Methylation-specific Multiplex Ligation Probe Amplification Research Articles

Beckwith–Wiedemann syndrome: Clinical, histopathological and molecular study of two Tunisian patients and review of literature

BackgroundBeckwith–Wiedemann syndrome (BWS) is a rare overgrowth syndrome characterized by congenital malformations and predisposition to embryonic tumors. Loss of methylation of imprinting center 2 (IC2) is the most frequent alteration and rarely associated with tumors compared to paternal uniparental disomy of chromosome 11 (UPD(11)pat) and gain of methylation of imprinting center 1.MethodsOur study aimed to describe the clinical, histopathological and genetic characteristics of two patients and establish genotype‐phenotype correlations. The clinical diagnosis was based on the criteria defined by the international expert consensus of BWS. Molecular study of 11p15.5 methylation status was assessed using methylation‐specific‐multiplex ligation probe amplification (MS‐MLPA).ResultsPatients were aged 12 months and 3 months and fulfilled the clinical score of BWS. MS‐MLPA showed molecular alterations consisting of loss of methylation in IC2 (IC2‐LOM) at the maternal allele for one patient and a mosaic UPD(11)pat for the second patient in whom follow‐up at 6months revealed adrenocortical carcinoma (ACC) with low grade of malignancy. Molecular subtypes guide the follow‐up and tumor surveillance, our major concern.ConclusionWe have to take into account the psychological impact of a possible tumor whatever the underlying mechanism is. Nevertheless, the tumor risk remains high for UPD(11)pat. Our study extended the phenotype of BWS with absence of macrosomia in Tunisian patients, contrasting with literature, and added a supplementary case of ACC in the tumor spectrum of BWS patients with UPD(11)pat.

Prader-Willi syndrome genetic subtypes and clinical neuropsychiatric diagnoses in residential care adults.

The historical diagnosis of Prader-Willi syndrome (PWS), a complex genetic disorder, in adults is often achieved by clinical presentation rather than by genetic testing and thus limited genetic subtype-specific psychometric investigations and treatment options. Genetic testing and clinical psychiatric evaluation using Diagnostic and Statistical Manual (DSM)-IV-TR criteria were undertaken on 72 adult residents (34 M; 38 F) from the Prader-Willi Homes of Oconomowoc (PWHO), a specialty PWS group home system. Methylation specific-multiplex ligation probe amplification and high-resolution microarrays were analyzed for methylation status, 15q11-q13 deletions and maternal uniparental disomy 15 (mUPD15). Seventy (33M; 37F) of 72 residents were genetically confirmed and 36 (51%) had Type I or Type II deletions; 29 (42%) with mUPD15 and 5 (7%) with imprinting defects from three separate families. Psychiatric comorbidities were classified as anxiety disorder (38%), excoriation (skin picking) (33%), intermittent explosive disorder ([30%-predominantly among males at 45% compared with females at 16% [OR = 4.3, 95%CI 1.4-13.1, P < 0.008]) and psychotic features (23%). Psychiatric diagnoses did not differ between mUPD15 vs deletion, but a greater number of psychiatric diagnoses were observed for the larger Type I (4.3) vs smaller Type II (3.6) deletions when age was controlled (F = 5.0, P < 0.04). Adults with PWS presented with uniformly higher rates of psychiatric comorbidities which differed by genetic subtype with gender-specific trends.

Methylation pattern analysis in prostate cancer tissue: identification of biomarkers using an MS-MLPA approach.

