Exome and immune cell score analyses reveal great variation within synchronous primary colorectal cancers

BACKGROUND: Approximately 4% of colorectal cancer (CRC) patients have at least two simultaneous cancers in the colon. Due to the shared environment, these synchronous CRCs (SCRCs) provide a unique setting to study colorectal carcinogenesis. Understanding whether these tumours are genetically similar or distinct is essential when designing therapeutic approaches. METHODS: We performed exome sequencing of 47 primary cancers and corresponding normal samples from 23 patients. Additionally, we carried out a comprehensive mutational signature analysis to assess whether tumours had undergone similar mutational processes and the first immune cell score analysis (IS) of SCRC to analyse the interplay between immune cell invasion and mutation profile in both lesions of an individual. RESULTS: The tumour pairs shared only few mutations, favouring different mutations in known CRC genes and signalling pathways and displayed variation in their signature content. Two tumour pairs had discordant mismatch repair statuses. In majority of the pairs, IS varied between primaries. Differences were not explained by any clinicopathological variable or mutation burden. CONCLUSIONS: The study shows major diversity within SCRCs. Rather than rely on data from one tumour, our study highlights the need to evaluate both tumours of a synchronous pair for optimised targeted therapy.Peer reviewe

Exome-wide somatic mutation characterization of small bowel adenocarcinoma

Small bowel adenocarcinoma (SBA) is an aggressive disease with limited treatment options. Despite previous studies, its molecular genetic background has remained somewhat elusive. To comprehensively characterize the mutational landscape of this tumor type, and to identify possible targets of treatment, we conducted the first large exome sequencing study on a population-based set of SBA samples from all three small bowel segments. Archival tissue from 106 primary tumors with appropriate clinical information were available for exome sequencing from a patient series consisting of a majority of confirmed SBA cases diagnosed in Finland between the years 2003-2011. Paired-end exome sequencing was performed using Illumina HiSeq 4000, and OncodriveFML was used to identify driver genes from the exome data. We also defined frequently affected cancer signalling pathways and performed the first extensive allelic imbalance (Al) analysis in SBA. Exome data analysis revealed significantly mutated genes previously linked to SBA (TP53, KRAS, APC, SMAD4, and BRAF), recently reported potential driver genes (SOX9, ATM, and ARID2), as well as novel candidate driver genes, such as ACVR2A, ACVR1B, BRCA2, and SMARCA4. We also identified clear mutation hotspot patterns in ERBB2 and BRAF. No BRAF V600E mutations were observed. Additionally, we present a comprehensive mutation signature analysis of SBA, highlighting established signatures 1A, 6, and 17, as well as U2 which is a previously unvalidated signature. Finally, comparison of the three small bowel segments revealed differences in tumor characteristics. This comprehensive work unveils the mutational landscape and most frequently affected genes and pathways in SBA, providing potential therapeutic targets, and novel and more thorough insights into the genetic background of this tumor type.Peer reviewe

Next-generation sequencing in a large pedigree segregating visceral artery aneurysms suggests potential role of COL4A1/COL4A2 in disease etiology

Abstract Background: Visceral artery aneurysms (VAAs) can be fatal if ruptured. Although a relatively rare incident, it holds a contemporary mortality rate of approximately 12%. VAAs have multiple possible causes, one of which is genetic predisposition. Here, we present a striking family with seven individuals affected by VAAs, and one individual affected by a visceral artery pseudoaneurysm. Methods: We exome sequenced the affected family members and the parents of the proband to find a possible underlying genetic defect. As exome sequencing did not reveal any feasible protein-coding variants, we combined whole-genome sequencing of two individuals with linkage analysis to find a plausible non-coding culprit variant. Variants were ranked by the deep learning framework DeepSEA. Results: Two of seven top-ranking variants, NC_000013.11:g.108154659C>T and NC_000013.11:g.110409638C>T, were found in all VAA-affected individuals, but not in the individual affected by the pseudoaneurysm. The second variant is in a candidate cis-regulatory element in the fourth intron of COL4A2, proximal to COL4A1. Conclusions: As type IV collagens are essential for the stability and integrity of the vascular basement membrane and involved in vascular disease, we conclude that COL4A1 and COL4A2 are strong candidates for VAA susceptibility genes

Clinicopathologic features of the patient cohort.

<p>Clinicopathologic features of the patient cohort.</p

Overview of AI events in SBA.

<p>Frequency of gains and losses in 106 SBA samples.</p

Mutational landscape of the most significant genes in MSS SBAs.

<p>The figure includes the 25 highest-ranking genes in MSS tumors (n = 91) according to OncodriveFML, ranked by the <i>P</i>-value (right, red line at <i>P</i> = 0.05). Of these, <i>TP53</i>, <i>KRAS</i>, <i>APC</i>, <i>SOX9</i>, <i>SMAD4</i>, <i>BRAF</i>, and <i>ACVR2A</i> were significant also after correction for multiple testing. Different colors distinguish between the different types of mutations (in the middle). “Double hit” refers to two truncating mutations. The percentage of mutated tumors by gene are shown on the left. The upper bars represent the total number of both synonymous and non-synonymous mutations per tumor.</p

Mutation pattern in ERBB receptor family.

<p>Mutations in <i>ERBB2</i> (ENST00000269571) grouped into four hotspots (top). Samples (n = 29) with a mutated member of ERBB receptor family are presented in columns (below). In addition to a hotspot mutation, some samples displayed simultaneously a non-hotspot mutation in the same gene, thus all mutations are not shown in the figure. Recep_L = Receptor L domain; Furin-like = Furin-like cysteine rich region; GF_recep = Growth factor receptor domain; Pkinase_Tyr = Protein tyrosine kinase.</p

Mutations in <i>BRAF</i> (ENST00000288602).

<p>In total, 12 mutations were identified in 11 tumors (MSS n = 10, MSI n = 1). RBD = Raf-like Ras-binding domain; C1_1 = C1 domain; Pkinase_Tyr = Protein tyrosine kinase.</p

Signature contexts.

<p>The 15 MSI tumors displayed signature 6. There were three signatures (1A, 17, and U2) that could be extracted from the 91 MSS tumors.</p