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The Molecular Network, Key Biomarkers, and Therapeutic Targets in Colorectal Cancer

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: 30 July 2025 | Viewed by 70

Special Issue Editor


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Guest Editor
Hiram C. Polk Jr. MD Department of Surgery, University of Louisville, Louisville, KY 40202, USA
Interests: inflammation; metabolism; colorectal cancer; tumor-associated macrophages; intestinal macrophage; obesity, cytokines; necrotizing enterocolitis; preterm infant

Special Issue Information

Dear Colleagues,

Colorectal cancer (CRC) is the third most common cancer worldwide with significantly improved mortality among high-income countries due to national and regional screening programs. Paradoxically, in adults younger than 50 years of age, the incidence of CRC is dramatically increasing, with frequent diagnoses at an advanced tumor stage. While surgical resection is the primary therapy in CRC, patients with advanced-stage tumors only have limited therapeutic options, and new targeted therapies are urgently needed. The pathophysiology of CRC is multifactorial, with most cancers being non-hereditary. They result from a series of somatic mutations acquired over time due to environmental and lifestyle stressors, which are leading to genomic instability. Key biomarkers and novel molecular targets can potentially be identified in signaling pathways that are altered by these stressors. This is crucial to develop novel treatment mechanisms translating into clinical practice to decrease mortality and improve outcomes in advanced CRC, particularly among the young.

Dr. Katharina M. Robertson
Guest Editor

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Keywords

  • inflammation
  • metabolism
  • tumor-associated macrophages
  • tumor microenvironment
  • early-onset colorectal cancer
  • colorectal neoplasms
  • obesity
  • immunotherapy
  • epigenetics
  • cytokines
  • microbiome

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Published Papers (1 paper)

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Research

24 pages, 4048 KiB  
Article
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
by 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, Rania Harati, Kadria Sayed, Ali AlFazari, Riyad Bendardaf and Rifat Hamoudi
Int. J. Mol. Sci. 2025, 26(9), 4194; https://doi.org/10.3390/ijms26094194 - 28 Apr 2025
Viewed by 45
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 [...] Read more.
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 (n = 10), carcinoma in situ (CIS) (n = 8) and adenocarcinoma (n = 11) samples. Using absGSEA, we identified significant cellular pathways and putative molecular biomarkers associated with each stage of CRC progression. Key findings were then validated in a large independent CRC patient cohort (n = 1926), with survival analysis conducted from 1336 patients to assess the prognostic relevance of the candidate biomarkers. The key differentially expressed genes were experimentally validated using real-time PCR (RT-qPCR). Pathway analysis revealed that in CIS, apoptotic processes and Wnt signaling pathways were more prominent than in adenoma samples, while in adenocarcinoma, transcriptional co-regulatory mechanisms and protein kinase activity, which are critical for tumor growth and metastasis, were significantly enriched compared to adenoma. Additionally, extracellular matrix organization pathways were significantly enriched in adenocarcinoma compared to CIS. Distinct gene signatures were identified across CRC stages that differentiate between adenoma, CIS and adenocarcinoma. In adenoma, ARRB1, CTBP1 and CTBP2 were overexpressed, suggesting their involvement in early tumorigenesis, whereas in CIS, RPS3A and COL4A5 were overexpressed, suggesting their involvement in the transition from benign to malignant stage. In adenocarcinoma, COL1A2, CEBPZ, MED10 and PAWR were overexpressed, suggesting their involvement in advanced disease progression. Functional analysis confirmed that ARRB1 and CTBP1/2 were associated with early tumor development, while COL1A2 and CEBPZ were involved in extracellular matrix remodeling and transcriptional regulation, respectively. Experimental validation with RT-qPCR confirmed the differential expression of the candidate biomarkers (ARRB1, RPS3A, COL4A5, COL1A2 and MED10) across the three CRC stages reinforcing their potential as stage-specific biomarkers in CRC progression. These findings provide a foundation to distinguish between the CRC stages and for the development of accurate stage-specific diagnostic and prognostic biomarkers, which helps in the development of more effective therapeutic strategies for CRC. Full article
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