BackgroundEpigenetic silencing mediated by CpG island methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with prostate carcinogenesis could potentially identify a tumour-specific methylation pattern, facilitating the early diagnosis of prostate cancer. The objective of the study was to assess the methylation status of 40 tumour suppressor genes in prostate cancer and healthy prostatic tissues.MethodsWe used methylation specific-multiplex ligation probe amplification (MS-MLPA) assay in two independent case series (training and validation set). The training set comprised samples of prostate cancer tissue (n = 40), healthy prostatic tissue adjacent to the tumor (n = 26), and healthy non prostatic tissue (n = 23), for a total of 89 DNA samples; the validation set was composed of 40 prostate cancer tissue samples and their adjacent healthy prostatic tissue, for a total of 80 DNA samples. Methylation specific-polymerase chain reaction (MSP) was used to confirm the results obtained in the validation set.ResultsWe identified five highly methylated genes in prostate cancer: GSTP1, RARB, RASSF1, SCGB3A1, CCND2 (P < 0.0001), with an area under the ROC curve varying between 0.89 (95 % CI 0.82–0.97) and 0.95 (95 % CI 0.90–1.00). Diagnostic accuracy ranged from 80 % (95 % CI 70–88) to 90 % (95 % CI 81–96). Moreover, a concordance rate ranging from 83 % (95 % CI 72–90) to 89 % (95 % CI 80–95) was observed between MS-MLPA and MSP.ConclusionsOur preliminary results highlighted that hypermethylation of GSTP1, RARB, RASSF1, SCGB3A1 and CCND2 was highly tumour-specific in prostate cancer tissue.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-016-1014-6) contains supplementary material, which is available to authorized users.

TP53 alterations in pancreatic acinar cell carcinoma: new insights into the molecular pathology of this rare cancer.

The molecular alterations of pancreatic acinar cell carcinomas (ACCs) are poorly understood and have been reported as being different from those in ductal adenocarcinomas. Loss of TP53 gene function in the pathogenesis of ACCs is controversial since contradictory findings have been published. A comprehensive analysis of the different possible genetic and epigenetic mechanisms leading to TP53 alteration in ACC has never been reported and hence the role of TP53 in the pathogenesis and/or progression of ACC remains unclear. We investigated TP53 alterations in 54 tumor samples from 44 patients, including primary and metastatic ACC, using sequencing analysis, methylation-specific multiplex ligation probe amplification, fluorescence in situ hybridization, and immunohistochemistry. TP53 mutations were found in 13 % of primary ACCs and in 31 % of metastases. Primary ACCs and metastases showed the same mutational profile, with the exception of one case, characterized by a wild-type sequence in the primary carcinoma and a mutation in the corresponding metastasis. FISH analysis revealed deletion of the TP53 region in 53 % of primary ACCs and in 50 % of metastases. Promoter hypermethylation was found in one case. The molecular alterations correlated well with the immunohistochemical findings. A statistically significant association was found between the combination of mutation of one allele and loss of the other allele of TP53 and worse survival.

Microsatellite unstable gastrointestinal neuroendocrine carcinomas: a new clinicopathologic entity.

Gastroenteropancreatic (GEP) neuroendocrine carcinomas (NECs) and mixed adenoneuroendocrine carcinomas (MANECs) are heterogeneous neoplasms characterized by poor outcome. Microsatellite instability (MSI) has recently been found in colorectal NECs showing a better prognosis than expected. However, the frequency of MSI in a large series of GEP-NEC/MANECs is still unknown. In this work, we investigated the incidence of MSI in GEP-NEC/MANECs and characterized their clinicopathologic and molecular features. MSI analysis and immunohistochemistry for mismatch repair proteins (MLH1, MSH2, MSH6 and PMS2) were performed in 89 GEP-NEC/MANECs (six esophageal, 77 gastrointestinal, three pancreatic, and three of the gallbladder). Methylation of 34 genes was studied by methylation-specific multiplex ligation probe amplification. Mutation analysis of BRAF and KRAS was assessed by PCR-pyrosequencing analysis. MSI was observed in 11 NEC/MANECs (12.4%): seven intestinal and four gastric. All but two MSI-cases showed MLH1 methylation and loss of MLH1 protein. The remaining two MSI-cancers showed lack of MSH2 or PMS2 immunohistochemical expression. MSI-NEC/MANECs showed higher methylation levels than microsatellite stable NEC/MANECs (40.6% vs 20.2% methylated genes respectively, P<0.001). BRAF mutation was detected in six out of 88 cases (7%) and KRAS mutation was identified in 15 cases (17%). BRAF mutation was associated with MSI (P<0.0008), while KRAS status did not correlate with any clinicopathologic or molecular feature. Vascular invasion (P=0.0003) and MSI (P=0.0084) were identified as the only independent prognostic factors in multivariate analysis. We conclude that MSI identifies a subset of gastric and intestinal NEC/MANECs with distinct biology and better prognosis. MSI-NEC/MANECs resemble MSI-gastrointestinal adenocarcinomas for frequency, molecular profile and pathogenetic mechanisms.

