Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers.

Somatic single-nucleotide variants (SNVs) occur every time a cell divides, appearing even in healthy tissues at low frequencies. These mutations may accumulate as neutral variants during aging, or eventually, promote the development of neoplasia. Here, we present the SP-ddPCR, a droplet digital PCR (ddPCR) based approach that utilizes customized SuperSelective primers aiming at quantifying the proportion of rare SNVs. For that purpose, we selected five potentially pathogenic variants identified by whole-exome sequencing (WES) occurring at low variant allele frequency (VAF) in at-risk colon healthy mucosa of patients diagnosed with colorectal cancer or advanced adenoma. Additionally, two APC SNVs detected in two cancer lesions were added to the study for WES-VAF validation. SuperSelective primers were designed to quantify SNVs at low VAFs both in silico and in clinical samples. In addition to the two APC SNVs in colonic lesions, SP-ddPCR confirmed the presence of three out of five selected SNVs in the normal colonic mucosa with allelic frequencies ≤ 5%. Moreover, SP-ddPCR showed the presence of two potentially pathogenic variants in the distal normal mucosa of patients with colorectal carcinoma. In summary, SP-ddPCR offers a rapid and feasible methodology to validate next-generation sequencing data and accurately quantify rare SNVs, thus providing a potential tool for diagnosis and stratification of at-risk patients based on their mutational profiling.

Adherence to Mediterranean diet and its association with multiple colonic polyps of unknown origin: a case-control study.

Introduction: Multiple colonic polyps do not have a genetic origin in most patients, and the cause of this phenotype remains elusive. Environmental factors, such as diet, could be related to this phenotype. Our aim was to investigate the relationship between the adherence to Mediterranean diet and multiple colonic polyps of unknown origin. Methods: A case-control pilot study was carried out with a sample of 38 individuals, including 23 cases with more than 10 adenomatous or serrated polyps from the national multicenter project EPIPOLIP and 15 healthy controls with normal colonoscopy. A validated Spanish version of the MEDAS questionnaire was administered to cases and controls. Results: Adherence to Mediterranean diet was higher in controls than in patients with multiple colonic polyps (MEDAS score: 8.6 ± 1.4 vs. 7.0 ± 1.6; p = 0.01). Optimal overall adherence to the Mediterranean diet pattern was significantly higher among the controls than among cases (MEDAS score >9: 46% vs. 13%; OR 0.17; 95% CI 0.03-0.83). Non-optimal adherence to the Mediterranean diet acts as a risk factor for developing colorectal cancer derived from colorectal polyps. Conclusion: Our results suggest that environmental factors play a role in the pathogenesis of this phenotype.

A novel non-invasive colorectal cancer diagnostic method: Volatile organic compounds as biomarkers.

INTRODUCTION: Population-based fecal tests for colorectal cancer (CRC) screening have shown to reduce mortality thanks to the early detection of the disease. However, currently available fecal tests are limited in their sensitivity and specificity. Our aim is to look for volatile organic compounds in fecal samples as biomarkers for CRC detection. MATERIAL AND METHODS: Eighty participants were included; 24 had adenocarcinoma, 24 had adenomatous polyps and 32 presented no neoplasms. Fecal samples were collected 48 h preceding the colonoscopy from all participants, except CRC patient samples that were collected after 3-4 weeks from the colonoscopy. Magnetic headspace adsorptive extraction (Mag-HSAE) followed by thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) was performed on stool samples to identify volatile organic compounds as biomarkers. RESULTS: p-Cresol was significantly more abundant in the cancer samples (P < 0.001) with an area under the curve (AUC) of 0.85 (CI 95%; 0.737-0.953), having a sensitivity and specificity of 83% and 82%, respectively. In addition, 3(4H)-dibenzofuranone,4a,9b-dihydro-8,9b-dimethyl- (3(4H)-DBZ) was also more abundant in the cancer samples (P < 0.001) with an AUC of 0.77 (CI 95%; 0.635-0.905), sensitivity of 78% and specificity of 75%. When combined (p-cresol and 3(4H)-DBZ), the AUC was 0.86, sensitivity 87% and specificity 79%. p-Cresol also appeared to be promising as a biomarker for pre-malignant lesions with an AUC of 0.69 (CI 95%; 0.534-0.862), sensitivity 83% and specificity 63%, P = 0.045. CONCLUSIONS: Volatile organic compounds emitted from feces and determined by a sensitive analytical methodology (Mag-HSAE-TD-GC-MS), employing a magnetic graphene oxide as extractant phase, could be used as a potential screening technology for CRC and pre-malignant lesions.

Lynch-like Syndrome: Potential Mechanisms and Management.

