Microsatellite Alterations Research Articles

Immunological Features with DNA Microsatellite Alterations in Patients with Colorectal Cancer.

Competent human DNA mismatch repair (MMR) corrects DNA polymerase mistakes made during cell replication to maintain complete DNA fidelity in daughter cells; faulty DNA MMR occurs in the setting of inflammation and neoplasia, creating base substitutions (e.g. point mutations) and frameshift mutations at DNA microsatellite sequences in progeny cells. Frameshift mutations at DNA microsatellite sequences are a detected biomarker termed microsatellite instability (MSI) for human disease, as this marker can prognosticate and determine therapeutic approaches for patients with cancer. There are two types of MSI: MSI-High (MSI-H), defined by frameshifts at mono- and di-nucleotide microsatellite sequences, and elevated microsatellite alterations at selected tetranucleotide repeats or EMAST, defined by frameshifts in di- and tetranucleotide microsatellite sequences but not mononucleotide sequences. Patients with colorectal cancers (CRCs) manifesting MSI-H demonstrate improved survival over patients without an MSI-H tumor, driven by the generation of immunogenic neoantigens caused by novel truncated proteins from genes whose sequences contain coding microsatellites; these patients' tumors contain hundreds of somatic mutations, and show responsiveness to treatment with immune checkpoint inhibitors. Patients with CRCs manifesting EMAST demonstrate poor survival over patients without an EMAST tumor, and may be driven by a more dominant defect in double strand break repair attributed to the MMR protein MSH3 over its frameshift correcting function; these patients' tumors often have a component of inflammation (and are also termed inflammation-associated microsatellite alterations) and show less somatic mutations and lack coding mononucleotide frameshift mutations that seem to generate the neoantigens seen in the majority of MSI-H tumors. Overall, both types of MSI are biomarkers that can prognosticate patients with CRC, can be tested for simultaneously in marker panels, and informs the approach to specific therapy including immunotherapy for their cancers.

IBCL-327: Genetic Instability (MSI, EMAST) in Patients with Follicular Lymphoma and Diffuse Large B-Cell Lymphoma

Context: Genetic instability is one of the characteristic features of tumor cells and is associated with tumor progression and transformation. An integral measure of genetic instability could be assessed through STR (short tandem repeats) analysis in terms of MSI (microsatellite instability) and EMAST (elevated microsatellite alteration at selected tetranucleotides). MSI and EMAST occur as a result of DNA repair complex malfunction in tumor cells. The study presents MSI and EMAST data in patients with non-Hodgkin B-cell lymphomas: follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Objective: To determine the frequency of MSI and EMAST as predictors of the clinical course of the disease at the early stages of diagnosis in patients with FL and DLBCL. Design: FL patients (n=7) and DLBCL patients (n=5) who followed up at the National Research Center for Hematology were included in the study after receiving their informed consent. DNA samples from tumor and control DNA samples from healthy somatic cells of the same patient were isolated according to a standard protocol. Genetic instability was assessed by multiplex PCR of STR loci with COrDIS Plus and COrDIS MSI kits (Gordiz Ltd, Russia). The fragment analysis was performed on an ABI3130 Genetic Analyzer. Results: The observed frequency of MSI and EMAST in FL was 15% (1/7) and 28% (2/7); in DLBCL, 0% (0/5) and 20% (1/5), respectively. STR profiles also revealed allelic imbalance due to loss of heterozygosity (LOH) with a high incidence: 71% (5/7) and 60% (3/5) in FL and DLBCL, respectively. LOH is an independent form of genetic instability and probably associated with recombination complex disruption in tumor cells. LOH reflects the loss of a significant amount of genetic material from a single chromosome via deletions or uniparental disomy. Conclusions: Statistically significant measures could not be reported here due to the small sample size. However, the findings show that STR instability is not a rare event in non-Hodgkin B-cell lymphomas; therefore, further detailed analysis of extended patient cohorts to determine its clinical significance is required.

