Molecular characterisation of pancreatic ductal adenocarcinoma with NTRK fusions and review of the literature.

AIMS: The majority of pancreatic ductal adenocarcinomas (PDACs) harbour oncogenic mutations in KRAS with variants in TP53, CDKN2A and SMAD4 also prevalent. The presence of oncogenic fusions including NTRK fusions are rare but important to identify. Here we ascertain the prevalence of NTRK fusions and document their genomic characteristics in a large series of PDAC. METHODS: Whole genome sequencing and RNAseq were performed on a series of patients with resected or locally advanced/metastatic PDAC collected between 2008 and 2020 at a single institution. A subset of specimens underwent immunohistochemistry (IHC) analysis. Clinical and molecular characterisation and IHC sensitivity and specificity were evaluated. RESULTS: 400 patients were included (resected n=167; locally advanced/metastatic n=233). Three patients were identified as harbouring an NTRK fusion, two EML4-NTRK3 (KRAS-WT) and a single novel KANK1-NTRK3 fusion. The latter occurring in the presence of a subclonal KRAS mutation. Typical PDAC drivers were present including mutations in TP53 and CDKN2A. Substitution base signatures and tumour mutational burden were similar to typical PDAC. The prevalence of NTRK fusions was 0.8% (3/400), while in KRAS wild-type tumours, it was 6.25% (2/32). DNA prediction alone documented six false-positive cases. RNA analysis correctly identified the in-frame fusion transcripts. IHC analysis was negative in the KANK1-NTRK3 fusion but positive in a EML4-NTRK3 case, highlighting lower sensitivity of IHC. CONCLUSION: NTRK fusions are rare; however, with emerging therapeutic options targeting these fusions, detection is vital. Reflex testing for KRAS mutations and subsequent RNA-based screening could help identify these cases in PDAC.

hENT1 Expression Predicts Response to Gemcitabine and Nab-Paclitaxel in Advanced Pancreatic Ductal Adenocarcinoma.

PURPOSE: Modified FOLFIRINOX (mFFX) and gemcitabine/nab-paclitaxel (GnP) remain standard first-line options for patients with advanced pancreatic ductal adenocarcinoma (PDAC). Human equilibrative nucleoside transporter 1 (hENT1) was hypothesized to be a biomarker of gemcitabine in the adjuvant setting, with conflicting results. In this study, we explore hENT1 mRNA expression as a predictive biomarker in advanced PDAC. EXPERIMENTAL DESIGN: COMPASS was a prospective observational trial of patients with advanced PDAC. A biopsy was required prior to initiating chemotherapy, as determined by treating physician. Biopsies underwent laser capture microdissection prior to whole genome and RNA sequencing. The cut-off thresholds for hENT1 expression were determined using the maximal χ2 statistic. RESULTS: 253 patients were included in the analyses with a median follow-up of 32 months, with 138 patients receiving mFFX and 92 receiving GnP. In the intention to treat population, median overall survival (OS) was 10.0 months in hENT1high versus 7.9 months in hENT1low (P = 0.02). In patients receiving mFFX, there was no difference in overall response rate (ORR; 35% vs. 28%, P = 0.56) or median OS (10.6 vs. 10.5 months, P = 0.45). However, in patients treated with GnP, the ORR was significantly higher in hENT1high compared with hENT1low tumors (43% vs. 21%, P = 0.038). Median OS in this GnP-treated cohort was 10.6 months in hENT1high versus 6.7 months hENT1low (P < 0.001). In an interaction analysis, hENT1 was predictive of treatment response to GnP (interaction P = 0.002). CONCLUSIONS: In advanced PDAC, hENT1 mRNA expression predicts ORR and OS in patients receiving GnP.

Clinical implementation of circulating tumour DNA testing for EGFR T790M for detection of treatment resistance in non-small cell lung cancer.

