENTER · PI Ioannis Vlachos · 2022 to 2026
$2.9M
NCI NIH HHS R01 CA258776NCI NIH HHS R35 CA232105U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA258776U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R35CA232105
6 · The paper itself

Abstract

The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3' untranslated region (3'-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3'-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3'-UTR eQTLs in immune-related genes. Our approach identifies numerous 3'-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.

Indexed as

3' Untranslated RegionsQuantitative Trait LociStomach NeoplasmsTumor EscapeB7-H1 AntigenFemaleGene Expression Regulation, NeoplasticHumansImmunotherapyMaleMutation3' Untranslated RegionsB7-H1 AntigenCD274 protein, human

Identifiers

PMID38773080
PMCPMC11109163

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Registered trials

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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.