Differences In Methylation Status Research Articles

O-028 DNA methylation testing with cervical secretion can serve as a non-invasive biomarker for predicting successful implantation in frozen-thawed embryo transfer

Abstract Study question Is cervical secretion gene methylation profile associated with embryo implantation outcome, and can be used as a non-invasive biomarker for pregnancy prediction in FET cycles? Summary answer Cervical secretion gene methylation profiles show significant associations with implantation outcomes, and can serve as a non-invasive predictor of successful pregnancy in FET cycles. What is known already Cause of implantation failure remains a black box in reproductive medicine, and the exact mechanism of how endometrial receptivity is still behind the curtain. Epigenetic modifications including DNA methylation regulate gene expression and may alter endometrium receptivity. Endometrial DNA methylation changes vigorously only during the reconstruction of a new endometrium throughout each menstrual cycle, suggesting a unique methylation landscape in each regenerated endometrium. Cervical secretions contain implantation-related cytokines and genetic material from endometrium, and the DNA methylation profiles of cervical secretions is highly correlated with endometrium. Therefore, cervical secretions can be used as non-invasive surrogates for investigating endometrial condition. Study design, size, duration This multi-centered, case-control study enrolled 72 infertile females who entered the FET cycle with at least one high-quality blastocyst available between Aug 2017 and Dec 2022. Embryos assessed by Gardner scoring system with grade 3BB or above were defined as high-quality. Cervical secretions were collected on the day right before embryo transfer, and then DNA methylation profile were assessed. Participants/materials, setting, methods These females aged between 20-45 years-old with regular menstruation cycle (24-35 days) and normal BMI (17.5–32.0 kg/m2). Uterine cavity lesions and hydrosalpinx without treatment, adenomyosis, large uterine myoma that distorted endometrium, and thin endometrium (<7mm) were excluded. The association between the cervical secretion gene methylation profile and pregnancy outcome was evaluated via quantitative methylation-specific PCR (qMSP), methylation array, and genome-wide analysis. Different machine learning algorithms were utilized for differential methylation analysis and implantation prediction. Main results and the role of chance Cervical secretion DNA methylome differed between receptive (pregnant) and non-receptive (non-pregnant) FET cycle with genome-wide methylation array. The accuracy of pregnancy outcome prediction using top 2000 differential methylation probes (DMPs) in promoter region can be as high as 86% in all tested sample and 96.4% in pregnant samples. Bioinformatic analysis of six selected candidate genes related to implantation from literature review showed significant differences in DNA methylation between receptive and non-receptive endometrium. The methylation level of the six candidate genes with eight regions were measured by the qMSP platform and showed varying degrees of differential methylation status between the pregnancy and non-pregnancy groups. The AUCs for a single gene/region ranged from 0.53–0.67 for implantation prediction. Ten different machine learning models were applied and the results showed that the combination of candidate genes’ DNA methylation profiles could differentiate pregnant from non-pregnant samples with an accuracy as high as 86.67% and an AUC of 0.81 by logistic regression model. The best model from different machine learning algorithms using selected DMPs of genes related to window of implantation (WOI) can predict ongoing pregnancy with accuracy rates as high as 86.78% and AUC values up to 0.91. Limitations, reasons for caution The results obtained from a relatively small cohort size, and the timing of sample collection is on the day right before embryo transfer. Further investigation of methylation profiles in late follicular phase along with large sample size with euploid embryo transfer are mandatory for validation and clinical applications. Wider implications of the findings We firstly demonstrated the feasibility of cervical secretion methylation profile as a non-invasive testing for pregnancy prediction. The promising result may contribute to predicting endometrial receptivity for cycles with a favorable endometrium and maximize the successful pregnancy rate of embryo transfer. Trial registration number not applicable

Genome-Wide Methylation Analysis in Two Wild-Type Non-Small Cell Lung Cancer Subgroups with Negative and High PD-L1 Expression.