AIMS: Epidermal growth factor receptor (EGFR) T790M mutations can be detected in the circulating tumour DNA from plasma of patients with non-small cell lung cancer (NSCLC) to triage patients for osimertinib eligibility and monitor patients longitudinally for development of T790M-mediated resistance. METHODS: Using droplet digital PCR (ddPCR), we examined the EGFR T790M status of 343 sequential patients with NSCLC and correlated mutational status with demographic and clinical features. Where available, serial T790M blood test results were assessed to identify clinical triggers and timing of repeat testing. RESULTS: Of the 343 patients with liquid biopsy test results, 24% were T790M positive. No clear clinical correlation with a T790M positive test result was identified in this study, although the number of metastatic sites did correlate significantly with the presence of EGFR sensitising mutations (L858R or exon 19 deletion) in patient plasma, as a measure of tumour DNA shedding. Of the 59 serial blood tests from patients that initially tested negative, 14% were positive on sequential testing, at a time interval up to 6 months after an initially negative blood test. CONCLUSIONS: The ddPCR test for EGFR T790M mutations effectively triaged 24% of patients for treatment with osimertinib, avoiding the need for invasive tissue biopsy in these patients. Our findings suggest that initial and repeat ctDNA testing can be used to monitor for acquired EGFR T790M resistance for NSCLC.

A novel complex mutation in MSH2 contributes to both Muir-Torre and Lynch Syndrome.

Mutations in mismatch repair genes lead to Lynch Syndrome, the most common form of inherited colorectal cancer. In this report, we describe a novel complex germline mutation c.[1601_1661+92dup; 1591_1611del] of the mismatch repair gene, MSH2. This mutation, which segregates with the disease phenotype, was discovered in a Lynch syndrome kindred that also shows a history of the Muir-Torre syndrome. Interestingly, several tumors from this family displayed microsatellite instability, a hallmark of Lynch syndrome tumors but no consistent, concomitant loss of MSH2 protein expression. In addition, a subset of tumors showed neither prototypical feature of microsatellite instability nor immunohistochemistry deficiency, highlighting the importance of a detailed molecular analysis of rare genetic alterations. This mutation and the atypical clinical manifestations observed underscore the genetic complexity underlying Lynch syndrome, and the importance of comprehensive molecular screening in the diagnosis and early detection of colorectal and other associated cancers.

Equity and Gender Issues Among Members of the Canadian Association of Gastroenterology.

BACKGROUND: Gender equity has historically been a challenge within gastroenterology. AIMS: The Canadian Association of Gastroenterology (CAG) developed a survey to identify issues pertaining to equity and gender faced by its membership and to determine areas of action. METHODS: In 2014, the survey was emailed to all 1155 CAG members, and the data were analyzed using statistical methods. RESULTS: One hundred eleven CAG members responded to the survey. Of those, 52% were male, 75% were between 26 and 45 years of age, and 55% were in their first decade of practice. More males held the status of full professor (21% versus 0%; P=0.022). Male CAG members reported working more hours per week than their female counterparts (58.3 ± 15.4 versus 52.3 ± 11.8, P=0.025). Regarding commitments outside the workplace, 81% of respondents had a spouse/partner, and 52% had children under 18 years of age, both of which did not significantly differ based on gender. Overall, 70% were satisfied or very satisfied with their career path. However, significantly more females felt their age/ethnicity/gender/marital status hindered career advancement (36% versus 14%; P=0.008). Furthermore, more females reported difficulties attaining work-life balance (45% versus 22%; P=0.015). CONCLUSIONS: This survey highlights that gender and equity challenges continue to exist within gastroenterology. The needs assessment highlights that work-life balance, physician well-being, negotiation skills and mentorship are areas of importance to many CAG members.

The MLH1 variants p.Arg265Cys and p.Lys618Ala affect protein stability while p.Leu749Gln affects heterodimer formation.

Germline mutations in the mismatch repair genes lead to the Lynch syndrome/ HNPCC, and genetic testing is offered to identify individuals at risk of developing this disease. About a third of all genetic alterations detected in the mismatch repair gene MutL homolog 1 (MLH1) are missense variants. The majority of these variants are of equivocal clinical significance. In this report, we investigate the molecular basis of the pathogenicity of three missense variants localized to distinct functional domains. Our results demonstrate that the MLH1 variants p.Arg265Cys (c.793C>T) and p.Lys618Ala (c.1852_1853AA>GC) significantly decrease the stability of the protein, while another missense variant p.Leu749Gln (c.2246T>A) is able to compromise heterodimerization of the MLH1-PMS2 complex.

