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. 2017 May 24;9(1):46.
doi: 10.1186/s13073-017-0434-0.

Multilevel genomics of colorectal cancers with microsatellite instability-clinical impact of JAK1 mutations and consensus molecular subtype 1

Anita Sveen  1   2   3   4 , Bjarne Johannessen  1   2   3   4 , Torstein Tengs  1   2   3   4 , Stine A Danielsen  1   2   3   4 , Ina A Eilertsen  1   2   4 , Guro E Lind  1   2   4 , Kaja C G Berg  1   2   4 , Edward Leithe  1   2   4 , Leonardo A Meza-Zepeda  3   5   6 , Enric Domingo  7 , Ola Myklebost  3   5 , David Kerr  8 , Ian Tomlinson  7 , Arild Nesbakken  2   3   4   9 , Rolf I Skotheim  1   2   3   4 , Ragnhild A Lothe  10   11   12   13
Affiliations

Multilevel genomics of colorectal cancers with microsatellite instability-clinical impact of JAK1 mutations and consensus molecular subtype 1

Anita Sveen et al. Genome Med. .

Abstract

Background: Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations-the microsatellite instability (MSI) phenotype. We investigated molecular heterogeneity and tumor immunogenicity in relation to clinical endpoints within this distinct subtype of colorectal cancers.

Methods: A total of 333 primary MSI+ colorectal tumors from multiple cohorts were analyzed by multilevel genomics and computational modeling-including mutation profiling, clonality modeling, and neoantigen prediction in a subset of the tumors, as well as gene expression profiling for consensus molecular subtypes (CMS) and immune cell infiltration.

Results: Novel, frequent frameshift mutations in four cancer-critical genes were identified by deep exome sequencing, including in CRTC1, BCL9, JAK1, and PTCH1. JAK1 loss-of-function mutations were validated with an overall frequency of 20% in Norwegian and British patients, and mutated tumors had up-regulation of transcriptional signatures associated with resistance to anti-PD-1 treatment. Clonality analyses revealed a high level of intra-tumor heterogeneity; however, this was not associated with disease progression. Among the MSI+ tumors, the total mutation load correlated with the number of predicted neoantigens (P = 4 × 10-5), but not with immune cell infiltration-this was dependent on the CMS class; MSI+ tumors in CMS1 were highly immunogenic compared to MSI+ tumors in CMS2-4. Both JAK1 mutations and CMS1 were favorable prognostic factors (hazard ratios 0.2 [0.05-0.9] and 0.4 [0.2-0.9], respectively, P = 0.03 and 0.02).

Conclusions: Multilevel genomic analyses of MSI+ colorectal cancer revealed molecular heterogeneity with clinical relevance, including tumor immunogenicity and a favorable patient outcome associated with JAK1 mutations and the transcriptomic subgroup CMS1, emphasizing the potential for prognostic stratification of this clinically important subtype. See related research highlight by Samstein and Chan 10.1186/s13073-017-0438-9.

Keywords: Colorectal cancer; Consensus molecular subtypes; Immunogenicity; Immunotherapy resistance; JAK1; Microsatellite instability; Mutation; Neoantigen; Prognosis.