ABCL-349: Genetic Instability of Microsatellite Loci in Primary Mediastinal B-cell Lymphoma

Context: Loss of heterozygosity (LOH) in STR loci, elevated microsatellite alteration at selected tetranucleotides (EMAST) and instability of mononucleotide tandem repeats (MSI - microsatellite instability) are intrinsic features of diverse tumor cells. For primary mediastinal B-cell lymphoma (PMBCL) these molecular factors to determine the prognosis of the disease have not been described yet. Objective: To analyze the frequency of LOH, EMAST, and MSI in tumor cells of PMBCL patients at diagnosis and to check possible association with disease features. Design: STR profiles of the DNA of tumor cells were analyzed on a cohort of 36 PMBCL patients undergoing treatment at the National Research Center for Hematology (Moscow, Russia). Setting: DNA was isolated from tumor biopsy samples taken at diagnosis. Control DNA samples were taken from the blood of patients in complete remission or from the buccal epithelium. STR-profiles for LOH and EMAST analysis were assessed by PCR with COrDIS Plus multiplex kit for amplification of 19 STR-markers and amelogenin loci (Gordiz Ltd, Russia). COrDIS MSI (BAT-25, BAT-26, NR-21, NR-24 and NR-27) kit was used for MSI testing. The fragment analysis was performed on ABI3130 Genetic Analyzer. Patients: Inclusion criteria: de novo diagnosed PMBCL patients. There were 10 males and 26 females, the median age at presentation was 30 years (range 21–61). Main outcome measures: Progression-free survival (PFS) and overall survival (OS) at 24 months from diagnosis were used to assess the independent impact of the genetic instability as a risk factor. Results: LOH was revealed in 21 out of 36 patients (58%). EMAST was found in 18 patients (50%); in 12 of them EMAST was accompanied by LOH, and in one by MSI. MSI was found in three patients only. OS and PFS were highest in the group with stable STR profile of a tumor, but not formally significant because of the small sample size. Conclusions: The high incidence of LOH and EMAST in PMBCL can cause standard therapy failure in a significant number of patients. EMAST as a variant of microsatellite instability might be useful for further consideration as a predictor of response to checkpoint inhibitor therapy.

Abstract 5296: Instability of non standard microsatellites in metastatic colorectal cancer patients treated with a bevacizumab based chemotherapy

Abstract Bevacizumab (B) is a biological agent frequently included in the treatment of metastatic colon cancer (mCRC), although at present there is no effective biomarker that can predict its efficacy. Few studies report a positive association of microsatellite instability (MSI) with the response to anti-angiogenic therapy, but the role of MSI in relation to B efficacy needs to be better understood. Elevated microsatellite alterations at selected tetranucleotides repeats (EMAST) can be observed at higher rate in mCRC patients compared to MSI. The predictive and prognostic role of EMAST has not been completely investigated so far. Moreover, it is known that angiogenesis in mCRC goes through the activation of VEGF-A, but VEGF-B can be involved in some compensatory effect during anti-VEGF-A treatments. By exploring the UCSC Genome Browser database, we found that the VEGF-B gene possesses a poly-dinucleotide microsatellite (normally 19xAG) which somatic instability has never been reported. In this study, we analyzed the status of MSI, five EMAST markers (D20S82, D20S85, D8S321, D9S242, MYCL1) and the VEGF-B microsatellite in relation to prognosis in 145 mCRC patients treated with chemotherapy alone (n=51) or chemotherapy plus B (n=94). MSI high (MSI-H) was detected in four patients (3%) out of 141 participants. Using a multivariable model and adjusting for patient characteristics, microsatellite status remains significantly associated with progression free survival (PFS) and overall survival (OS). The PFS hazard ratio (HR) for MSI-H patients was 3.18 (95% CI 1.09-9.25; p=0.034) and the OS HR was 6.45 (95% CI 2.08-19.99; p=0.001). Eleven (7.8%) patients out of 140 were positive to at least two EMAST markers. EMAST instability was associated with a general worse prognosis, trend that become significant in the group of patients treated with CT plus B in term of PFS (median survival 5 months vs 11. months, p=0.0006) and OS (median survival 6.1 months vs 29.1 months, p<0.0001). The interaction test showed a significant association of D20S82 (PFS p=0.004) and MYCL1(PFS p=0.029), with worse prognosis when treated with CT plus B, adding a possible predictive value in mCRC patients. The 24.2% of patients (29 out of 120) showed a VEGF-B-poly-AG instability. Amplification of the poly-AG is associated with worse outcome in PSF (7.0 month of median survival vs 28.0 months for patients with shortened poly-AG; p=0.005) in patients treated with CT alone, suggesting that an extended microsatellite in VEGF-B might have a role in the resistance to chemotherapy. In conclusion, MSI, EMAST and VEGF-B poly-AG instability are associated with prognosis in mCRC patients treated with CT or CT plus B. MSI and EMAST instability are associated with worse prognosis in CT+B patients, while VEGF-B microsatellite instability is linked to worse prognosis in CT patients. Further investigations are needed but we can hypothesize that MSI, EMAST and VEGF-B poly-AG instability can have some relevance for the clinical outcome of the disease. Citation Format: Francesca Pirini, Luigi Pasini, Sara Ravaioli, Gianluca Tedaldi, Emanuela Scarpi, Giorgia Marisi, Chiara Molinari, Daniele Calistri, Alessandro Passardi, Paola Ulivi. Instability of non standard microsatellites in metastatic colorectal cancer patients treated with a bevacizumab based chemotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5296.

