Single-center study of Lynch syndrome screening in colorectal polyps

Rare single-nucleotide variants of MLH1 and MSH2 genes in patients with Lynch syndrome

BACKGROUND

Approximately 5% of colorectal cancers (CRCs) are hereditary. Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is the most common form of recognized hereditary CRC. Although Iran, as a developing country, has a high incidence of CRC, the spectrum of variants has yet to be thoroughly investigated.

AIMS

This study aimed to investigate pathogenic and non-pathogenic variants in MLH1 and MSH2 genes in Iranian patients with suspected Lynch syndrome (sLS).

METHODS AND RESULTS

In the present study, 25 peripheral blood samples were collected from patients with sLS and high microsatellite instability (MSI-H). After DNA extraction, all samples underwent polymerase chain reaction and Sanger sequencing to identify the variants in the exons of MLH1 and MSH2 genes. The identified variants were interpreted using prediction tools, and were finally reported under ACMG guidelines. In our study population, 13 variants were found in the MLH1 gene and 8 in the MSH2 gene. Interestingly, 7 of the 13 MLH1 variants and 3 of the 8 MSH2 variants were novel, whereas the remaining variants were previously reported or available in databases. In addition, some patients with sLS did not have variants in the exons of the MLH1 and MSH2 genes. The variants detected in the MLH1 and MSH2 genes had specific characteristics regarding the number, area of occurrence, and their relationship with demographic and clinicopathologic features.

CONCLUSION

Overall, our results suggest that analysis of MLH1 and MSH2 genes alone is insufficient in the Iranian population, and more comprehensive tests are recommended for detecting LS.

Genetic testing decision-making experiences within families of colorectal cancer patients: A qualitative study

PURPOSE

Genetic testing is the gold standard for the diagnosis of hereditary colorectal cancer syndromes but is currently inadequate and nonideal. The decision-making processes regarding genetic testing are even less well known. The present study aims to explore the decision-making experience of genetic testing for colorectal cancer patients and their family members.

METHOD

A descriptive qualitative study was employed. Data were collected using individual semi-structured interviews with 5 colorectal cancer patients and 20 family members from November 2020 to April 2021. Interviews were transcribed and analysed using inductive content analysis.

RESULTS

Four categories were identified: 1) the source of information for genetic testing, 2) the differentiated attitudes towards genetic testing, 3) genetic testing decisional needs, and 4) the factors influencing genetic testing decision-making. Colorectal cancer patients and their families engaged in two distinct pathways to genetic testing decisions: direct decision-making and indirect decision-making. Throughout these processes, due to the limited source of information, they had information needs that were met and facilitated genetic testing decision-making.

CONCLUSIONS

Colorectal cancer patients and family members need knowledge related to genetic testing, but they have limited access to information, which prevents them from making informed decisions. Providing decision aid interventions and informational support are significant steps towards addressing the support needs of this population.

PMS2 Pathogenic Variant in Lynch Syndrome-Associated Colorectal Cancer with Polyps

Background  Lynch syndrome (LS) is an autosomal dominant condition due to the germline mutation in the mismatch repair (MMR) genes including MLH1 , MSH2 , MSH6, and PMS2 (post-meiotic segregation increased 2). The MMR mutation carriers have high risk for cancers. Pathogenic PMS2 variants are rarely reported in LS-associated colorectal cancer (CRC) with colorectal polyps. The aim of the study was to investigate the genetic etiology of CRC in an individual with CRC with multiple colorectal polyps and a family history of cancers. Patients and Methods  The index patient was an African male affected by CRC with multiple colorectal polyps. The clinical diagnostic for LS was based on the Amsterdam II criteria and pedigree. Next-generation sequencing with inherited cancer genes panel was used to detect the pathogenic variant. Results  The patient fulfilled the Amsterdam II criteria and the pedigree revealed a family history of recurrent CRC. A deleterious PMS2 germline heterozygous mutation c.2192_2196delTAACT was detected. Conclusion  Our study supports the notion that LS may be associated with polyps and shows the predisposition of PMS2 heterozygous mutation in LS-associated CRC at young age.

Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS

Lynch syndrome (LS), caused by heterozygous pathogenic variants affecting one of the mismatch repair (MMR) genes (MSH2, MLH1, MSH6, PMS2), confers moderate to high risks for colorectal, endometrial, and other cancers. We describe a four-generation, 13-branched pedigree in which multiple LS branches carry the MSH2 pathogenic variant c.2006G>T (p.Gly669Val), one branch has this and an additional novel MSH6 variant c.3936_4001+8dup (intronic), and other non-LS branches carry variants within other cancer-relevant genes (NBN, MC1R, PTPRJ). Both MSH2 c.2006G>T and MSH6 c.3936_4001+8dup caused aberrant RNA splicing in carriers, including out-of-frame exon-skipping, providing functional evidence of their pathogenicity. MSH2 and MSH6 are co-located on Chr2p21, but the two variants segregated independently (mapped in trans) within the digenic branch, with carriers of either or both variants. Thus, MSH2 c.2006G>T and MSH6 c.3936_4001+8dup independently confer LS with differing cancer risks among family members in the same branch. Carriers of both variants have near 100% risk of transmitting either one to offspring. Nevertheless, a female carrier of both variants did not transmit either to one son, due to a germline recombination within the intervening region. Genetic diagnosis, risk stratification, and counseling for cancer and inheritance were highly individualized in this family. The finding of multiple cancer-associated variants in this pedigree illustrates a need to consider offering multicancer gene panel testing, as opposed to targeted cascade testing, as additional cancer variants may be uncovered in relatives.

Prevalence of Mismatch Repair-Deficient Colorectal Adenoma/Polyp in Early-Onset, Advanced Cases: a Cross-Sectional Study Based on Iranian Hereditary Colorectal Cancer Registry

BACKGROUND

Lynch syndrome (LS) increases the risk of many types of cancer, mainly colorectal cancer (CRC). The purpose of this study was to assess the prevalence of mismatch repair (MMR) deficiency in patients under the age of 50 with advanced adenomatous polyps, aiming at an early diagnosis of LS.

METHODS

This retrospective, cross-sectional study included eligible patients with advanced adenomas diagnosed ≤ 50 years of age registered between April 2014 and February 2017 at three pathology centers in Mashhad. Pathological records were reviewed, and colon tissue specimens were analyzed by immunohistochemistry (IHC) staining to identify proteins which serve as markers for LS as they are related to loss of MMR gene (MLH1, MSH2, MSH6, and PMS2) expression.

RESULTS

Of 862 consecutive patients, a total of 50 adenomas (54% males, 46% females of mean age 41.24 ± 6.5) met the eligibility criteria. Of the adenomas examined, 20 (40%) had a tubulovillous component, 34 (68%) had high-grade dysplasia, and 30 (60%) had were larger than 10 mm protrusions. None of the patients had loss of MMR protein expression.

CONCLUSION

No individual with MMR genetic disorder was identified by IHC screening of early-onset advanced colorectal adenomas. This strategy is therefore not an effective strategy for detecting MMR mutation carriers.

Overview on population screening for carriers with germline mutations in mismatch repair (MMR) genes in China

DNA mismatch repair (MMR) genes play an important role in maintaining genome stability. Germline mutations in MMR genes disrupt the mismatch repair function and cause genome instability. Carriers with MMR germline mutations are more likely to have MMR deficiency and microsatellite instability (MSI) than non-carriers and are prone to develop colorectal cancer (CRC) and extracolorectal malignancies, known as Lynch syndrome (LS). MMR gene testing for suspected mutation carriers is a reliable method to identify the mutation types and to discover mutation carriers. Given that carriers of MMR germline mutations have a higher risk of LS-related cancers (LS-RC) and a younger age at onset than non-carriers, early surveillance and regular screening of relevant organs of carriers are very important for early detection of related cancers. This review mainly focuses on the general status of MMR carriers, the approaches for early detection and screening, and the surveillance of MMR mutation carriers in China. Population screening of MMR germline mutation carriers in China will be helpful for early detection, early diagnosis and treatment of MMR mutation carriers, which may improve the 5-year survival, and reduce mortality and incidence rate in the long term.

