Polymerase proofreading-associated polyposis is a dominantly inherited colorectal cancer syndrome caused by exonuclease domain missense variants in the DNA polymerases POLE and POLD1. Manifestations ...may also include malignancies at extracolonic sites. Cancer risks in this syndrome are not yet accurately quantified.
We sequenced POLE and POLD1 exonuclease domains in 354 individuals with early/familial colorectal cancer (CRC) or adenomatous polyposis. We assessed the pathogenicity of POLE variants with yeast fluctuation assays and structural modeling. We estimated the penetrance function for each cancer site in variant carriers with a previously published nonparametric method based on survival analysis approach, able to manage unknown genotypes.
Pathogenic POLE exonuclease domain variants P286L, M294R, P324L, N363K, D368N, L424V, K425R, and P436S were found in ten families. The estimated cumulative risk of CRC at 30, 50, and 70 years was 11.1% (95% confidence interval CI: 4.2-17.5), 48.5% (33.2-60.3), and 74% (51.6-86.1). Cumulative risk of glioblastoma was 18.7% (3.2-25.8) at 70 years. Variants interfering with DNA binding (P286L and N363K) had a significantly higher mutagenic effect than variants disrupting ion metal coordination at the exonuclease site.
The risk estimates derived from this study provide a rational basis on which to provide genetic counseling to POLE variant carriers.
Purpose:
DNA methylation is a mechanism for gene expression silencing in cancer. Limited information is available for adrenocortical tumors. Abnormal methylation at the IGF2/H19 locus is common in ...adrenocortical carcinomas. Our aim was to characterize the methylation in adrenocortical carcinomas at a whole-genome scale and to assess its clinical significance and its impact on gene expression.
Experimental Design:
Methylation patterns of CpG islands in promoter regions of 51 adrenocortical carcinomas and 84 adenomas were studied by the Infinium HumanMethylation27 Beadchip (Illumina, San Diego, CA). Methylation of 33 genes was studied by methylation-specific multiplex ligation-dependent probe amplification (MRC-Holland, Amsterdam, The Netherlands) in 15 carcinomas. Gene expression data were available for 87 tumors from a previous study (HG-U133Plus2.0 AffymetrixGeneChip; Affymetrix, Santa Clara, CA). Clinical information, including patient features and survival, were available for all tumors.
Results:
Methylation was higher in carcinomas than in adenomas (t test P = 3.1 × 10−9). Unsupervised clustering of DNA methylation profiles identified two groups of carcinomas, one with an elevated methylation level, evoking a CpG island methylator phenotype (CIMP). The subgroup of hypermethylated carcinomas was further divided in two subgroups, with different levels of methylation (CIMP-high and CIMP-low). This classification could be confirmed by methylation-specific multiplex ligation-dependent probe amplification. Hypermethylation was associated with a poor survival (Cox model P = 0.02). The transcriptome/methylation correlation showed 1741 genes (of 12,250) negatively correlated; among the top genes were H19 and other tumor suppressors (PLAGL-1, G0S2, and NDRG2).
Conclusions:
This genome-wide methylation analysis reveals the existence of hypermethylated adrenocortical carcinomas, with a poorer prognosis. Hypermethylation in these tumors is important for silencing specific tumor suppressor genes.
Background & Aims Cyclooxygenase-2 inhibitors reduce colon cancer risk by mechanisms that are not fully understood. We performed microarray analysis of adenomas from ApcΔ14/+ mice to identify genes ...that respond to these drugs. Methods ApcΔ14/+ mice were given a single daily injection of parecoxib for up to 9 weeks; intestinal tracts of these and control mice were analyzed by microarray analysis, immunohistochemistry, in situ hybridization, and quantitative real-time polymerase chain reaction. Findings were further assessed using Apclox/lox vil-CreERT2 mice, the CT26 cancer cell line, and human colon tumor samples. Results Microarray analysis revealed that osteopontin, a marker of colon cancer progression, was down-regulated in polyps from ApcΔ14/+ mice given parecoxib compared with controls. ApcΔ14/+ mice given parecoxib had longer survival times and reduced polyp burdens. Osteopontin was quickly down-regulated by parecoxib in intestinal polyps from ApcΔ14/+ mice, and 2 components of the osteopontin regulatory network—the orphan nuclear receptor NR4A2 and Wnt/β-catenin signaling—were sequentially repressed. NR4A2 activated the osteopontin promoter in CT26 cells; this effect was blocked by mutation of the NR4A2 binding response element, cotransfection of a dominant-negative form of NR4A2, and small inhibitory RNA against NR4A2. NR4A2 levels were increased throughout tumor progression in ApcΔ14/+ mice but, unlike osteopontin, did not correlate with tumor stage. NR4A2 levels were reduced in adenomas from patients treated with rofecoxib. Conclusions Down-regulation of osteopontin, probably through blockade of NR4A2 and Wnt signaling, is an important component of the antitumor activity of cyclooxygenase-2 inhibitors. These factors might be developed as therapeutic targets for intestinal cancers.
Some patients with Lynch syndrome (LS) have extreme phenotypes, i.e. cancer before the recommended screening age, or cancer for which there are no screening guidelines. We made the hypothesis that ...additional germline variants in cancer susceptibility genes (CSG) could explain some of these phenotypes. We compared the prevalence of additional CSG variants in LS patients with a cancer diagnosis before age 30 (early-onset, EO group) and after 40 (usual-onset, UO group). While there was no overall difference, we did find an excess of pathogenic variants and variants of unknown significance in EO cases when only gastrointestinal CSG were considered (OR 2.25; 95% CI: 1.01-5.06, p value = 0.04). Four EO cases stood out: two with POLE/POLD1 variants in the key exonuclease domain, one with a BMPR1A duplication and one with an EPCAM deletion. Additional germline variants should be considered in future screening recommendations, as they might influence cancer risk.
