Transcriptional Framework for the Molecular Diagnosis of Response to Immunotherapy in Lung Cancer With Agnostic Potential

Recruiting

• Conditions: NSCLC

• Registration Number: NCT06807307
• Lead Sponsor: Regina Elena Cancer Institute

Brief Summary

Through genomic and transcriptomic sequencing techniques (whole exome sequencing, WES; whole transcriptome sequencing, WTS) patients with enrichment for KEAPness and specific gene interactions associated with it.

Detailed Description

Retrospective-prospective, non-pharmacological, biological, multicenter observational study, for which the collection and use of tissue samples from patients suffering from NSCLC and/or other tumor types. Through genomic and transcriptomic sequencing techniques (whole exome sequencing, WES; whole transcriptome sequencing, WTS) patients with enrichment for KEAPness and specific gene interactions associated with it. Subsequently, through the same techniques, applied to different tumor regions taken from operating site it will be possible to identify the evolution of the tumor at a spatio-temporal level and the immune subtype associated with the presence/absence of KEAPness. Finally, cell lines will be used to recapitulate what was observed in the patient and per-patient cohorts identify new pharmacological vulnerabilities associated with the characteristics of KEAPness.

Study Timeline

• Study Start: 2024-06-04
• Status Verified: 2025-01
• Study First Submitted: 2025-01-29
• Study First Submitted QC: 2025-01-29
• Last Update Submitted: 2025-01-29
• Study First Posted: 2025-02-04
• Last Update Posted: 2025-02-04
• Primary Completion: 2026-06-04
• Study Completion: 2026-06-04

Recruitment & Eligibility

• Status: RECRUITING
• Sex: All
• Target Recruitment: 256

Inclusion Criteria

Not provided

Exclusion Criteria

Not provided

Study & Design

• Study Type: OBSERVATIONAL
• Study Design: Not specified

Primary Outcome Measures

Name	Time	Method
Innovative molecular tool	24 months	To generate an innovative molecular tool for prediction DNA/RNA will be extracted from 5μm FFPE tissue sections using the AllPrep DNA/RNA FFPE kit (Qiagen). The quality of the RNA will be evaluated with the Bioanalyzer, the integrity of genomic DNA through the Agilent NGS FFPE qPCR QC Kit (Agilent). The libraries for RNA-Seq will be prepared using the RNA TruSeq Exome Kit (Illumina). The quality of the libraries resulting will be checked using Bioanalyzer (high sensitivity DNA kit). The intermediate library before exon enrichment will be quantified with Qubit, the final library with qPCR. The samples will be sequenced in paired-end mode, sequencing 76 bp on each side. The Exome DNA sequencing will be performed using SureSelectXT Low Input Kit reagents for the initial preparation of the library followed by enrichment with Clinical Research Exome Kit (Agilent).

Secondary Outcome Measures

Name	Time	Method
Tracing the evolutionary path	24 months	Tracing the evolutionary path of NRF-2 dependent tumors, in his association with the microenvironment, and in particular the related immune subtypes, and characterize the interactions between pairs of genes (epistatic) underlying the KEAPness.i phenotype, the multi-region sequencing technology that will be used involves the use of surgical samples, taken in a single session. This allows you to isolate different regions of the tumor, corresponding to different time points (central region, R1; expansion zone, R2; locoregional metastases, R3).; Through this methodology it is possible to trace the evolution of the tumor over time, and in particular the interactions between pairs of mutant genes linked to the KEAPness phenotype.
Identification of therapeutic vulnerabilities specific	24 months	Identification of therapeutic vulnerabilities specific to biological processes related to KEAPness. Cell lines derived from patients affected by NSCLC and GC, already available in the laboratories of Promoter/IFO, will initially be characterized by genomic sequencing and transcriptomic (WES and WTS) to identify the enrichment in the KEAPness phenotype and previously identified epistatic interactions.

Trial Locations

Locations (1)

IRCCS National Cancer Institute "Regina Elena"; 🇮🇹 Rome, Italy