How Should We Test for Lynch Syndrome? A Review of Current Guidelines and Future Strategies

International guidelines for the diagnosis of Lynch syndrome (LS) recommend molecular screening of colorectal cancers (CRCs) to identify patients for germline mismatch repair (MMR) gene testing. As our understanding of the LS phenotype and diagnostic technologies have advanced, there is a need to review these guidelines and new screening opportunities. We discuss the barriers to implementation of current guidelines, as well as guideline limitations, and highlight new technologies and knowledge that may address these. We also discuss alternative screening strategies to increase the rate of LS diagnoses. In particular, the focus of current guidance on CRCs means that approximately half of Lynch-spectrum tumours occurring in unknown male LS carriers, and only one-third in female LS carriers, will trigger testing for LS. There is increasing pressure to expand guidelines to include molecular screening of endometrial cancers, the most frequent cancer in female LS carriers. Furthermore, we collate the evidence to support MMR deficiency testing of other Lynch-spectrum tumours to screen for LS. However, a reliance on tumour tissue limits preoperative testing and, therefore, diagnosis prior to malignancy. The recent successes of functional assays to detect microsatellite instability or MMR deficiency in non-neoplastic tissues suggest that future diagnostic pipelines could become independent of tumour tissue.

Is tumor testing efficiency for Lynch syndrome different in rectal and colon cancer?

BACKGROUND

Tumor testing utility in Lynch syndrome (LS) diagnosis is established.

AIMS

Analyze the differences between tumor testing efficiency in rectal (RC) and colon cancer (CC).

METHODS

We performed immunohistochemistry (IHC) for MisMatch Repair (MMR) proteins (IHC-MMR) and MicroSatellite Instability analysis (MSI) on 482 unselected primary tumors: 320 CCs and 162 RCs. Samples had proficient-IHC, deficient-IHC or borderline-IHC ("patchy" expression). MSI-H borderline-IHC tumors were considered as likely MMR-deficient. Germline testing was offered to MMR-deficient patients without BRAF mutation or MLH1 promoter hypermetilation (MLH1-Hy).

RESULTS

We identified 51/482 (10.6%) MMR-defective tumors. Multivariable analysis demonstrated a significant correlation between tumor testing results with histotype, lymph-node involvement and tumor location. In particular, RC showed a lower MMR-deficiency rate than CC (p<0.0001). Interestingly, MLH1 loss was detected in 0% RCs and 76.1% CCs, with 80% of them showing BRAF mutation/MLH1-Hy. A germline variant was detected in 12 out of 18 patients (mutation detection rate of 66.7%).

CONCLUSION

Tumor testing results showed molecular differences between CCs and RCs, in terms of MMR proteins expression, and presence of BRAF mutation/MLH1-Hy. MSH6 variants were the most frequent ones (50%). Although young age at diagnosis was associated with mutation detection (p = 0.045), 33.3% of LS patients were >50 years.

Genome-wide mutation analysis in precancerous lesions of endometrial carcinoma

Clinicopathological evidence supports endometrial atypical hyperplasia (AH) or endometrial intraepithelial neoplasia as the precursor of uterine endometrioid carcinoma (EC), the most common gynecologic malignancy. However, the pathogenic progression from AH to EC remains unclear. Here, we employed whole-exome sequencing to identify somatic mutations and copy number changes in micro-dissected lesions from 30 pairs of newly diagnosed AH and EC. We found that all but one pair of AHs shared the same DNA mismatch repair status as their corresponding ECs. The percentage of common mutations between AH lesions and corresponding ECs varied significantly, ranging from 0.1% to 82%. Microsatellite stable AHs had fewer cancer driver mutations than ECs (5 versus 7, p = 0.017), but among microsatellite unstable AHs and ECs there was no difference in mutational numbers (36 versus 38, p = 0.65). As compared to AH specimens, 19 (79%) of 24 microsatellite stable EC tumors gained new cancer driver mutations, most of which involved PTEN, ARID1A, PIK3CA, CTNNB1, or CHD4. Our results suggest that some AH lesions are the immediate precursor of ECs, and progression depends on acquisition of additional cancer driver mutations. However, a complex clonal relationship between AH and EC can also be appreciated, as in some cases both lesions diverge very early or arise independently, thus co-developing with distinct genetic trajectories. Our genome-wide profile of mutations in AH and EC shines new light on the molecular landscape of tumor progression. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Using chatbots to screen for heritable cancer syndromes in patients undergoing routine colonoscopy