Dna Methylation of Tumor Suppressor Gene is a Predictor of Pathologic Complete Response in Stage Iiia (N2) Nsclc Patients Treated with Neoadjuvant Ccrt Followed By Surgery

ABSTRACT Aim: The aim of this study was to evaluate the clinical implications of DNA methylation of tumor suppressor gene in pathologic complete responders in stage IIIA(N2) NSCLC patients treated with neoadjuvant CCRT followed by surgery. Methods: Methylation-specific multiplex ligation probe amplification (MS-MLPA) was used to analyze the DNA methylation status of 36 tumor suppressor genes in 15 stage IIIA (N2) NSCLC patients who were treated with neoadjuvant CCRT followed by surgery between October 2011 and January 2014. FFPE (formalin-fixed, paraffin-embedded) tissue samples obtained from 15 paired pre-CCRT lung biopsy and post-CCRT surgically resected tumor specimens were used. Factors predictive of pathologic CR were evaluated using logistic regression. Pre-treatment methylated DNA number less than 2, the ratio of unmethylated DNA after neoadjuvant CCRT and difference between pre-, posttreatment SUV max of primary tumor and mediastinal lymph node were analysed. Results: The median follow-up time was 17.4 months. One patient had recurrence at mediastinal lymph node. Factor predictive of pathologic complete response after neoadjuvant CCRT followed by surgery was pre-treatment methylated DNA number less than 2 (p = 0.03) in stage IIIA (N2) NSCLC patients. The change of the ratio of unmethylated DNA after neoadjuvant CCRT (p > 0.6) of the paired samples and difference between pre-, posttreatment SUV max of primary tumor and mediastinal lymph node were not a predictive factor of pathologic CR (p > 0.15). Conclusions: These results suggest that pre-treatment methylated DNA number less than 2 is a predictor of pathologic complete response in stage IIIA (N2) NSCLC patients treated with neoadjuvant CCRT followed by surgery. And we think that an analysis of the correlation between DNA methylation status and the long-term survival and recurrence rate is needed in these patients. Disclosure: All authors have declared no conflicts of interest.

APC alterations are frequently involved in the pathogenesis of acinar cell carcinoma of the pancreas, mainly through gene loss and promoter hypermethylation

Genetic and epigenetic alterations involved in the pathogenesis of pancreatic acinar cell carcinomas (ACCs) are poorly characterized, including the frequency and role of gene-specific hypermethylation, chromosome aberrations, and copy number alterations (CNAs). A subset of ACCs is known to show alterations in the APC/β-catenin pathway which includes mutations of APC gene. However, it is not known whether, in addition to mutation, loss of APC gene function can occur through alternative genetic and epigenetic mechanisms such as gene loss or promoter methylation. We investigated the global methylation profile of 34 tumor suppressor genes, CNAs of 52 chromosomal regions, and APC gene alterations (mutation, methylation, and loss) together with APC mRNA level in 45 ACCs and related peritumoral pancreatic tissues using methylation-specific multiplex ligation probe amplification (MS-MLPA), fluorescence in situ hybridization (FISH), mutation analysis, and reverse transcription-droplet digital PCR. ACCs did not show an extensive global gene hypermethylation profile. RASSF1 and APC were the only two genes frequently methylated. APC mutations were found in only 7 % of cases, while APC loss and methylation were more frequently observed (48 and 56 % of ACCs, respectively). APC mRNA low levels were found in 58 % of cases and correlated with CNAs. In conclusion, ACCs do not show extensive global gene hypermethylation. APC alterations are frequently involved in the pathogenesis of ACCs mainly through gene loss and promoter hypermethylation, along with reduction of APC mRNA levels.