Lynch syndrome is an autosomal dominant disorder caused by germline mutations in DNA mismatch repair (MMR) system genes, such as MLH1, MSH2, MSH6, or PMS2. It is the most common hereditary colorectal cancer syndrome. Screening is regularly performed by using microsatellite instability (MSI) or immunohistochemistry for the MMR proteins in tumor samples. However, in a proportion of cases, MSI is found or MMR immunohistochemistry is impaired in the absence of a germline mutation in MMR genes, BRAF mutation, or MLH1 hypermethylation. These cases are defined as Lynch-like syndrome. Patients with Lynch-like syndrome represent a mixture of truly hereditary and sporadic cases, with a risk of colorectal cancer in first-degree relatives that is between the risk of Lynch syndrome in families and relatives of sporadic colon cancer cases. Although multiple approaches have been suggested to distinguish between hereditary and sporadic cases, a homogeneous testing protocol and consensus on the adequate classification of these patients is still lacking. For this reason, management of Lynch-like syndrome and prevention of cancer in these families is clinically challenging. This review explains the concept of Lynch-like syndrome, potential mechanisms for its development, and methods for adequately distinguishing between sporadic and hereditary cases of this entity.

Risk of Colorectal Cancer and Advanced Polyps One Year After Excision of High-Risk Adenomas.

BACKGROUND: Patients with multiple or large adenomas are considered to be high-risk for metachronous colorectal cancer. OBJECTIVE: Evaluate the risks of detecting colorectal cancer, advanced adenoma, and advanced serrated polyps at 1-year surveillance colonoscopy in patients with >5 adenomas or adenomas >20 mm. DESIGN: Descriptive, retrospective, multicentric, cohort study. We calculated the absolute risk of developing colorectal cancer, advanced adenomas, and advanced serrated polyps at the 1-year surveillance colonoscopy. Potential risk factors for advanced neoplasia at follow-up were evaluated with univariable and multivariable logistic regression analyses. SETTINGS: This study included data from a multicenter cohort colorectal cancer screening program, conducted from January 2014 to December 2015, based on fecal immunochemical tests in Spain. PATIENTS: We included 2119 participants with at least 1 adenoma ≥20 mm or ≥5 adenomas of any size. MAIN OUTCOME MEASURES: We calculated the absolute risk of developing colorectal cancer, advanced adenomas, and advanced serrated polyps at the 1-year surveillance colonoscopy. Potential risk factors for advanced neoplasia at follow-up were evaluated with univariable and multivariable logistic regression analyses. RESULTS: At 1 year, participants displayed 6 colorectal cancers (0.3%), 228 advanced adenomas (10.5%), and 58 advanced serrated polyps (2.7%). The adjusted analysis identified 2 factors associated with advanced neoplasia: >5 adenomas (odds ratio 1.53; 95% CI: 1.15-2.03; p = 0.004) and polyps in a proximal location (OR 1.52; 95% CI: 1.15-2.02; p = 0.004). LIMITATIONS: First, the sample size was relatively small compared to other studies with similar aims. Another limitation was the lack of a comparison group, which could have provided more practical results in terms of surveillance recommendations. CONCLUSIONS: The colorectal cancer detection rate at a 1-year colonoscopy surveillance was low among patients classified at high risk of advanced neoplasia. The risk factors for advanced neoplasia were ≥5 adenomas and proximal polyps at baseline. See Video Abstract at http://links.lww.com/DCR/B820 . RIESGO DE CNCER COLORRECTAL Y DE PLIPOS AVANZADOS UN AO DESPUS DE LA RESECCIN DE ADENOMAS DE ALTO RIESGO: ANTECEDENTES:Los pacientes con adenomas múltiples o grandes se consideran de alto riesgo para desarrollar cáncer colorrectal metacrónico.OBJETIVO:Evaluar los riesgos de detectar cáncer colorrectal, adenoma avanzado y pólipos serrados avanzados en la colonoscopia de seguimiento al año, en pacientes con un número mayor o igual a 5 adenomas o adenomas de 20 mm o más.DISEÑO:Estudio descriptivo, retrospectivo, multicéntrico, de cohortes. Calculamos el riesgo absoluto de desarrollar cáncer colorrectal, adenomas avanzados y pólipos serrados avanzados en la colonoscopia de vigilancia al año. Los factores de riesgo potenciales para el desarrollo de una neoplasia avanzada en el seguimiento, fueron evaluados mediante un análisis de regresión logística univariable y multivariable.AJUSTES:Este estudio incluyó datos de un programa de cribado de cáncer colorrectal de cohorte multicéntrico, realizado entre enero de 2014 y diciembre de 2015, con base en pruebas inmunoquímicas de materia fecal, en España.PACIENTES:Incluimos 2119 participantes con al menos un adenoma ≥20 mm o con cinco o más adenomas de cualquier tamaño.PRINCIPALES MEDIDAS DE RESULTADO:Calculamos el riesgo absoluto de desarrollar cáncer colorrectal, adenomas avanzados y pólipos serrados avanzados en la colonoscopia de vigilancia al año. Los potenciales factores de riesgo para desarrollar una neoplasia avanzada en el seguimiento, se evaluaron mediante un análisis de regresión logística univariable y multivariable.RESULTADOS:Al año se encontraron en los pacientes participantes, 6 cánceres colorrectales (0,3%), 228 adenomas avanzados (10,5%) y 58 pólipos serrados avanzados (2,7%). Mediante el análisis ajustado se identificaron dos factores asociados con el desarrollo de neoplasia avanzada: un número igual o mayor a 5 adenomas (razón de probabilidades 1,53; IC del 95%: 1,15-2,03; p = 0,004) y la presencia de pólipos en una ubicación proximal (razón de probabilidades 1,52; IC del 95%: 1,15-2,02; p = 0,004).LIMITACIONES:Primero, el tamaño de la muestra fue relativamente pequeño en comparación con otros estudios con objetivos similares. Otra limitación fue la falta de un grupo comparativo, que podría haber proporcionado resultados más prácticos, en términos de recomendaciones de vigilancia.CONCLUSIÓNES:La tasa de detección de cáncer colorrectal mediante una colonoscopia de vigilancia al año, fue baja entre los pacientes clasificados como de alto riesgo de neoplasia avanzada. Los factores de riesgo para desarrollar una neoplasia avanzada fueron; un número igual o mayor a 5 adenomas y la presencia de pólipos proximales en la colonoscopia inicial de base. Consulte Video Resumen en http://links.lww.com/DCR/B820 . ( Traducción-Eduardo Londoño-Schimmer ).

