Aberrant Splicings Due to Microsatellite Instability in Colorectal Cancer : Physiopathological and Clinical Impact

NCT03447431 | Unknown

• 1 other identifier: NI14027
• Study Type: observational
• Target: 350
• Locations: 1 country
• Sites: 1

Brief Summary

MSI (Microsatellite Instability) colorectal cancer (CRC) show improved survival, are less prone to metastasis and show poor response to chemotherapy (compared to MSS tumors). The underlying reasons for these characteristics are still not understood and no specific therapeutic approach for MSI colon tumours (15% of CRC overall) has yet been developed. The MSI process is oncogenic when it affects DNA repeat sequences that have a functional role, e.g. Small Coding Repeats (SCR). MSI also frequently affects Long Non-Coding Repeats (LNCR) in tumour DNA. In contrast to SCR, only a few LNCR are endowed with biological activity. Consequently, this area has received very little attention. Our group recently identified HSP110 mutant chaperone protein in MSI CRC that was generated by somatic deletion of a LNCR. Of interest, HSP110 mutant (due to exon skipping) have anti-oncogenic properties and the survival of MSI CRC patients receiving chemotherapy is positively associated with HSP110 mutations in tumour DNA. The aim of the current project is to identify additional clinically relevant MSI-associated splicing aberrations due to mutations in LNCR located in splice acceptor sites. The four main steps are as follows:

1. 1.To identify exon/intron sites affected by aberrant splicing events due to MSI in CRC . All RNASeq data will be exploited to identify recurrent splicing aberrations (mostly exon skipping) that occur specifically in MSI colon tumours;
2. 2.To investigate for possible functional links between MSI and any detected aberrant splicing events . All specific aberrant splicing events detected by RNAseq in MSI CRC samples will be first confirmed (quantitative RT-PCR) in order to eliminate false positive cases. For validated exon candidates, the allelic profiles of adjacent intronic LNCR will be analysed (PCR and fluorescence genotyping) in CRC cell lines and primary tumours (MSI and MSS), as well as in matching normal mucosa samples in order to assess their polymorphic status;
3. 3.To identify splicing events and LNCR mutations with clinical relevance in MSI CRC patients . All LNCR with a confirmed role in gene splicing in MSI CRC will be analysed. The clinical relevance of candidate genes will be assessed using multivariate survival regression models for Relapse- Free Survival, with interaction terms (response to chemotherapy);
4. 4.To initiate functional studies on a limited number of clinically relevant, cancer-related genes whose splicing is perturbed in MSI cancer cells, and to develop biological tools to simplify screening in future clinical assays Similar to HSP110, we will focus on 4 or 5 mutant proteins that are promising drug therapeutic targets. Functional assays will be developed to further elucidate their role in the pathophysiology of MSI tumours. We also aim to develop biological tools for these candidate genes, such as the detection of wild-type or mutant proteins by immunohistochemistry.

Conditions

Colorectal Cancer; Microsatellite Instability

Keywords

colorectal cancers; Microsatellite Instability; Tumor development

Outcome Measures

Primary Outcomes (5)

• To identify exon/intron junctions that are specifically affected by aberrant splicing events in MSI CRC

  All RNASeq data will be exploited to identify recurrent splicing aberrations (mostly exon skipping) that occur specifically in MSI colon tumours compared to MSS CRCs and matching normal colonic mucosa.

  3 years

• To investigate for functional links between MSI and aberrant splicing events.

  All specific aberrant splicing events detected by RNAseq in MSI CRC samples will be first confirmed (quantitative RT-PCR) in order to eliminate false positive cases. For validated exon candidates, the allelic profiles of adjacent intronic LNCR will be analysed (PCR and fluorescence genotyping) in CRC cell lines and primary tumours (MSI and MSS), as well as in matching normal mucosa samples in order to assess their polymorphic status.

  3 years

• To identify splicing events and/or LNCR mutations with clinical relevance in MSI CRC patients.

  All LNCR with a confirmed role in gene splicing in MSI CRC will be analysed. The clinical relevance of candidate genes will be assessed using multivariate survival regression models for Relapse- Free Survival, with interaction terms (response to chemotherapy);

  3 years

• To initiate functional studies on a limited number of clinically relevant, cancer related genes whose splicing is highly perturbed in MSI cancer cells

  We will focus on 4 or 5 mutant proteins that are promising drug therapeutic targets. Functional assays will be developed to further elucidate their role in the pathophysiology of MSI tumours.

  3 years

• To develop biological tools to simplify screening in future clinical assays

  We aim to develop biological tools for these candidate genes, such as the detection of wild-type or mutant proteins by immunohistochemistry.

  3 years

Study Arms (1)

MSI colon tumours

MSI colon tumours (as compared to MSS CRCs and matching normal colonic mucosa) Identification of exon/intron sites affected by aberrant splicing events due to MSI in CRC

Eligibility Criteria

• Sex: all
• Healthy Volunteers: No
• Age Groups: Child (0-17), Adult (18-64), Older Adult (65+)
• Sampling Method: Non-Probability Sample

Study Population

MSI colon tumours

You may qualify if:

• All patients presenting a MSI CRC (second or third state, histologically confirmed) who have been operated at Saint Antoine Hospital between 1998 and 2013
• Clinical data of patients follow-up available on site
• non-opposition for tumour samples using from patient obtained

You may not qualify if:

• non-opposition for tumour samples using from patient not obtained

Sponsors & Collaborators

• Assistance Publique - Hôpitaux de Paris: lead
• Institut National de la Santé Et de la Recherche Médicale, France: collaborator

Study Sites (1)

Service d'Anatomie et de Cytologie Pathologique

Paris, 75012, France

RECRUITING

MeSH Terms

Conditions

Colorectal Neoplasms; Microsatellite Instability

Condition Hierarchy (Ancestors)

Intestinal Neoplasms; Gastrointestinal Neoplasms; Digestive System Neoplasms; Neoplasms by Site; Neoplasms; Digestive System Diseases; Gastrointestinal Diseases; Colonic Diseases; Intestinal Diseases; Rectal Diseases; Genomic Instability; Pathologic Processes; Pathological Conditions, Signs and Symptoms

Central Study Contacts

Jean-François FLÉJOU, PU-PH

CONTACT

0149283012; jean-francois.flejou@sat.aphp.fr

Alex DUVAL

CONTACT

0149286680; alex.duval@inserm.fr

Study Design

• Study Type: observational
• Observational Model: COHORT
• Time Perspective: RETROSPECTIVE
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: October 24, 2017
• First Posted: February 27, 2018
• Study Start: April 5, 2018
• Primary Completion: February 1, 2021
• Study Completion: February 1, 2021
• Last Updated: July 2, 2019

Record last verified: 2019-06

Locations

FR (1)