Revisiting epilepsy and the electroencephalogram patterns in Angelman syndrome

Angelman syndrome is a neurogenetic disorder that severely affects global neurodevelopment due to modifications in the structure or functioning of UBE3A gene. Its prevalence ranges from 1:10,000 to 1:40,000. There are four main genetic types of AS transmission. A maternal deletion in 15q11.2-q13 is the most common type. There are three well-established electroencephalogram (EEG) patterns used as an ancillary tool for AS diagnosis. The main objectives are to scrutinize the EEG patterns in Angelman syndrome, their correlation to different types of seizures and to review the role of the EEG as an ancillary screening tool in the diagnosis of clinically suspected patients. Forty-three patients' charts and their previously recorded EEGs were reviewed. A set of 34 patients with deletion type, paternal uniparental disomy type and imprint defect type AS were enrolled. AS diagnosis was confirmed either by fluorescent in situ hybridization test or Methylation Specific-Multiplex Ligation Probe Amplification test. Sequencing of UBE3A was not available. Frequencies and Chi-square tests were used for statistic analysis. Pattern I type EEG was observed in 22 (64.7 %) individuals. Pattern II accounted for 6 (17.6 %); Pattern III was evident in 11 (32.4 %). The three distinguished EEG patterns, more frequently Pattern I, when observed in the appropriate clinical setting, may heighten the index of suspicion for selecting patients who will need a molecular biology test to confirm the diagnosis of AS.

HPV and methylation indicators in paired tumor and saliva in HNSCC

Human papilloma virus type 16 (HPV16) is a causative agent for some head and neck squamous cell carcinoma (HNSCC) and an independent risk factor for oropharyngeal SCC. The goal of this study was to examine HPV16 associated gene methylation in paired saliva and tumor DNA with assessment of the sensitivity, specificity, positive predictive, and negative predictive value for saliva HPV as a test for HNSCC. HPV16 status was determined by quantitative PCR (qPCR) in 35 primary HNSCC paired tumor and saliva specimens. Tumor cut points >=0.03 and >=0.1 and saliva cut points >0 and ?0.001 were used to classify results as HPV positive or negative. Aberrant methylation was determined by the methylation-specific multiplex ligation probe amplification (MS-MLPA) assay. The frequency of promoter hypermethylation in tumor samples was 66% (23/35) versus 17% (6/35) in saliva. Two of 35 paired tumor and saliva samples had commonly methylated genes. HPV and methylation were correlated for IGSF4 (p=0.01) in tumor samples (cut point ?0.03) and for ESR1 in saliva samples (cut point >0). Although the sensitivity of HPV detection in saliva was significantly reduced when saliva cut points were increased from >0 to >=0.001, the specificity and positive predictive values were 100% at saliva cut point of >=0.001, regardless of tumor cut points. Within clearly defined parameters, HPV detection in saliva DNA shows promise as a non invasive approach for tumor HPV status. Methylated genes detected in saliva may be useful in early detection and as potential predictive markers of HNSCC. Further confirmation and validation in larger cohorts is required.

Prognostic Impact of the Number of Methylated Genes in Myelodysplastic Syndromes and Acute Myeloid Leukemias Treated with 5-Azacytidine

