Evidence map›Paper›PMID 39673574›Full record

ArticleJournal of cancer research and clinical oncology2024

Identification of a distinctive immunogenomic gene signature in stage-matched colorectal cancer.

Pankaj Ahluwalia, Ashis K Mondal, Ashutosh Vashisht, Harmanpreet Singh, Ahmet Alptekin, Kalyani Ballur, Nivin Omar, Meenakshi Ahluwalia, Kimya Jones, Amanda Barrett and 2 more

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Article in Journal of cancer research and clinical oncology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Pankaj AhluwaliaDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Ashis K MondalDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Ashutosh VashishtDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Harmanpreet SinghDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Ahmet AlptekinDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Kalyani BallurDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Nivin OmarDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Meenakshi AhluwaliaGeorgia Cancer Center at Augusta University, Augusta, GA, 30912, USA.
Kimya JonesDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Amanda BarrettDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA.
Vamsi KotaGeorgia Cancer Center at Augusta University, Augusta, GA, 30912, USA.
Ravindra KolheDepartment of Pathology, Medical College of Georgia at Augusta University, 1120 15th Street, Augusta, GA, 30912, BF-207, USA. rkolhe@augusta.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundColorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Despite advances in diagnosis and treatment, including surgery, chemotherapy, and immunotherapy, accurate clinical markers are still lacking. The development of prognostic and predictive indicators, particularly in the context of personalized medicine, could significantly improve CRC patient management.

methodIn this retrospective study, we used FFPE blocks of tissue samples from CRC patients at Augusta University (AU) to quantify a custom 15-gene panel. To differentiate the tumor and adjacent normal regions (NAT), H&E staining was utilized. For the quantification of transcripts, we used the NanoString nCounter platform. Kaplan-Meier and Log-rank tests were used to perform survival analyses. Several independent datasets were explored to validate the gene signature. Orthogonal analyses included single-cell profiling, differential gene expression, immune cell deconvolution, neoantigen prediction, and biological pathway assessment.

resultsA 3-gene signature (GTF3A, PKM, and VEGFA) was found to be associated with overall survival in the AU cohort (HR = 2.26, 95% CI 1.05-4.84, p = 0.02, 93 patients), TCGA cohort (HR = 1.57, 95% CI 1.05-2.35, p < 0.02, 435 patients) and four other GEO datasets. Independent single-cell analysis identified relatively higher expression of the 3-gene signature in the tumor region. Differential analysis revealed dysregulated tissue inflammation, immune dysfunction, and neoantigen load of cell cycle processes among high-risk patients compared to low-risk patients.

conclusionWe developed a 3-gene signature with the potential for prognostic and predictive clinical assessment of CRC patients. This gene-based stratification offers a cost-effective approach to personalized cancer management. Further research using similar methods could identify therapy-specific gene signatures to strengthen the development of personalized medicine for CRC patients.

Indexed as

Biomarkers, TumorColorectal NeoplasmsAgedFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMaleMiddle AgedNeoplasm StagingPrognosisRetrospective StudiesTranscriptomeBiomarkers, TumorColonColorectal cancerGene signatureImmune infiltrationImmunotherapy responsivenessPersonalized medicinePrecision medicinePrognostic genesStratified medicine

Identifiers

PMID39673574
PMCPMC11646222

What Socratic holds

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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 Socratic graph.