A transient increase in the activity of Src-family kinases induced by cell detachment delays anoikis of intestinal epithelial cells.

Detachment of epithelial cells from the basement membrane (BM) induces apoptosis, a phenomenon now widely known as anoikis. Studies in mammary and intestinal epithelial cells have shown that the loss of attachment to the BM rapidly triggers reversible proapoptotic events from which the cells can recover if they reattach within a certain period. Thus, cells seem to be transiently protected from the initial detachment-induced proapoptotic events. The molecular mechanisms underlying such transient protection against anoikis are unknown. In this paper, we present evidence indicating that detachment of intestinal epithelial cells triggers a transient, yet significant increase in the activity of the tyrosine kinases c-Src and c-Fyn, and that this activation of Src-family kinases (SFK) contributes to the transient protection against anoikis in these cells. The protective signals from SFK are mediated by the PI3K pathway, and caveolin-1. In addition, we show that the MEK1-ERK1/2 pathway acts in a synergistic manner with SFK to protect intestinal epithelial cells from anoikis.

Functional effects of the MLH1-93G>A polymorphism on MLH1/EPM2AIP1 promoter activity.

Defective mismatch repair leads to the microsatellite instability (MSI) phenotype of colorectal cancer (CRC). We previously showed that the MLH1-93G>A promoter polymorphism is strongly associated with MSI tumours, suggesting a modifier role for this polymorphism in CRC. The MLH1 promoter is bi-directional with the EPM2AIP1 gene located on the antisense strand. In order to evaluate the functional effects of this polymorphism, we transfected a panel of CRC, endometrial cancer and non-tumourigenic cell lines with MLH1 luciferase promoter constructs. We used constructs in reverse orientation to assess the effect of this polymorphism on EPM2AIP1. The luciferase activities were compared using a two-sided Student's t-test. Electrophoretic mobility shift assays (EMSAs) were used to evaluate whether differential protein binding was responsible for the differences in promoter activity. We observed a higher level of activity with the -93G allele in all the cell lines observed; including the CRC cell line, HCT116 (P=0.002), the endometrial cancer cell line, HEC-1-A (P<0.001) and the normal colonic cell line, CCD-841-CoTr (P=0.002). This polymorphism also affected EPM2AIP1 transcription with the -93A allele demonstrating higher promoter activity in the HCT116 (P=0.007) and HEC-1-A (P=0.004) cells. The EMSA results suggest that this polymorphism alters the affinity of nuclear factors that bind to this region. Our findings indicate that the -93G>A polymorphism modifies the efficiency of MLH1/EPM2AIP1 transcription.

A novel and rapid method of determining the effect of unclassified MLH1 genetic variants on differential allelic expression.

Germline mutations in mismatch repair genes predispose patients to Lynch Syndrome and the majority of these mutations have been detected in two key genes, MLH1 and MSH2. In particular, about a third of the missense variants identified in MLH1 are of unknown clinical significance. Using the PeakPicker software program, we have conducted a proof-of-principle study to investigate whether missense variants in MLH1 lead to allelic imbalances. Lymphocyte RNA extracted from patients harboring known MLH1 variants was used to quantify the ratio of variant to wild-type transcript, while patient lymphocyte DNA was used to establish baseline allelic expression levels. Our analysis indicated that the missense variants c.350C>T, c.793C>T, and c.1852_1853AA>GC, as well as the truncating variant c.1528C>T were all associated with significantly unbalanced allelic expression. However, the variants c.55A>T and c.2246T>C did not demonstrate an allelic imbalance. These results illustrate a novel and efficient method to investigate the pathogenicity of unclassified genetic variants discovered in mismatch repair genes, as well as genes implicated in other inherited diseases. In addition, the PeakPicker methodology has the potential to be applied in the diagnostic setting, which, in conjunction with results from other assays, will help increase both the accuracy and efficiency of genetic testing of colorectal cancer, as well as other inherited diseases.