AbstractAbstract 1717 Background:Aberrant DNA methylation of tumor suppressor genes is a common event in myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML). Therefore hypomethylating agents like azacytidine (AZA) and decitabine seem to be a good therapeutic approach for the treatment of these diseases. Clinical experience and recent published data have demonstrated that AZA is effective for the treatment of MDS and AML patients. However, the prognostic impact of the aberrant hypermethylation on response and outcome to AZA treatment remains to be determined. For this reason the influence of the methylation status of a selected set of tumor suppressor genes on the overall survival and clinical response in MDS and AML patients, prior to treatment with AZA was studied. Patients and Methods:A total of 78 patients with MDS or AML who had been treated with AZA were evaluated. Among these, 25 were excluded because they had received less than 4 cycles, AZA was used after allogeneic stem cell transplantation, response was not assessable, or there was not enough quality DNA available. So finally, the study was focused in 53 patients: 36 MDS and 17 AML. Most of the AML included in the study had low blast count (20–30%). Responses were assessed according to the IWG MDS criteria in accordance to Fenaux et.al, and IWG AML criteria following European LeukemiaNet recommendations. DNA methylation status was analyzed using the Methylation Specific Multiplex Ligation Probe Amplification (MS-MLPA), with a panel of 24 different tumor suppressor genes related to cell cycle control, apoptosis regulation, DNA repair, cell adhesion and cell growth. Results:In the study cohort 47% of patients had cytogenetic alterations prior to AZA treatment, 4 with isolated -5/del(5q), 7 with isolated −7/del(7q), 4 with trisomy 8, 4 with not isolated -5/del(5q), 1 with trisomy 14, and 5 with complex cytogenetics. Methylation analysis showed that most patients (74%) had at least one methylated gene, but only 10% of patients displayed more than 3 methylated genes. The most frequently methylated genes were IGSF4 (28.3%), CDKN2B (24.5%), ESR1 (22.6%), CDH13 (17%) and CDKN1B (11.3%).The presence of a high number (≥2) of methylated genes (p=0.02), an adverse cytogenetics (p=0.03) or anemia (p=0.04) were independent prognostic factors associated with shorter overall survival. Moreover, the analysis of those patients displaying “no methylation”, patients with 1 methylated gene, patients with 2 methylated genes and those with more than 3 methylated genes, showed that as the number of methylated genes increases, the survival was shorter. The patients displaying the highest level of methylation (more than 3 genes), had a very short survival (median OS of 9.3 months, p<0.001).Forty-nine per cent of all patients responded to azacytidine. The statistical analysis revealed that the number of methylated genes did not correlate in general with the clinical response to AZA, although four of the five patients with more than 3 genes methylated did not respond. By contrast, cytogenetics was the only factor that independently influenced the response to AZA. Thus 64.7% of patients with favorable cytogenetics responded to AZA, while only 28.6% of those with adverse cytogenetics responded (p=0.03). Interestingly, our study included 3 MDS patients with isolated chromosome 7 alterations, and all of them responded. Conclusion:In summary, these results suggest that the analysis of the methylation status before AZA treatment by a feasible methodology such as MS-MLPA could be used in a clinical setting in order to identify a group of patients with poor survival, in which other alternative therapeutic approaches might be considered. [Display omitted] [Display omitted] Disclosures:Ramos:Celgene, Novartis, Amgen, Pfizer, and Merck Sharp & Dohme: Honoraria. Hernández:Celgene: Research Funding.

The Changes in MGMT Promoter Methylation Status in Initial and Recurrent Glioblastomas

To evaluate the mechanism of the development of therapeutic resistance after temozolomide treatment, we focused on changes in O(6)-methylguanine DNA methyltransferase (MGMT) and mismatch repair (MMR) between initial and recurrent glioblastomas. Tissue samples obtained from 24 paired histologically confirmed initial and recurrent adult glioblastoma patients who were initially treated with temozolomide were used for MGMT and MMR gene promoter methylation status and protein expression analysis using methylation-specific multiplex ligation probe amplification (MS-MLPA), methylation-specific polymerase chain reaction (MSP), and immunohistochemical staining. There was a significant decrease in the methylation ratio of the MGMT promoter determined by MS-MLPA, which was not detectable with MSP, and MGMT protein expression changes were not remarkable. However, there was no epigenetic variability in MMR genes, and a relatively homogeneous expression of MMR proteins was observed in initial and recurrent tumors. We conclude that the development of reduced methylation in the MGMT promoter is one of the mechanisms for acquiring therapeutic resistance after temozolomide treatment in glioblastomas.

