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Proteogenomic analysis reveals a compendium of therapeutic targets for treatment-resistant subtypes of locally advanced cervical cancers

ABSTRACT: Proteogenomic analysis reveals a compendium of therapeutic targets for treatment-resistant subtypes of locally advanced cervical cancers

PROVIDER: PRJNA1175711 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31065000.fastq.gz	Fastqsanger.gz
	SRR31065001.fastq.gz	Fastqsanger.gz
	SRR31065002.fastq.gz	Fastqsanger.gz
	SRR31065003.fastq.gz	Fastqsanger.gz
	SRR31065004.fastq.gz	Fastqsanger.gz

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Project description:Purpose: We aimed to investigate the distinct transcriptional landscape in the poor responders to concurrent chemoradiotherapy (CCRT) and to gain mechanistic insights on treatment resistance in cervical cancer. Methods: RNA sequencing was performed using archived pre-treatment tissue biopsies of patients with locally advanced cervical cancer treated with concurrent platinum-based CCRT. Transcriptome data of patients with no durable benefit (NDB; progression-free period < 3 years) and durable clinical benefit (DCB; progression-free period > 5 years) after were compared. NDB score was estimated for each patient using the differentially expressed genes between NDB and DCB patients. Three independent cohorts, including The Cancer Genome Atlas cervical cancer (TCGA-CESC) cohort, were utilized for validation of NDB score. Potential response to PD-1 blockade was estimated with Tumor Immune Dysfunction and Exclusion (TIDE) score and T-cell-inflamed gene expression profile (GEP). Results: Patients with NDB exhibited a distinct transcriptional profile compared to those with DCB such as higher signatures of extracellular matrix organization and epithelial-to-mesenchymal transition. The fraction of cancer-associated fibroblasts (CAFs) within the tumor was significantly higher in NDB than DCB patients. Higher NDB score was significantly associated with poor survival in the TCGA-CESC cohort (n = 274; P = 0.015), but only in patients that received curative aim radiotherapy (P = 0.002) and not in patients who received other treatments (P = 0.57). The transcriptomic characteristics of patients with NDB were recapitulated in patients with high NDB score in TCGA-CESC. Patients with high NDB score displayed significantly higher TIDE prediction score and lower T-cell-inflamed GEP score compared to patients with low NDB scores. Conclusion: Cervical cancer patients with poor treatment outcome following CCRT exhibited a distinct gene signature that was able to predict treatment outcomes. For poor responders, immune checkpoint inhibitors may be less effective and CAF-targeting treatments may be a promising approach.

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Proteogenomic analysis reveals a compendium of therapeutic targets for treatment-resistant subtypes of locally advanced cervical cancers

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