Abnormal ERV Expression and Its Clinical Relevance in Colon Cancer
Abstract
1. Introduction
2. Materials and Methods
2.1. Manually Compiled ERV Set
2.2. RNA-Seq Data
2.3. RNA-Seq Data Pre-Processing and Analysis
2.4. ERV-Defined Tumor Subtypes and Their Association with Clinical and Other Molecular Phenotypes
2.5. ERV Expression Association with Patient Survival
3. Results
3.1. Comparable ERV Expression Measurement in CRC Cell Lines Between Total RNA rRNA Depleted- and Poly a-Enriched RNA-Seq Data
3.2. Low Number and Expression of ERVs in Normal Cells Compared to CRC Cells
3.3. Most ERVs Are Overexpressed in Primary Tumor Tissue Samples Compared to Their Paired Normal Colon Samples
3.4. ERV Expression-Defined “Subtypes” of COAD Are Associated with Immunogenic Scores and Tumor Mutation Burden
3.5. Individual ERVs Associated with Disease Specific Survival
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ERVs | Human endogenous retroviruses |
COAD/CRC | Colon adenocarcinoma/colorectal carcinoma |
TCGA | The Cancer Genome Atlas |
DSS | Disease-specific survival |
GEO | Gene expression omnibus |
IIS | Immune infiltration score |
APM | Antigen processing and presenting machinery |
TMB | Tumor mutation burden |
RPKM | Reads per kilobase of transcript per million mapped reads |
GO | Gene ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
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ERV | DSS HR | Surv Pval | DE log2FC | DE Pval | DE Padj | DE Direction |
---|---|---|---|---|---|---|
chr14:73702885–73716167 | 1.63 | 2.31 × 10−2 | −1.11 | 3.18 × 10−7 | 4.82 × 10−6 | Down |
chr19:56494761–56501703 | 1.44 | 1.36 × 10−2 | −1.83 | 1.79 × 10−11 | 8.44 × 10−10 | Down |
chr17:43872266–43876352 | 1.43 | 1.55 × 10−2 | −2.34 | 1.00 × 10−15 | 1.08 × 10−13 | Down |
chr19:38935163–38941835 | 1.41 | 1.05 × 10−2 | −1.12 | 6.47 × 10−6 | 6.43 × 10−5 | Down |
chr12:76291617–76300850 | 1.31 | 1.87 × 10−2 | 2.00 | 1.82 × 10−6 | 2.12 × 10−5 | Up |
chr19:36323747–36332422 | 1.25 | 4.85 × 10−2 | −1.08 | 1.16 × 10−6 | 1.49 × 10−5 | Down |
chr16:86739328–86747655 | 1.19 | 3.98 × 10−2 | 3.34 | 2.06 × 10−17 | 3.59 × 10−15 | Up |
chr6:144923391–144932448 | 1.14 | 4.54 × 10−2 | 2.92 | 8.27 × 10−11 | 3.30 × 10−9 | Up |
chr7:4590929–4600359 | 1.11 | 9.14 × 10−3 | 1.33 | 3.19 × 10−3 | 1.16 × 10−2 | Up |
chr15:51357586–51367580 | 1.10 | 2.55 × 10−2 | −1.04 | 1.01 × 10−2 | 3.01 × 10−2 | Down |
chr2:64886311–64899831 | 1.10 | 2.55 × 10−2 | −1.18 | 1.30 × 10−3 | 5.55 × 10−3 | Down |
chr4:179720511–179728321 | 1.09 | 1.92 × 10−2 | 1.84 | 7.08 × 10−4 | 3.36 × 10−3 | Up |
chr6:118574055–118578291 | 1.09 | 6.39 × 10−3 | −1.31 | 4.95 × 10−4 | 2.49 × 10−3 | Down |
chr8:12037971–12041523 | 1.09 | 1.60 × 10−2 | 1.66 | 4.30 × 10−3 | 1.47 × 10−2 | Up |
chr1:247898555–247905892 | 1.08 | 2.17 × 10−2 | −2.42 | 6.05 × 10−6 | 6.12 × 10−5 | Down |
chr11:23882492–23892875 | 1.08 | 3.05 × 10−2 | 2.80 | 7.56 × 10−6 | 7.30 × 10−5 | Up |
chr12:38123075–38131103 | 1.08 | 3.44 × 10−2 | 3.21 | 1.14 × 10−6 | 1.47 × 10−5 | Up |
chr19:54894290–54900597 | 1.08 | 2.55 × 10−2 | 2.26 | 3.24 × 10−4 | 1.74 × 10−3 | Up |
chr21:38224030–38229830 | 1.08 | 4.06 × 10−2 | 4.42 | 3.08 × 10−10 | 1.06 × 10−8 | Up |
chr4:4130683–4133908 | 1.08 | 1.19 × 10−2 | −1.56 | 3.73 × 10−3 | 1.32 × 10−2 | Down |