Is elevated microsatellite alterations at selected tetranucleotide repeats (EMAST)-negative/MSI-high colorectal cancer a distinct subtype of the disease?

Microsatellite instability (MSI) plays a prognostic and predictive role in colorectal cancer (CRC). Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), a novel type of MSI, was recently identified. A retrospective analysis of a prospective cohort database was performed. Patients who attempted curative surgery for MSI-high (MSI-H) CRC and had available testing results of EMAST were included for analysis. The difference in clinical characteristics, immunohistochemistry profile, and 3-year recurrence-free and overall survival between EMAST-negative and EMAST-positive tumors was measured. EMAST status was successfully evaluated in 86 cases among patients who received EMAST testing, and only 16.3% (14/86) of these patients were EMAST-negative/MSI-H. Patients with EMAST-negative tumors were younger; their tumors exhibited well differentiation, less venous invasion, and greater mutS homolog 3 expression. There was no distant metastasis or cancer-specific death among EMAST-negative patients. Yet no statistically significant difference was found between the two groups in 3-year overall or recurrence-free survival. Patients with EMAST-negative/MSI-H CRC seem to have different clinicopathological characteristics. Future large-scale studies could clarify the role of EMAST genotype as a sub-classifier of MSI-H CRC.

EMAST frequency in colorectal cancer: a meta-analysis and literature review.

Aim: The prognostic and predictive value of Elevated Microsatellite Alterations at Selected Tetranucleotide (EMAST) has been reported in colorectal cancer (CRC). The prevalence of EMAST in CRC varied across the literature. We conducted a meta-analysis to determine the prevalence of EMAST in CRC. Materials & methods: Three international databases including PubMed, ISI and Scopus were searched to identify related articles that described the frequency of EMAST. Results: Analysis was performed on 16 eligible studies including 4922 patients. The overall EMAST prevalence among CRCs patients was 33% (95% CI: 23-43%, I2=98%). Conclusion: This study indicated that approximately a third of the CRC patients are diagnosed with EMAST, hereupon EMAST as a prognostic and predictive biomarker should be more studied clinically.

The Human DNA Mismatch Repair Protein MSH3 Contains Nuclear Localization and Export Signals That Enable Nuclear-Cytosolic Shuttling in Response to Inflammation.

Inactivation of DNA mismatch repair propels colorectal cancer (CRC) tumorigenesis. CRCs exhibiting elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) show reduced nuclear MutS homolog 3 (MSH3) expression with surrounding inflammation and portend poor patient outcomes. MSH3 reversibly exits from the nucleus to the cytosol in response to the proinflammatory cytokine interleukin-6 (IL-6), suggesting that MSH3 may be a shuttling protein. In this study, we manipulated three putative nuclear localization (NLS1 to -3) and two potential nuclear export signals (NES1 and -2) within MSH3. We found that both NLS1 and NLS2 possess nuclear import function, with NLS1 responsible for nuclear localization within full-length MSH3. We also found that NES1 and NES2 work synergistically to maximize nuclear export, with both being required for IL-6-induced MSH3 export. We examined a 27-bp deletion (Δ27bp) within the polymorphic exon 1 that occurs frequently in human CRC cells and neighbors NLS1. With oxidative stress, MSH3 with this deletion (Δ27bp MSH3) localizes to the cytoplasm, suggesting that NLS1 function in Δ27bp MSH3 is compromised. Overall, MSH3's shuttling in response to inflammation enables accumulation in the cytoplasm; reduced nuclear MSH3 increases EMAST and DNA damage. We suggest that polymorphic sequences adjacent to NLS1 may enhance cytosolic retention, which has clinical implications for inflammation-associated neoplastic processes.

