Evidence map›Paper›PMID 40362431›Full record

ArticleInternational journal of molecular sciences2025

Transcriptome-Wide Analysis and Experimental Validation from FFPE Tissue Identifies Stage-Specific Gene Expression Profiles Differentiating Adenoma, Carcinoma In-Situ and Adenocarcinoma in Colorectal Cancer Progression.

Faisal Alhosani, Reem Sami Alhamidi, Burcu Yener Ilce, Alaa Muayad Altaie, Nival Ali, Alaa Mohamed Hamad, Axel Künstner, Cyrus Khandanpour, Hauke Busch, Basel Al-Ramadi and 5 more

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Article in International journal of molecular sciences, 2025. 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.

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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

15 authors.

Faisal AlhosaniResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.ORCID 0000-0002-3553-7217
Reem Sami AlhamidiResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.ORCID 0009-0006-2893-2872
Burcu Yener IlceResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.ORCID 0009-0009-2068-1089
Alaa Muayad AltaieResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.
Nival AliResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.
Alaa Mohamed HamadCollege of Health Sciences, Abu Dhabi University, Abu Dhabi P.O. Box 59911, United Arab Emirates.
Axel KünstnerMedical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.ORCID 0000-0003-0692-2105
Cyrus KhandanpourDepartment of Hematology and Oncology, University Cancer Center Schleswig-Holstein, University Hospital Schleswig-Holstein, University of Lübeck, 23562 Lübeck, Germany.ORCID 0000-0003-4655-6269
Hauke BuschMedical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.ORCID 0000-0003-4763-4521
Basel Al-RamadiDepartment of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates.ORCID 0000-0002-1657-1938
Rania HaratiResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.ORCID 0000-0001-6672-2944
Kadria SayedDepartment of Pathology and Laboratory Medicine, American Hospital Dubai, Dubai P.O. Box 3050, United Arab Emirates.
Ali AlFazariMediclinic Welcare Hospital, Dubai P.O. Box 31500, United Arab Emirates.
Riyad BendardafOncology Unit, University Hospital Sharjah, Sharjah P.O. Box 72772, United Arab Emirates.
Rifat HamoudiResearch Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates.ORCID 0000-0002-1402-0868

Funding

ASPIRE Precision Medicine Research Institute grant VRI-20-10
6 · The paper itself

Abstract

Colorectal cancer (CRC) progression occurs through three stages: adenoma (pre-cancerous lesion), carcinoma in situ (CIS) and adenocarcinoma, with tumor stage playing a pivotal role in the prognosis and treatment outcomes. Despite therapeutic advancements, the lack of stage-specific biomarkers hinders the development of accurate diagnostic tools and effective therapeutic strategies. This study aims to identify stage-specific gene expression profiles and key molecular mechanisms in CRC providing insights into molecular alterations across disease progression. Our methodological approach integrates the use of absolute gene set enrichment analysis (absGSEA) on formalin-fixed paraffin-embedded (FFPE)-derived transcriptomic data, combined with large-scale clinical validation and experimental confirmation. A comparative whole transcriptomic analysis (RNA-seq) was performed on FFPE samples including adenoma (

Indexed as

AdenocarcinomaAdenomaCarcinoma in SituColorectal NeoplasmsGene Expression ProfilingTranscriptomeAgedBiomarkers, TumorDisease ProgressionFemaleGene Expression Regulation, NeoplasticHumansMaleMiddle AgedNeoplasm StagingParaffin EmbeddingBiomarkers, Tumoradenocarcinomaadenomabiomarker discoverycolorectal cancer (CRC)GSEAtumor immune microenvironment

Identifiers

PMID40362431
PMCPMC12071244

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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.