Effects of Somatic Methylation in Colonic Polyps on Risk of Developing Metachronous Advanced Colorectal Lesions.

The utility of molecular markers for predicting the risk of metachronous advanced colorectal lesions (MACLs) remains poorly investigated. We examined the relationship between somatic hypermethylation in polyps at baseline and the risk of developing MACL. This retrospective cohort study included 281 consecutive patients with colonic polyps who were enrolled between 2007 and 2009 and followed-up until 2014. MACLs were defined as adenomas of ≥10 mm, high-grade dysplasia, or with a villous component; and serrated lesions of ≥10 mm or with dysplasia. In total, 595 polyps were removed at baseline colonoscopy and analyzed for pathological characteristics and CpG island methylator phenotype (CIMP) using the MS-MLPA (Methylation-Specific -- Multiplex Ligation-dependent Probe Amplification) technique. Forty-five patients (16.0%) showed at least one CIMP+ polyp. MACL risk was higher in patients with CIMP+ polyps (odds ratio (OR), 4.50; 95% CI, 1.78-11.4; p = 0.002). Patients with CIMP+ polyps also exhibited shorter time to MACL development (33.8 months vs. 50.1 months; p < 0.001), even with adjustment for polyp size and number (OR, 2.40; 95% CI, 1.33-4.34). Adding CIMP analysis improved the sensitivity (57.0% to 70.9%), negative predictive value (71.1% to 77.3%), and overall accuracy (49.8% to 52.0%) for MACL risk estimation. These results highlight that CIMP may be a useful marker for endoscopic surveillance.

Increased Th17-Related Cytokine Serum Levels in Patients With Multiple Polyps of Unexplained Origin.

OBJECTIVES: Most patients with multiple colonic polyps do not have a known genetic or hereditary origin. Our aim was to analyze the presence of inflammatory cytokines and levels of glucose, insulin, and C-reactive protein (CRP) in patients with multiple colonic polyps. METHODS: Eighty-three patients with 10 or more adenomatous or serrated polyps and 53 control people with normal colonoscopy were included. Smoking habits were registered, and glucose, CRP, and basal insulin in the serum/blood were measured. Quantification of IL-2, IL-4, IL-6, IL-10, IL-11, IL-17A, and IL-23 cytokine levels in the serum was performed by a high-sensitivity enzyme-linked immunosorbent assay. RESULTS: Smoking and diabetes were more prevalent in those with colonic polyps than in the control people (67% vs 16%, P = 0.001; 11% vs 2%, P = 0.048). In addition, the cytokine serum levels were higher, i.e., IL-2 (P = 0.001), IL-4 (P = 0.001), IL-6 (P = 0.001), IL-17A (P = 0.001), IL-23 (P = 0.014), and CRP (P = 0.003). Adjusting for sex, smoking, and diabetes in a multivariate analysis, IL-2, IL-4, IL-6, IL-17A, and IL-23 remained independently elevated in cases with multiple polyps. DISCUSSION: These results indicate that immune responses mediated by Th17 cells may be involved in the pathogenesis of multiple colonic polyps.