De novo germline pathogenic variants (gPV) of the BReast CAncer 1 (BRCA1) gene are very rare. Only a few have been described up to date, usually in patients with a history of ovarian or breast ...cancer. Here, we report the first case of an incidental de novo BRCA1 germline pathogenic variant which was identified within the framework of the Plan France Médecine Génomique (PFMG) 2025 French national tumor sequencing program. The proband was a 29-year-old man diagnosed with metastatic osteosarcoma. Tumor whole exome sequencing identified a BRCA1 c.3756_3759del p.(Ser1253Argfs*10) pathogenic variant without loss-of-heterozygosity. A low genomic instability score and the absence of single base substitution signatures of homologous recombination deficiency suggested that the BRCA1 variant was not driver in the osteosarcoma tumorigenesis. Germline whole genome sequencing asserted the germline nature of this variant, with a 36% allele frequency, suggesting a mosaicism caused by a post-zygotic mutational event. The proband's family (parents and siblings) were not carriers of this variant confirming the de novo occurrence. Tumor sequencing programs like the French PFMG 2025 have been implemented worldwide and may help identify new gPV, including de novo variants.
Missense mutations in the polymerase epsilon (POLE) gene have been reported to generate proofreading defects resulting in an ultramutated genome and to sensitize tumors to checkpoint blockade ...immunotherapy. However, many POLE-mutated tumors do not respond to such treatment. To better understand the link between POLE mutation variants and response to immunotherapy, we prospectively assessed the efficacy of nivolumab in a multicenter clinical trial in patients bearing advanced mismatch repair-proficient POLE-mutated solid tumors. We found that only tumors harboring selective POLE pathogenic mutations in the DNA binding or catalytic site of the exonuclease domain presented high mutational burden with a specific single-base substitution signature, high T-cell infiltrates, and a high response rate to anti-PD-1 monotherapy. This study illustrates how specific DNA repair defects sensitize to immunotherapy. POLE proofreading deficiency represents a novel agnostic biomarker for response to PD-1 checkpoint blockade therapy.
POLE proofreading deficiency leads to high tumor mutational burden with high tumor-infiltrating lymphocytes and predicts anti-PD-1 efficacy in mismatch repair-proficient tumors. Conversely, tumors harboring POLE mutations not affecting proofreading derived no benefit from PD-1 blockade. POLE proofreading deficiency is a new tissue-agnostic biomarker for cancer immunotherapy. This article is highlighted in the In This Issue feature, p. 1397.
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but highly variable expressivity. In most patients, Next Generation Sequencing (NGS) technologies allow the ...identification of a loss-of-function pathogenic variant in the
NF1
gene, a negative regulator of the RAS-MAPK pathway. We describe the 5-year diagnosis wandering of a patient with a clear NF1 clinical diagnosis, but no molecular diagnosis using standard molecular technologies. The patient presented with a typical NF1 phenotype but
NF1
targeted NGS,
NF1
transcript analysis, MLPA, and array comparative genomic hybridization failed to reveal a genetic aberration. After 5 years of unsuccessful investigations, trio WGS finally identified a de novo mosaic (VAF ~ 14%) 24.6 kb germline deletion encompassing the promoter and first exon of
NF1
. This case report illustrates the relevance of WGS to detect structural variants including copy number variants that would be missed by alternative approaches. The identification of the causal pathogenic variant allowed a tailored genetic counseling with a targeted non-invasive prenatal diagnosis by detecting the deletion in plasmatic cell-free DNA from the proband’s pregnant partner. This report clearly highlights the need to make WGS a clinically accessible test, offering a tremendous opportunity to identify a molecular diagnosis for otherwise unsolved cases.
Context:Adrenocortical cancer (ACC) is an aggressive tumor with heterogeneous outcome. Prognostic stratification is difficult even based on tumor stage and Ki67 index. Recently integrated genomics ...studies have demonstrated that CpG islands hypermethylation is correlated with poor survival.Objective:To confirm the prognostic value of CpG islands methylation on an independent cohort with a single commonly available methylation assay.Design:CpG islands methylation was measured by methylation-specific-multiplex-ligation-dependent-probe-amplification (MS-MLPA) using the ME002 kit (MRC-Holland).Setting:MS-MLPA was performed in a training cohort of 50 ACC to identify the best set of probes correlating with disease-free (DFS) and overall survival (OS). These were then validated in an independent cohort from 21 ENSAT centers.Patients:The validation cohort included 203 ACC: 64% females, median age 50 years, 80% localized tumors.Intervention:None.Main Outcome Measures:DFS and OS (Cox models).Results:In the training cohort, mean methylation in CpG islands of 4 genes (PAX5,GSTP1,PYCARD,PAX6) was the strongest methylation marker. In the validation cohort, methylation was a significant prognostic factor of DFS (p<0.0001) and OS (p<0.0001). Methylation, Ki67 and ENSAT stage were combined in multivariate models. For DFS, methylation (p=0.0005) and ENSAT stage (p<0.0001) but not Ki67 (p=0.19) remained highly significant. For OS, methylation (p=0.0006), ENSAT stage (p<0.0001) and Ki67 (p=0.024) were independent prognostic factors.Conclusions:Tumor DNA methylation emerges as an independent prognostic factor in ACC. MS-MLPA is readily compatible with clinical routine, and above clinical and pathological features, should enhance our ability for prognostication and precision medicine.
PDF