Usefulness of MS-MLPA for detection of MGMT promoter methylation in the evaluation of pseudoprogression in glioblastoma patients

Pseudoprogression is a major diagnostic dilemma in current treatment protocols for malignant gliomas that involve concurrent chemoradiotherapy. We hypothesized that methylation-specific multiplex ligation probe amplification (MS-MLPA), an assay that permits semiquantitative evaluation of promoter methylation, may be used to diagnose pseudoprogression based on the quantification of the methylation status of the O(6)-methylguanine DNA methyltransferase (MGMT) promoter. We examined the methylation ratio of the MGMT promoter with MS-MLPA in 48 samples from glioblastoma patients. The results were compared with those from methylation-specific polymerase chain reaction (MSP), and protein levels were confirmed by immunohistochemical staining. We then evaluated the correlation between those molecular signatures and clinical outcomes. With regard to radiological progression after chemoradiotherapy, the diagnostic accuracy of the MS-MLPA method was 80% (using a cut-off value of 0.2). These results are better than those obtained with MSP (diagnostic accuracy of 68%). Combining the MS-MLPA and MSP methods resulted in a diagnostic accuracy of 93% for the identification of pseudoprogression among patients to whom these results were coherent. These results demonstrate that MS-MLPA is a useful method to predict radiological progression vs pseudoprogression in glioblastoma patients and that the interpretation of these results in combination with MSP results will provide good practical guidelines for clinical decision making in glioblastoma treatment.

Abstract 150: HPV and aberrant DNA methylation status in paired saliva and tumor samples in HNSCC

Abstract To examine the utility of non-invasive detection of high risk HPV and aberrant DNA methylation in matched saliva and tumor DNA in squamous head and neck cancer (HNSCC). In a cohort of 35 primary HNSCC with matched tumor (cases) and saliva specimens, HPV status was initially determined using the Linear Array HPV Genotyping kit and confirmed by PCR for HPV subtypes 16, 31, 33 and 45. Aberrant methylation of 24 tumor suppressor genes was interrogated using the methylation specific multiplex ligation probe amplification (MS-MLPA) assay. Of the 35 cases, 20 were negative for HPV in the saliva and tumor, 9 were positive for HPV in both and in 6 cases HPV was positive in the tumor specimen but not detected in the corresponding saliva. In the 9 cases that were positive for HPV in the tumor and matched saliva, 6 were HPV 16 positive and 1 case each was positive for HPV 31, 33 and 45. The sensitivity and specificity for HPV in this cohort were 100% and 60%, respectively. Promoter hypermethylation frequency in tumor samples was 60% (21/35) as compared to 14% (5/35) in saliva. The most frequently methylated genes in tumors included RARB-10/21, APC- 9/21, TIMP3 and CDKN2B- 7/21, CDKN2A and IGSF4- 5/21 tumor samples. The most frequently methylated genes in saliva samples included TIMP3, ESR1 and IGSF4 (3/5 saliva samples), followed by APC, CDKN2B and DAPK1 (2/3). Two of the 35 tumor and saliva pairs had commonly methylated genes, APC in one pair, and TIMP3, CDKN2B, ESR1 and IGSF4 in the other. There was no association between HPV and methylation. PCR analysis of HPV DNA in salivary rinses allows for detection of HPV and promoter methylation status in HNSCC and is a feasible noninvasive alternative to more invasive procedures. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 150.