chr6:123556843–123562657 | 1.08 | 2.29 × 10−2 | −3.46 | 4.42 × 10−12 | 2.46 × 10−10 | Down |
chr6:123582329–123588017 | 1.08 | 3.02 × 10−2 | 1.65 | 7.54 × 10−3 | 2.36 × 10−2 | Up |
chr4:11653551–11659272 | 1.07 | 3.66 × 10−2 | 3.81 | 1.21 × 10−7 | 2.05 × 10−6 | Up |
chr8:11931841–11936717 | 1.07 | 2.34 × 10−2 | 1.60 | 1.30 × 10−3 | 5.55 × 10−3 | Up |
chrX:77077094–77086082 | 1.07 | 4.51 × 10−2 | −1.26 | 5.94 × 10−3 | 1.95 × 10−2 | Down |
chrY:8994259–9004253 | 1.07 | 4.17 × 10−2 | 3.56 | 1.29 × 10−5 | 1.14 × 10−4 | Up |
chr11:89381303–89387559 | 1.06 | 3.61 × 10−2 | 2.13 | 4.48 × 10−4 | 2.26 × 10−3 | Up |
chr12:4018995–4025863 | 0.93 | 1.13 × 10−2 | 2.13 | 3.79 × 10−5 | 2.87 × 10−4 | Up |
chr8:60493460–60499925 | 0.93 | 2.21 × 10−2 | 1.48 | 1.84 × 10−3 | 7.30 × 10−3 | Up |
chr18:51112855–51117176 | 0.92 | 2.42 × 10−2 | 3.46 | 5.00 × 10−8 | 9.42 × 10−7 | Up |
chr4:23722376–23727827 | 0.92 | 2.25 × 10−2 | −2.38 | 1.00 × 10−9 | 3.07 × 10−8 | Down |
chr5:34461058–34468430 | 0.92 | 1.89 × 10−2 | 2.05 | 1.34 × 10−6 | 1.65 × 10−5 | Up |
chrX:151550923–151562615 | 0.92 | 1.34 × 10−2 | 3.17 | 1.32 × 10−8 | 2.91 × 10−7 | Up |
chr8:7402289–7408615 | 0.92 | 3.54 × 10−2 | 1.51 | 1.36 × 10−2 | 3.84 × 10−2 | Up |
chr20:25394210–25403221 | 0.91 | 6.26 × 10−3 | 1.22 | 8.64 × 10−3 | 2.66 × 10−2 | Up |
chr6:137717275–137724946 | 0.91 | 5.27 × 10−3 | 3.14 | 1.20 × 10−10 | 4.65 × 10−9 | Up |
chr14:103234947–103242530 | 0.91 | 2.92 × 10−2 | 1.54 | 6.25 × 10−5 | 4.41 × 10−4 | Up |
chrX:97841727–97849389 | 0.91 | 1.71 × 10−2 | −1.43 | 1.78 × 10−3 | 7.10 × 10−3 | Down |
chr9:64870612–64878934 | 0.90 | 1.98 × 10−2 | 3.24 | 1.45 × 10−9 | 4.26 × 10−8 | Up |
chr11:58996950–59006462 | 0.90 | 8.61 × 10−3 | 1.31 | 5.78 × 10−4 | 2.82 × 10−3 | Up |
chr4:115950630–115956482 | 0.90 | 3.20 × 10−2 | −1.72 | 2.70 × 10−3 | 1.01 × 10−2 | Down |
chr6:63321317–63335844 | 0.90 | 1.23 × 10−3 | −2.48 | 5.14 × 10−10 | 1.67 × 10−8 | Down |
chr4:77630582–77637015 | 0.90 | 3.47 × 10−2 | 2.62 | 1.47 × 10−9 | 4.28 × 10−8 | Up |
chr4:58458021–58466147 | 0.89 | 2.10 × 10−2 | 1.81 | 3.38 × 10−3 | 1.22 × 10−2 | Up |
chr9:29775512–29780684 | 0.89 | 4.75 × 10−2 | 1.77 | 2.88 × 10−3 | 1.06 × 10−2 | Up |
chr22:30676787–30679926 | 0.84 | 1.49 × 10−4 | 1.37 | 4.00 × 10−6 | 4.26 × 10−5 | Up |
chr3:11247257–11254838 | 0.82 | 4.36 × 10−3 | −1.00 | 4.07 × 10−5 | 3.03 × 10−4 | Down |
chr11:17370179–17379293 | 0.68 | 1.46 × 10−2 | 1.07 | 7.14 × 10−6 | 6.97 × 10−5 | Up |
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Bhagwate, A.; Taylor, W.; Kisiel, J.; Sun, Z. Abnormal ERV Expression and Its Clinical Relevance in Colon Cancer. Genes 2025, 16, 988. https://doi.org/10.3390/genes16080988
Bhagwate A, Taylor W, Kisiel J, Sun Z. Abnormal ERV Expression and Its Clinical Relevance in Colon Cancer. Genes. 2025; 16(8):988. https://doi.org/10.3390/genes16080988
Chicago/Turabian StyleBhagwate, Aditya, William Taylor, John Kisiel, and Zhifu Sun. 2025. "Abnormal ERV Expression and Its Clinical Relevance in Colon Cancer" Genes 16, no. 8: 988. https://doi.org/10.3390/genes16080988
APA StyleBhagwate, A., Taylor, W., Kisiel, J., & Sun, Z. (2025). Abnormal ERV Expression and Its Clinical Relevance in Colon Cancer. Genes, 16(8), 988. https://doi.org/10.3390/genes16080988