BACKGROUND

Hereditary colorectal cancer (HCRC) syndromes account for 10% of colorectal cancers but remain underdiagnosed. This feasibility project tested the utility of an artificial intelligence-based chatbot deployed to patients scheduled for colonoscopy to identify HCRC risk factors, educate participants about HCRC and obtain consent to genetic testing as an extension of genetic counselling of appropriate subjects. Genetic counsellor (GC) and genetic counselling assistant (GCA) time spent per subject was also measured.

METHODS

Patients scheduled for colonoscopy at Cleveland Clinic were invited via electronic medical record patient portal or letter prior to colonoscopy with a link to a chatbot administering the Colon Cancer Risk Assessment Tool (CCRAT) to screen for HCRC syndromes. Those with ≥1 positive response to a CCRAT question received chatbot-deployed genetic education and the option to receive genetic testing. An order for a 55-gene pan-cancer panel was placed for those consenting, and the subject had blood drawn on the day of colonoscopy. Results were disclosed by a GC or GCA by telephone. Subject demographics, progression through the chat, responses to CCRAT, personal and family history, genetic test results and communication with the subject were recorded. Descriptive statistics and two-tailed unpaired t-test and Fisher's exact test were used.

RESULTS

506/4254 (11.9%) initiated and 487 (96.2%) completed the chat with the chatbot. 215 (44.1%) answered 'yes' to ≥1 CCRAT question and all completed pretest education. 129/181 (71.3%) subjects who consented completed testing, and 12 (9.3%) were found to have a germline pathogenic variant. Per subject, the GC spent a mean of 14.3 (SD 7.3) and the GCA a mean of 19.2 (SD 9.8) minutes.

CONCLUSION

The use of a chatbot in this setting was a novel and feasible method, with the potential of increasing genetic screening and testing in individuals at risk of HCRC syndromes.

Challenges Facing the Detection of Colonic Polyps: What Can Deep Learning Do?

Colorectal cancer (CRC) is one of the most common causes of cancer mortality in the world. The incidence is related to increases with age and western dietary habits. Early detection through screening by colonoscopy has been proven to effectively reduce disease-related mortality. Currently, it is generally accepted that most colorectal cancers originate from adenomas. This is known as the "adenoma-carcinoma sequence", and several studies have shown that early detection and removal of adenomas can effectively prevent the development of colorectal cancer. The other two pathways for CRC development are the Lynch syndrome pathway and the sessile serrated pathway. The adenoma detection rate is an established indicator of a colonoscopy's quality. A 1% increase in the adenoma detection rate has been associated with a 3% decrease in interval CRC incidence. However, several factors may affect the adenoma detection rate during a colonoscopy, and techniques to address these factors have been thoroughly discussed in the literature. Interestingly, despite the use of these techniques in colonoscopy training programs and the introduction of quality measures in colonoscopy, the adenoma detection rate varies widely. Considering these limitations, initiatives that use deep learning, particularly convolutional neural networks (CNNs), to detect cancerous lesions and colonic polyps have been introduced. The CNN architecture seems to offer several advantages in this field, including polyp classification, detection, and segmentation, polyp tracking, and an increase in the rate of accurate diagnosis. Given the challenges in the detection of colon cancer affecting the ascending (proximal) colon, which is more common in women aged over 65 years old and is responsible for the higher mortality of these patients, one of the questions that remains to be answered is whether CNNs can help to maximize the CRC detection rate in proximal versus distal colon in relation to a gender distribution. This review discusses the current challenges facing CRC screening and training programs, quality measures in colonoscopy, and the role of CNNs in increasing the detection rate of colonic polyps and early cancerous lesions.