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Golkaram M, Salmans ML, Kaplan S, Vijayaraghavan R, Martins M, Khan N, Garbutt C, Wise A, Yao J, Casimiro S, Abreu C, Macedo D, Costa AL, Alvim C, Mansinho A, Filipe P, Marques da Costa P, Fernandes A, Borralho P, Ferreira C, Aldeia F, Malaquias J, Godsey J, So A, Pawlowski T, Costa L, Zhang S, Liu L. HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome. NPJ Genom Med 2021; 6:13. [PMID: 33589643 PMCID: PMC7884730 DOI: 10.1038/s41525-021-00177-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/12/2021] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal malignancies. The extreme heterogeneity in survival rate is driving the need for new prognostic biomarkers. Human endogenous retroviruses (hERVs) have been suggested to influence tumor progression, oncogenesis and elicit an immune response. We examined multiple next-generation sequencing (NGS)-derived biomarkers in 114 CRC patients with paired whole-exome and whole-transcriptome sequencing (WES and WTS, respectively). First, we demonstrate that the median expression of hERVs can serve as a potential biomarker for prognosis, relapse, and resistance to chemotherapy in stage II and III CRC. We show that hERV expression and CD8+ tumor-infiltrating T-lymphocytes (TILs) synergistically stratify overall and relapse-free survival (OS and RFS): the median OS of the CD8-/hERV+ subgroup was 29.8 months compared with 37.5 months for other subgroups (HR = 4.4, log-rank P < 0.001). Combing NGS-based biomarkers (hERV/CD8 status) with clinicopathological factors provided a better prediction of patient survival compared to clinicopathological factors alone. Moreover, we explored the association between genomic and transcriptomic features of tumors with high hERV expression and establish this subtype as distinct from previously described consensus molecular subtypes of CRC. Overall, our results underscore a previously unknown role for hERVs in leading to a more aggressive subtype of CRC.
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Affiliation(s)
| | | | | | | | - Marta Martins
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | | | | | | | - Sandra Casimiro
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina Abreu
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Daniela Macedo
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Ana Lúcia Costa
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Cecília Alvim
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - André Mansinho
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Pedro Filipe
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Pedro Marques da Costa
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal.,Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Afonso Fernandes
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Borralho
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Cristina Ferreira
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Fernando Aldeia
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - João Malaquias
- Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | | | - Alex So
- Illumina Inc., San Diego, CA, USA
| | | | - Luis Costa
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal.
| | | | - Li Liu
- Illumina Inc., San Diego, CA, USA.
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