Prevalence of PD-L1 expression is associated with EMAST, density of peritumoral T-cells and recurrence-free survival in operable non-metastatic colorectal cancer

IntroductionMicrosatellite instability (MSI) predict response to anti-PD1 immunotherapy in colorectal cancer (CRC). CRCs with MSI have higher infiltration of immune cells related to a better survival. Elevated Microsatellite Alterations at Tetranucleotides (EMAST) is a form of MSI but its association with PD-L1 expression and immune-cell infiltration is not known.MethodsA consecutive, observational cohort of patients undergoing surgery for CRC. EMAST and clinicopathological characteristics were investigated against PD-L1, as well as CD3 and CD8 expression in the invasive margin or tumour centre (Immunoscore). Difference in survival between groups was assessed by log rank test.ResultsA total of 149 stage I–III CRCs patients, with a median follow up of 60.1 months. Patients with PD-L1+ tumours (7%) were older (median 79 vs 71 years, p = 0.045) and had EMAST+ cancers (OR 10.7, 95% CI 2.2–51.4, p = 0.001). Recurrence-free survival was longer in cancers with PD-L1+ immune cells (HR 0.35, 95% CI 0.16–0.76, p = 0.008, independent of EMAST) and high Immunoscore (HR 0.10, 95% CI 0.01–0.72, p = 0.022). Patients expressing PD-L1 in immune cells had longer disease-specific survival (HR 0.28, 95% CI 0.10–0.77, p = 0.014).ConclusionsHigher Immunoscore (CD3/CD8 cells) and expression of tumour PD-L1 is found in CRCs with EMAST. Lymphocytic infiltrate and peritumoral PD-L1 expression have prognostic value in CRC.

The Clinicopathological Features and Genetic Mutations in Gastric Cancer Patients According to EMAST and MSI Status.

Background: There has been no report regarding the clinicopathological features and genetic mutations regarding elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) in gastric cancer (GC). Methods: The correlation among EMAST status, microsatellite instability (MSI) status, mutations of common GC-related genes and 16 DNA repair-associated genes, and the clinicopathological features were analyzed. Results: Among the 360 GC patients enrolled, there were 76 (21.1%) with EMAST+ tumors and 284 with EMAST− tumors, and 59 (16.4%) were MSI-high (MSI-H) tumors, and 301 were microsatellite stable (MSS) tumors. Patients with EMAST+ tumors exhibited an earlier pathological T category and had more genetic mutations in the PI3K/AKT pathway, ARID1A and DNA repair-associated genes than those with EMAST− tumors. Patients with MSI-H tumors have more genetic mutations in the PI3K/AKT pathway and DNA repair-associated genes than those with MSS tumors. In the subgroup analysis for MSI-H GC, EMAST+ tumors were associated with earlier pathological T and N categories, earlier TNM stages, higher frequency of DNA-repair-associated genetic mutations, and a better survival rate than EMAST− tumors. Conclusions: PI3K/AKT pathway mutations may play an important role in EMAST+ and/or MSI-H GC. EMAST+/MSI-H tumors seem to represent a different subtype of gastric cancer from EMAST−/MSI-H tumors.

Application of msh3 immunohistochemistry and tetranucleotide microsatellite analysis to identify Elevated Microsatellite Alterations at Selected Tetranucleotide repeats (EMAST) in colorectal tumours

