Evidence map›Paper›PMID 35088383›Full record

ArticleJournal of endocrinological investigation2022

Transcriptome-guided resolution of tumor microenvironment interactions in pheochromocytoma and paraganglioma subtypes.

S Batchu, A Hakim, O S Henry, J Madzo, U Atabek, F R Spitz, Y K Hong

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Article in Journal of endocrinological investigation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
1.1field-weighted citation impact, top 24% 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

7 citing papers in PubMed, 12 citations in OpenAlex.

  1. Review
  2. [Advance in HIF expression and immune microenvironment in pseudohypoxic HNPGL].Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery · 2024
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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 3 institutions in 1 country.

S BatchuCooper Medical School at Rowan University, 401 Broadway, Camden, NJ, 08103, USA. batchu94@rowan.edu.ORCID http://orcid.org/0000-0003-1531-9682
A HakimDepartment of Surgery, Cooper University Hospital, Camden, NJ, USA.
O S HenryCooper Medical School at Rowan University, 401 Broadway, Camden, NJ, 08103, USA.
J MadzoCoriell Institute, Camden, NJ, USA.
U AtabekDepartment of Surgery, Cooper University Hospital, Camden, NJ, USA.
F R SpitzDepartment of Surgery, Cooper University Hospital, Camden, NJ, USA.
Y K HongDepartment of Surgery, Cooper University Hospital, Camden, NJ, USA.
Cooper University Hospital · USCooper Medical School of Rowan University · USCoriell Institute For Medical Research · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundPheochromocytomas and paragangliomas (PCPG) are rare catecholamine-secreting endocrine tumors deriving from chromaffin cells of the embryonic neural crest. Although distinct molecular PCPG subtypes have been elucidated, certain characteristics of these tumors have yet to be fully examined, namely the tumor microenvironment (TME). To further understand tumor-stromal interactions in PCPG subtypes, the present study deconvoluted bulk tumor gene expression to examine ligand-receptor interactions.

methodsRNA-sequencing data primary solid PCPG tumors were derived from The Cancer Genome Atlas (TCGA). Tumor purity was estimated using two robust algorithms. The tumor purity estimates and bulk tumor expression values allowed for non-negative linear regression to predict the average expression of each gene in the stromal and tumor compartments for each PCPG molecular subtype. The predicted expression values were then used in conjunction with a previously curated ligand-receptor database and scoring system to evaluate top ligand-receptor interactions.

resultsAcross all PCPG subtypes compared to normal samples, tumor-to-tumor signaling between bone morphogenic proteins 7 (BMP7) and 15 (BMP15) and cognate receptors ACVR2B and BMPR1B was increased. In addition, tumor-to-stroma signaling was enriched for interactions between predicted tumor-originating delta-like ligand 3 (DLL3) and predicted stromal NOTCH receptors. Stroma-to-tumor signaling was enriched for interactions between ephrins A1 and A4 with ephrin receptors EphA5, EphA7, and EphA8. Pseudohypoxia subtype tumors displayed increased predicted stromal expression of genes related to immune-exhausted T-cell response, including those for inhibitory receptors HAVCR2 and CTLA4.

conclusionThe current exploratory study predicted stromal and tumor through compartmental deconvolution and yielded previously unrecognized interactions and putative biomarkers in PCPG.

Indexed as

Adrenal Gland NeoplasmsParagangliomaPheochromocytomaBiomarkers, TumorHumansIntracellular Signaling Peptides and ProteinsLigandsMembrane ProteinsTranscriptomeTumor MicroenvironmentBiomarkers, TumorDLL3 protein, humanIntracellular Signaling Peptides and ProteinsLigandsMembrane ProteinsLigand–receptor interactionsParagangliomaPheochromocytomaPseudohypoxiaRNA deconvolutionTumor microenvironment

Identifiers

PMID35088383
OpenAlexW4210497016

What OpenQuestion holds

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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.