M1929 Utility of MS-Mlpa Methylation Analysis in the Diagnosis of Lynch Syndrome

Despite the advances in the selection of patients for genetic testing in Lynch syndrome at least a third of patients with Bethesda criteria and lack of MLH1 expression have sporadic tumours and should not receive genetic testing. The aim of this study is to investigate the role of the methylation analysis using MS-MLPA in the diagnosis of Lynch syndrome. MSMLPA is a novel and methodologically easy technique for quantitative measure of gene methylation. Methods. Sixty colorectal cancer (CRC) specimens with loss of MLH1 expression were selected. DNA from paraffin-embedded tumours was tested for 2 quantitative methylation detection methods: Methylight (Applied biosystems) and MS-MLPA (Methylation Specific-Multiplex Ligation Probe Amplification) (MCR Holland) calculating Methylation Ratio in MLH1. Somatic mutation in BRAF V600E was investigated from tumour DNA. Germline mutations in MLH1 were analyzed by sequentiation. Results: Correlation of quantitative results of the 2 methylation analysis techniques (Methylation and MS-MLPA) was 96.7% (p <0,001). Germline mutations in MLH1 were found in 8 out of 60 patients (13,3%). None of the tumours from these patients with Lynch syndrome showed significant methylation. Forty-two out of 52 (80%) tumours from patients without germline mutation in MLH1 showed significant methylation using Methylight. Using MS-MLPA, methylation was found in 44 out of 52 patients (85%). Both techniques had sensitivity and negative predictive value of 100 % to detect germline mutation patients. Specificity was 80 % for Methylight and 85 % for MS-MLPA, and positive predictive value (PPV) was 44 % for Methylight and 50 % for MS-MLPA. These values were clearly better than the obtained using BRAF V600E mutation, with a specificity of 53,8%. Conclusion: Methylation analysis is a high sensitivity and specific method for detecting sporadic CRC unstable cases. These results highlight the role of MS-MLPA assays as a simple and reliable method for selection of patients for genetic testing in Lynch syndrome.

M1933 A Comprehensive Analysis of the Phenotypic Manifestations of Mismatch Repair Gene Mutations: Comparing MSH6 with MLH1 and MSH2 Mutation Carriers

Despite the advances in the selection of patients for genetic testing in Lynch syndrome at least a third of patients with Bethesda criteria and lack of MLH1 expression have sporadic tumours and should not receive genetic testing. The aim of this study is to investigate the role of the methylation analysis using MS-MLPA in the diagnosis of Lynch syndrome. MSMLPA is a novel and methodologically easy technique for quantitative measure of gene methylation. Methods. Sixty colorectal cancer (CRC) specimens with loss of MLH1 expression were selected. DNA from paraffin-embedded tumours was tested for 2 quantitative methylation detection methods: Methylight (Applied biosystems) and MS-MLPA (Methylation Specific-Multiplex Ligation Probe Amplification) (MCR Holland) calculating Methylation Ratio in MLH1. Somatic mutation in BRAF V600E was investigated from tumour DNA. Germline mutations in MLH1 were analyzed by sequentiation. Results: Correlation of quantitative results of the 2 methylation analysis techniques (Methylation and MS-MLPA) was 96.7% (p <0,001). Germline mutations in MLH1 were found in 8 out of 60 patients (13,3%). None of the tumours from these patients with Lynch syndrome showed significant methylation. Forty-two out of 52 (80%) tumours from patients without germline mutation in MLH1 showed significant methylation using Methylight. Using MS-MLPA, methylation was found in 44 out of 52 patients (85%). Both techniques had sensitivity and negative predictive value of 100 % to detect germline mutation patients. Specificity was 80 % for Methylight and 85 % for MS-MLPA, and positive predictive value (PPV) was 44 % for Methylight and 50 % for MS-MLPA. These values were clearly better than the obtained using BRAF V600E mutation, with a specificity of 53,8%. Conclusion: Methylation analysis is a high sensitivity and specific method for detecting sporadic CRC unstable cases. These results highlight the role of MS-MLPA assays as a simple and reliable method for selection of patients for genetic testing in Lynch syndrome.