Background and aims: Reduced function of the DNA mismatch repair enzyme MSH3 in tumour cells results in elevated microsatellite alterations at selected tetranucleotide repeats (EMAST). In contrast to microsatellite instability (MSI) caused by MLH1/PMS2/MSH2/MSH6 defects, EMAST in CRCs is a marker of poor prognosis. This study examined the prevalence of EMAST-positive CRCs in a Western Australian population and critically evaluated immunohistochemical and molecular detection methods. Methods and results: MSH3 immunostaining of 250 archival CRCs identified aberrant MSH3 expression (focal or widespread reduction of nuclear MSH3, cytoplasmic MSH3 mis-localisation) in 66% cases. Tetranucleotide MSI (EMAST) was detected in 46% cases, a proportion consistent with limited previous reports. Discordance between MSH3 immunostaining and molecular detection of tetranucleotide MSI resulted from over-detection of abnormal MSH3 immunostaining, which is focal and confounded by common tissue damage (crush, autolysis). Summary and conclusions: Aberrant MSH3 function in CRCs results from elevated inflammatory signalling, a potentially modifiable risk factor that may be targeted to reduce or prevent disease relapse. A combination of MSH3 immunostaining and molecular methods can be used to identify EMAST-positive CRCs, however further antibody development and establishment of consistent tetranucleotide panels will improve the reliability and reproducibility of its detection in routine practice.

Loss of MSH3 Is Not Related to EMAST in Colorectal Cancer. Digitalised Automated Expression Analysis in a Population-Based Cohort

Background: Elevated microsatellite alterations at selected tetranucleotides (EMAST) is a form of microsatellite instability (MSI) that is present at high frequencies in colorectal cancer (CRC). Some reports have recently pointed at mismatch-repair member MSH3 being the putative culprit of its development. MSH3 is part of a complex crucial in repairing both natural and potentially oncogenic mismatches during DNA synthesis and as such it is a ubiquitously expressed protein whose subtle loss might go unnoticed under manual review. This study aims at assessing MSH3 aptness to identifying EMAST-positive tumors and to develop a sensitive, automated and digitalised method of MSH3 protein analysis in immunohistochemically stained tumor slides.

Utility of the immunohistochemical analysis of DNA mismatch-repair proteins in endometrial hyperplasia

The utility of the expression lack of DNA mismatch-repair (MMR) proteins in the detection of Lynch syndrome in endometrial hyperplasia as precursor lesion of endometrial carcinoma has not been well-established. The study investigated the immunoexpression pattern of MMR proteins in endometrial hyperplasia from Tunisian patients. We carried out a retrospective study of 60 endometrial hyperplasias diagnosed among Tunisian patients. Expression of MLH1, MSH2, MSH6, and PMS2 proteins was performed by immunohistochemistry on whole-slide sections of archival tissues. Analysis of MLH1 promoter methylation and microsatellite alterations was conducted in appropriate cases. Microsatellite instability screening was assessed using the Bethesda panel, including BAT25, BAT26, D17S250, D2S123, and D5S346 markers. Expression of MMR proteins was observed in all hyperplasias without atypia as well as in 27 out of 29 atypical hyperplasias. Only two atypical hyperplasias exhibited expression loss of MMR proteins. A single case revealed MSH6 expression lack. Expression loss of MLH1 and PMS2 was identified in another atypical hyperplasia and was associated with hypermethylation of MLH1 promoter. This patient had no familial history of endometrial cancer at the diagnostic time. The two deficient MMR cases showed microsatellite stable pattern. In conclusion, only two endometrial hyperplasias displayed an altered pattern of MMR expression. Our results suggest the limited utility of the immunohistochemical analysis of MMR protein in the early detection of Lynch syndrome in Tunisian patients diagnosed with endometrial hyperplasias. Multicenter studies with larger sample size are needed to more explore these findings.

Tetranucleotide Microsatellite Mutational Behavior Assessed in Real Time: Implications for Future Microsatellite Panels.