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Figures

Fig. 1
Fig. 1
Patient samples and data analyses. a A total of 333 MSI+ CRCs were analyzed, including 192 in-house tumor samples and publicly available data from 141 patients; 248 were analyzed for gene mutations and 213 for gene expression. Among the 68 samples in Norwegian series I analyzed for JAK1 mutations by PCR-based analysis, 33 were exome sequenced, 27 were analyzed for DNA copy number aberrations, and 63 were analyzed for gene expression. b Molecular result parameters are shown in red, clinical endpoints in green, and the data types used for analysis in grey. Significant associations are indicated by red arrows and the red cross indicates no association
Fig. 2
Fig. 2
Somatic exonic mutation profiles of 33 MSI+ CRCs. a The total number of amino acid-changing mutations per tumor ranged from 957 to 4614 (median 1676). The tumors are sorted by mutation load. b The MSI score, calculated as the percentage of somatically unstable microsatellites in the exome of each tumor (microsatellites with indels), was more strongly associated with the number of indels than substitutions (Spearman correlations 0.7 and 0.4, respectively). c MLH1 promoter hypermethylation and BRAF V600E mutations were found in 28 (85%) and 21 (64%) of the tumors, respectively. There was no difference in the MSI score between tumors with and without MLH1 methylation. d Collection across all 33 tumors of substitutions in each of six categories (indicated in the top panel), classified according to sequence context (flanking nucleotides are indicated on the horizontal axis). The mutation distribution corresponds to mutation signature 6, as designated in COSMIC, which is associated with defective MMR
Fig. 3
Fig. 3
Cancer-critical genes with frequent frameshift mutations. a Mutation frequency of cancer-critical genes with most frequent indels affecting the reading frame, splice sites, or stop codons. CRTC1 (mutation frequency 42%), BCL9 (30%), JAK1 (24%), and PTCH1 (24%) were identified as novel frequently mutated genes. b Mutation validation analyses in MSI+ CRCs in independent patient series. c The JAK1 frameshift indels were found in four hotspot amino acid positions (GenBank accession NP_002218; 1154 amino acids). The number of mutations detected in each patient series and mutation hotspot is shown, confirming frequent mutations upstream of the JAK1 kinase domain (JH1). The patient series analyzed are indicated (top left) using the same color code as in b. All four homopolymers of length ≥6 in JAK1 are indicated below the protein. Protein domains are indicated by color; SH2 Src Homology 2, FERM (F, 4.1 protein; E, ezrin; R, radixin; M, moesin), JH1 kinase domain, JH2 pseudokinase domain. d Gene signatures of five processes previously found to be associated with innate resistance to anti-PD-1 treatment in melanomas were over-expressed in MSI+ CRCs with versus without JAK1 mutations in both Norwegian series I and TCGA. e Six of the tumors in Norwegian series I with JAK1 indels were available for clonality analyses. All these tumors had at least one JAK1 indel (asterisk) scored as truncal, and all JAK1 mutations were heterozygous. Each plot represents one sample and separate tumor clones, identified as mutation clusters with different variant allele frequencies, are indicated with different colors
Fig. 4
Fig. 4
Predicted neoantigen load correlates with mutation load, while immune infiltration is highest in CMS1. a Among the 33 exome-sequenced tumors, there was a strong correlation between the number of exonic mutations (including synonymous) and predicted neoantigens. b There was not a one-to-one correspondence among the number of mutations (left), mutations predicted to create neoantigens (middle), and predicted neoantigens (right) per tumor (each tumor is indicated with a separate color), showing that individual mutations generate several neoantigens per tumor. c The individual mutations (represented by a dot) predicted to create most neoantigens per tumor (horizontal axis) were typically not recurrent in a large proportion of the tumors (vertical axis). However, several mutations (indicated by colors) created neoantigens in several tumors. d The number of amino acid changing mutations per tumor (horizontal axis) was not associated with the level of infiltration of cytotoxic lymphocytes (Spearman’s correlation −0.06, P = 0.8). e In contrast, among all MSI+ tumors in Norwegian series I, infiltration of cytotoxic lymphocytes and the ESTIMATE immune-score, as well as PD-1 and JAK-STAT signaling (based on gene expression) were significantly higher in CMS1 compared to CMS2-4 (Welch’s t-test; although high also in CMS4)
Fig. 5
Fig. 5
JAK1 mutations, mutation load, and CMS1 are associated with a good patient outcome. a Among 175 patients with MSI+ CRC from Norwegian series I and II and the VICTOR trial, tumors with JAK1 frameshift indels were associated with a better 5-year overall survival rate (94%) than wild-type tumors (75%; P value from Wald’s test). b Among the 33 exome-sequenced tumors in Norwegian series I, tumors with a mutation load above the median number of mutations were associated with a better 5-year relapse-free survival rate (100%) than tumors with a low mutation load (63%; P value from the log-rank test). c Among 119 patients in Norwegian series I and a publicly available dataset (GEO accession number GSE39582), patients in CMS1 had a significantly better 5-year relapse-free survival rate (81%) than patients in CMS2-4 (57%, P value from Wald’s test)
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References

    1. Ionov Y, Peinado MA, Malkhosyan S, Shibata D, Perucho M. Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature. 1993;363:558–61. doi: 10.1038/363558a0. - DOI - PubMed
    1. Aaltonen LA, Peltomaki P, Leach FS, Sistonen P, Pylkkanen L, Mecklin JP, et al. Clues to the pathogenesis of familial colorectal cancer. Science. 1993;260:812–6. doi: 10.1126/science.8484121. - DOI - PubMed
    1. Thibodeau SN, Bren G, Schaid D. Microsatellite instability in cancer of the proximal colon. Science. 1993;260:816–9. doi: 10.1126/science.8484122. - DOI - PubMed
    1. Kane MF, Loda M, Gaida GM, Lipman J, Mishra R, Goldman H, et al. Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res. 1997;57:808–11. - PubMed
    1. Cunningham JM, Christensen ER, Tester DJ, Kim CY, Roche PC, Burgart LJ, et al. Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability. Cancer Res. 1998;58:3455–60. - PubMed

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