Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
by
, ,
Susana Iraola-Guzmán
1,2,†, 
Anna Brunet-Vega
3,4,†,
Cinta Pegueroles
1,2,†,
Ester Saus
1,2,
Hrant Hovhannisyan
1,2,
Alex Casalots
5,
Carles Pericay
4 and
Toni Gabaldón
1,2,6,* 1
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
2
Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain
3
Institut d’Investigació i Innovació Parc Taulí I3PT, Parc Taulí Hospital Universitari, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain
4
Oncology Service, Parc Taulí Hospital Universitari, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain
5
Pathology Service, Parc Taulí Hospital Universitari, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain
6
Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work and share first authorship.
Cancers 2020, 12(10), 2844; https://doi.org/10.3390/cancers12102844
Submission received: 24 August 2020
/
Revised: 20 September 2020
/
Accepted: 23 September 2020
/
Published: 1 October 2020
(This article belongs to the Special Issue Switching Off Cancer: Epigenetic Modifiers (miRNA, lncRNA and Methylation) in Cancers)
Simple Summary
Alterations in long noncoding RNAs and their mutations have been increasingly recognized in tumorogenesis and cancer progression awakening especial interest as potential novel cancer biomarkers and therapeutic targets. The use of adjuvant chemotherapy in stage II colorectal cancer patients is challenging, and new biomarkers are required to identify patients with high probability of relapse. We focused on translational potential of non-coding RNAs in colorectal cancer. In this study, we aim to validate a new tool which couples target enrichment and RNAseq for transcriptomics studies of lncRNAs in formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that this new approach efficiently detects lncRNAs and differences in their expression between healthy and tumor FFPE tissues, as well as somatic mutations in expressed lncRNAs, identifying novel lncRNAs as potential candidates for colorectal cancer. This new approach could represent a promising avenue that would reduce costs and enable more efficient translational research.
Abstract
Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.
Keywords:
lncRNAs enrichment; CRC; FFPE samples