Background & AimsFifty percent of colorectal cancers show elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) and are associated with inflammation, metastasis, and poor patient outcome. EMAST results from interleukin 6–induced nuclear-to-cytosolic displacement of the DNA mismatch repair protein Mutated S Homolog 3, allowing frameshifts of dinucleotide and tetranucleotide but not mononucleotide microsatellites. Unlike mononucleotide frameshifts that universally shorten in length, we previously observed expansion and contraction frameshifts at tetranucleotide sequences. Here, we developed cell models to assess tetranucleotide frameshifts in real time.MethodsWe constructed plasmids containing native (AAAG)18 and altered-length ([AAAG]15 and [AAAG]12) human D9S242 locus that placed enhanced green fluorescent protein +1 bp/-1 bp out-of-frame for protein translation and stably transfected into DNA mismatch repair–deficient cells for clonal selection. We used flow cytometry to detect enhanced green fluorescent protein–positive cells to measure mutational behavior.ResultsFrameshift mutation rates were 31.6 to 71.1 × 10-4 mutations/cell/generation and correlated with microsatellite length (r2 = 0.986, P = .0375). Longer repeats showed modestly higher deletion over insertion rates, with both equivalent for shorter repeats. Accumulation of more deletion frameshifts contributed to a distinct mutational bias for each length (overall: 77.8% deletions vs 22.2% insertions), likely owing to continual deletional mutation of insertions. Approximately 78.9% of observed frameshifts were 1 AAAG repeat, 16.1% were 2 repeats, and 5.1% were 3 or more repeats, consistent with a slipped strand mispairing mutation model.ConclusionsTetranucleotide frameshifts show a deletion bias and undergo more than 1 deletion event via intermediates, with insertions converted into deletions. Tetranucleotide markers added to traditional microsatellite instability panels will be able to determine both EMAST and classic microsatellite instability, but needs to be assessed by multiple markers to account for mutational behavior and intermediates.

Inflammation-Associated Microsatellite Alterations Caused by MSH3 Dysfunction Are Prevalent in Ulcerative Colitis and Increase With Neoplastic Advancement.

OBJECTIVES:Inflammation-associated microsatellite alterations (also known as elevated microsatellite alterations at selected tetranucleotide repeats [EMAST]) result from IL-6–induced nuclear-to-cytosolic displacement of the DNA mismatch repair (MMR) protein MSH3, allowing frameshifts of dinucleotide or longer microsatellites within DNA. MSH3 also engages homologous recombination to repair double-strand breaks (DSBs), making MSH3 deficiency contributory to both EMAST and DSBs. EMAST is observed in cancers, but given its genesis by cytokines, it may be present in non-neoplastic inflammatory conditions. We examined ulcerative colitis (UC), a preneoplastic condition from prolonged inflammatory duration.METHODS:We assessed 70 UC colons without neoplasia, 5 UC specimens with dysplasia, 14 UC-derived colorectal cancers (CRCs), and 19 early-stage sporadic CRCs for microsatellite instability (MSI) via multiplexed polymerase chain reaction capable of simultaneous detection of MSI-H, MSI-L, and EMAST. We evaluated UC specimens for MSH3 expression via immunohistochemistry.RESULTS:UC, UC with dysplasia, and UC-derived CRCs demonstrated dinucleotide or longer microsatellite frameshifts, with UC showing coincident reduction of nuclear MSH3 expression. No UC specimen, with or without neoplasia, demonstrated mononucleotide frameshifts. EMAST frequency was higher in UC-derived CRCs than UC (71.4% vs 31.4%, P = 0.0045) and higher than early-stage sporadic CRCs (66.7% vs 26.3%, P = 0.0426). EMAST frequency was higher with UC duration >8 years compared with ≤8 years (40% vs 16%, P = 0.0459).DISCUSSION:Inflammation-associated microsatellite alterations/EMAST are prevalent in UC and signify genomic mutations in the absence of neoplasia. Duration of disease and advancement to neoplasia increases frequency of EMAST. MSH3 dysfunction is a potential contributory pathway toward neoplasia in UC that could be targeted by therapeutic intervention.

Patterns of germline and somatic mutations in 16 genes associated with mismatch repair function or containing tandem repeat sequences.

BackgroundWe assumed that targeted next‐generation sequencing (NGS) of mismatch repair‐associated genes could improve the detection of driving mutations in colorectal cancers (CRC) with microsatellite instability (MSI) and microsatellite alterations at selected tetranucleotide repeats (EMAST) and clarify the somatic mutation patterns of CRC subtypes.Material and methodsDNAs from tumors and white blood cells were obtained from 81 patients with EMAST(+)/MSI‐high (MSI‐H), 78 patients with EMAST(+)/microsatellite stable (MSS), and 72 patients with EMAST(−)/MSI‐H. The germline and somatic mutations were analyzed with a 16‐genes NGS panel.ResultsIn total, 284 germline mutations were identified in 161 patients. The most common mutations were in EPCAM (24.8%), MSH6 (24.2%), MLH1 (21.7%), and AXIN2 (21.7%). Germline mutations of AXIN2, POLE, POLD1, and TGFBR2 also resulted in EMAST and MSI. EMAST(+)/MSI‐H tumors had a significant higher mutation number (205.9 ± 95.2 mut/MB) than tumors that were only EMAST(+) or MSI‐H (118.6 ± 64.2 and 106.2 ± 54.5 mut/MB, respectively; both P < .001). In patients with AXIN2 germline mutations, the number of pathological somatic mutations in the tumors was significantly higher than those without AXIN2 germline mutations (176.7 ± 94.2 mut/MB vs 139.6 ± 85.0 mut/MB, P = .002).ConclusionNext‐generation sequencing could enhance the detection of familial CRC. The somatic mutation burden might result from not only the affected genes in germline mutations but also through the dysfunction of downstream effectors. The AXIN2 gene might associate with hypermutation in tumors. Further in vitro experiments to confirm the causal relationship is deserved.