Concurrent methylation of promoters from tumor associated genes predicts outcome in acute myeloid leukemia

By assessment of the methylation status of 25 candidate tumor suppressor genes (TSGs) in 119 acute myeloid leukemia (AML) patients and 5 controls, we aimed to determine whether simultaneous methylation of multiple TSGs exerts prognostic impact. Methylation-specific multiplex ligation probe amplification (MS-MLPA) revealed methylation of at least one TSG in 59/119 patients, while no methylation was found in controls. Methylation of different TSGs within patients was substantially correlated (intra-class correlation; 0.38). ESR1 methylation (34/119) strongly predicted concurrent methylation of other genes, OR 7.33 (95%CI 4.13–12.99). A Cox regression model that included the three most frequently methylated TSGs ESR1, CDKN2B/p15 and IGSF4, showed ESR1 to have opposite effects on overall survival (OS) compared with the other two, HR 0.22 (95% CI 0.09–0.53) and HR 1.66 (95% CI 0.73–3.79), HR 1.61 (95%CI 0.66–3.93). By assessment of CDKN2B/p15 and IGSF4 methylation, patients with methylation at multiple loci can be identified. Accumulation of methylation aberrancies is much more pronounced in ESR1 methylated patients. When combined, the methylation status of ESR1, CDKN2B/p15 and IGSF4 enable identification of patient subgroups with large differences in OS (p <0.0001). This study shows that methylation profiling allows risk stratification in AML. In addition, ESR1 methylation may reflect a biological pathway that leads to hypermethylation of multiple genes, which is reflected by methylation of IGSF4 and/or CDKN2B/p15.

Methylation of ESR1 and Tumour Suppressor Genes Together Constitute an Independent Outcome Predictor in Acute Myeloid Leukemia.

In acute myeloid leukemia (AML) promoter methylation has been observed for the estrogen receptor (ESR1) as well as for a number of Tumor Suppressor Genes (TSGs). These individual aberrancies were suggested to be part of a general methylation defect in subsets of AML patients, rather than random events. The objective of this study was to assess whether aberrant promoter methylation of multiple genes, as observed in AML samples, are associated and whether such associations render impact on clinical outcome. By Methylation-Specific Multiplex Ligation Probe Amplification (MS-MLPA) the methylation status of 26 TSGs was determined in bone marrow samples of 119 primary AML patients and 5 control individuals. No promoter methylation was detected in any of the controls, while at least one TSG was methylated in 59/119 patients. Methylation was observed in 12 out of 26 assessed sites, most frequently for ER, CDKN2B/p15, and IGSF4 (28–36% of all patients). A substantial intra-class correlation of 0.38 existed between methylation of different TGSs. ESR1 methylation (34/119) strongly predicted concurrent methylation of TSGs, OR 7.33 (95%CI 4.13–12.99). A regression model that included both the ESR1 methylation status and the number of methylated TSGs (methylation index), showed both parameters to be independent oppositely directed predictors for overall survival (OS), HR 0.06 (95%CI 0.01–0.33; p=.001) and HR 1.92 (95%CI 1.19–3.10; p=.007), respectively. In line with this observation, a higher methylation index was found to yield a significant negative effect on patient OS in both the ESR1 methylated (ESR1+) and ESR1 unmethylated (ESR1−) subgroups.Combining ESR1 methylation status with the absence or presence of promoter methylation of other TSGs (TSG+ or TSG−); yielded 4 patient subgroups with large differences in OS in univariate analysis (p=.0001, figure 1A). In multivariate analysis that included, FLT3-status, age at diagnosis, cytogenetics and achievement of CR, the predictive impact of the 4-group division on OS was maintained, HR 2.12 (95%CI 1.04–4.29; p=.037). Moreover, the combination identified a good prognostic patient subgroup (n=15, median OS 39 month) within the intermediate cytogenetic risk group (n=54, median OS 8.3 month), figure 1B. In conclusion, concurrent methylation occurs frequent in AML and is best predicted by ESR1 methylation. Methylation of ESR1 and methylation of other TSGs represent processes with independent predictivity. When combined, they constitute a unique and powerful factor for predicting overall survival, both in the total AML population as well as within the intermediate cytogenetic risk group. [Display omitted]