Elevated Microsatellite Alterations at Selected Tetranucleotides (EMAST) in Colorectal Cancer is Associated with an Elderly, Frail Phenotype and Improved Recurrence-Free Survival.

Elevated microsatellite alterations at selected tetranucleotides (EMAST) is a poorly investigated form of microsatellite instability (MSI) in colorectal cancer (CRC). The aim of this study was to investigate the clinicopathological features of EMAST in CRC and its relation to outcome. A population-based, consecutive cohort of surgically treated stage I-III CRC patients investigated for high-frequency MSI (MSI-H) and EMAST. Clinicopathological differences were reported as odds ratios (OR) and survival was presented as hazard ratios (HR) with 95% confidence intervals (CIs). Of 161 patients included, 25% were aged > 79years. There was a large overlap in the prevalence of EMAST (31.7%) and MSI-H (27.3%) [82.4% of EMAST were also MSI-H]. EMAST had the highest prevalence in the proximal colon (OR 15.9, 95% CI 5.6-45.1; p < 0.001) and in women (OR 4.1, 95% CI 1.9-8.6; p < 0.001), and were poorly differentiated (OR 5.0, 95% CI 2.3-10.7; p< 0.001). Compared with EMAST-negative patients, EMAST-positive patients were older (median age 77 vs. 69years; p < 0.001), leaner (median weight 67.5 vs. 77kg; p = 0.001), had significantly higher rates of hypoalbuminemia (24% vs. 6%; OR 2.3, 95% CI 1.5-3.6; p = 0.002) and anemia (45% vs. 20%; OR 3.3, 95% CI 1.6-6.8; p = 0.001), and had elevated preoperative C-reactive protein (CRP) levels (51% vs. 34%; OR 1.9, 95% CI 1.0-3.9; p = 0.046). Improved recurrence-free survival was found in both MSI-H and EMAST subtypes. In multivariable analysis, node status (pN +), together with elevated CRP and MSI-positive, were the strongest prognostic factors for recurrence-free survival. EMAST in CRC is associated with an older, leaner, and frailer phenotype with a lower risk of recurrence. The relevance of, and putative mechanisms to, EMAST warrants further investigation.

Global Characterization of Circulating Nucleic Acids.

Circulating nucleic acids (CNAs) include genomic and mitochondrial DNA fragments, small RNAs, and bacterial and viral DNA/RNA. Different mechanisms such as cell apoptosis, necrosis, and active CNA release from cells have been proposed to result in nucleic acids in the circulation. Application of next generation sequencing technology demonstrated that CNAs contain specific mutations, indels, microsatellite alterations, and epigenetic changes (DNA methylation) associated with various diseases. Their clinical implications have been demonstrated for diseases such as cancer, stroke, trauma, myocardial infarction, autoimmune disorders, and pregnancy-associated complications. Thus, CNAs in blood represent an attractive family of molecules that can serve as biomarkers and the analysis of CNAs can be alternative for immunohistochemical analyses of conventional biopsies. The methods described in this chapter provides details for circulating DNA and small RNA isolation, CNA(-derived cDNA) library preparation, and sequencing data analysis.

Elevated Microsatellite Alterations at Selected Tetranucleotides (EMAST) Is Not Attributed to MSH3 Loss in Stage I-III Colon cancer: An Automated, Digitalized Assessment by Immunohistochemistry of Whole Slides and Hot Spots

INTRODUCTION: EMAST is a poorly understood form of microsatellite instability (MSI) in colorectal cancer (CRC) for which loss of MSH3 has been proposed as the underlying mechanism, based on experimental studies. We aimed to evaluate whether MSH3 loss is associated with EMAST in CRC. METHODS: A consecutive cohort of patients with stage I-III CRC. Digital image analysis using heatmap-derived hot spots investigated MSH3 expression by immunohistochemistry. Fragment analysis of multiplex PCR was used to assess MSI and EMAST, and results cross-examined with MSH3 protein expression. RESULTS: Of 152 patients, EMAST was found in 50 (33%) and exclusively in the colon. Most EMAST-positive cancers had instability at all 5 markers, and EMAST overlapped with MSI-H in 42/50 cases (84%). The most frequently altered tetranucleotide markers were D8S321 (38.2% of tumors) and D20S82 (34.4%). Subjective evaluation of MSH3 expression by IHC in tumor found ≤10% negative tumor cells in all samples, most being ≤5% negative. Digital analysis improved the detection but showed a similar spread of MSH3 loss (range 0.1–15.7%, mean 2.2%). Hotspot MSH3 negativity ranged between 0.1 to 95.0%, (mean 8.6%) with significant correlation with the whole slide analysis (Spearman's rho=0.677 P<.001). Loss of MSH3 expression did not correlate with EMAST. CONCLUSIONS: In a well-defined cohort of patients with CRC, loss of MSH3 was not associated with EMAST. Further investigation into the mechanisms leading to EMAST in CRC is needed.

Association of intron microsatellite status and exon mutational profiles of TP53 in human colorectal cancer.

Microsatellite instability (MSI) and loss of heterozygosity (LOH), which cause genomic instability, contribute to cancer pathogenesis. However, only few studies have evaluated the association of a single microsatellite locus of the TP53 gene with the mutation spectra of TP53 exons. A total of 256 patients with colorectal cancer were enrolled in the present study. MSI/LOH alterations of a microsatellite in the TP53 intron (TP53ALU) were assessed via short tandem repeat scanning. The exon mutation profile was evaluated by direct sequencing. The mutation rate of TP53 exons was significantly higher in tumors with LOH alterations of TP53 introns compared with those in tumors with a microsatellite-stable status in the TP53 intron (P=0.0047). TNM stage II was significantly more frequent in MSI vs. LOH or MSS of the TP53 intron (P=0.027 and P=0.048, respectively). Thus, microsatellite alterations may be valuable predictors of TP53 exon mutation and the TNM stage of colorectal cancers.

EMAST status as a beneficial predictor of fluorouracil-based adjuvant chemotherapy for Stage II/III colorectal cancer.

Elevated microsatellite alteration at selected tetranucleotide repeats (EMAST) is a type of microsatellite instability that occurs in ∼60% of colorectal cancers (CRCs) and associated with MSH3 dysfunction. A 5-fluorouracil (5-FU)-related cytotoxicity is attenuated in MSH3-deficient colon cancer cells. Reported here is the predictive value of EMAST in CRCs with Stage II or III disease treated with 5-FU-based chemotherapy. EMAST status was analyzed in 157 patients with CRC with Stage II or III disease and MSH3 expression was analyzed using immunohistochemistry. The patients treated with 5-FU-based chemotherapy were studied in terms of the links of EMAST status with MSH3 expression, clinicopathological features, and overall survival (OS). A total of 63 patients (40.1%) had EMAST positive (EMAST+ ) CRC and 77 patients (49.0%) had low MSH3 expression. EMAST+ tumors were associated with advanced TNM stage and poor and moderately differentiated tumor. EMAST CRC was more frequently observed in tumors with low expression of MSH3 in the nucleus (n = 53; 84.1%, p < .001). On multivariate analysis, patients with EMAST+ status had a worse OS (hazard ratio: 2.489, 95% confidence interval [1.149-5.394], and p = .021). Worse OS in EMAST+ patients who received 5-FU-based chemotherapy was significantly more common compared with EMAST- CRCs. There is a link between EMAST and reduced nuclear expression of MSH3. There is worse survival in patients with EMAST+ CRC after 5-FU-based chemotherapy. According to our findings, adjuvant 5-FU-based chemotherapy might not be advantageous in EMAST+ CRCs with Stage II or III disease.