We conducted a pilot study to analyze the differential methylation status of 20 primary acinar adenocarcinomas of the lungs. These adenocarcinomas had to be wild type in mutation analysis and had either high (TPS > 50%; n = 10) or negative (TPS < 1%; n = 10) PD-L1 status to be integrated into our study. To examine the methylation of 866,895 specific sites, we utilized the Illumina Infinium EPIC bead chip array. Both hypermethylation and hypomethylation play significant roles in tumor development, progression, and metastasis. They also impact the formation of the tumor microenvironment, which plays a decisive role in tumor differentiation, epigenetics, dissemination, and immune evasion. The gained methylation patterns were correlated with PD-L1 expression. Our analysis has identified distinct methylation patterns in lung adenocarcinomas with high and negative PD-L1 expression. After analyzing the correlation between the methylation results of genes and promoters with their pathobiology, we found that tumors with high expression of PD-L1 tend to exhibit oncogenic effects through hypermethylation. On the other hand, tumors with negative PD-L1 expression show loss of their suppressor functions through hypomethylation. The suppressor functions of hypermethylated genes and promoters are ineffective compared to simultaneously activated dominant oncogenic mechanisms. The tumor microenvironment supports tumor growth in both groups.

Mapping Chemo-Resistance Profiles of Pediatric Acute Leukemia through Integration of Ex-Vivo Drug Screens with Molecular Data

Introduction While novel approaches for treatment of acute lymphoblastic leukemia (ALL) in children have resulted in significant improvements in survival rates, survivors are faced with potentially life-long challenges as a result of the highly toxic treatment and the outcome for patients who relapse remains poor. The current risk-adapted treatment for ALL in children includes multiple drugs administered sequentially or in combination, with little variation in timing or intensity. Factors that affect varying treatment response between patients and cellular mechanisms that underly response to individual drugs are still under exploration. In this study, we investigate the relationship between ex-vivo drug resistance, transcriptomes, epigenomes and clinical outcome, with the aim of better understanding underlying determinants of treatment response. Methods Pediatric patients diagnosed with B-ALL between 1992 and 2008 in the Nordic countries were included in the study (n = 598). For these patients, ex-vivo drug response to ten clinically used drugs was determined using the fluorometric microculture cytotoxicity assay (FMCA). Clinical data, including follow-up information (overall survival and relapse free survival) was available for all patients. Additionally, DNA-methylation (450K array, n = 383) and gene expression profiling (RNA-seq, n = 119) was performed on a subset of diagnostic patient samples. The patients were stratified into low, medium and high resistance groups based on ex-vivo drug response. The low and high resistance groups were compared with regard to differentially methylated CpG sites or expressed genes associated with individual drug response profiles. Results Overall survival was significantly lower for patients with higher ex-vivo drug resistance to dexamethasone, doxorubicin and thioguanine compared to patients that displayed sensitivity to these drugs (p &amp;lt; 0.05). Similarly, relapse free survival was significantly lower for patients with ex-vivo resistance to cytarabine, dexamethasone, doxorubicin, prednisolone and thioguanine (p &amp;lt; 0.05). After adjusting for sex and risk group, according to the Nordic Society of Pediatric Hematology and Oncology (NOPHO) protocol, in a Cox proportional hazards model, higher hazard ratios for relapse were observed in the highly resistant group across all drugs. We identified distinct DNA methylation and gene expression patterns in patients with low and high resistance, indicating the presence of predetermined molecular resistance fates. These resistance patterns included 665 genes that were differentially expressed (absolute log2FC &amp;gt; 1, Benjamini-Hochberg adjusted p value &amp;lt; 0.05) and 1 422 CpG sites with differential methylation status (absolute mean β-value difference &amp;gt; 0.2, Benjamini-Hochberg adjusted p value &amp;lt; 0.05) in resistant compared to sensitive groups, for one or multiple drugs. With the aim of identifying the genes with the largest impact on drug resistance, we selected the most differentially expressed genes and the genes with the largest difference in methylation status between resistant and sensitive samples. Among these, we identified ~20 putative genes of interest for future studies into resistance mechanisms based on potential functional prioritization. Conclusion Our findings confirm that drug response profiles are associated with outcome in pediatric ALL, reflecting response in vivo. We show molecular evidence for differentiating low- and high-resistant types based on diagnostic gene expression and DNA methylation profiles, suggesting contribution of certain molecular signatures to drug response. Our data integrating molecular data with drug response profiles may help identifying such changes of importance in drug resistance mechanisms.

Analysis of nerve growth factor (NGF) gene methylation in patients with schizophrenia

According to the neurotrophin hypothesis, schizophrenia can be caused by neurotrophic factors. One of these neurotrophic factors is the nerve growth factor (NGF), which has a critical role in cognitive functions. The present study aimed to investigate the NGF gene promoter methylation pattern in patients with schizophrenia and healthy individuals. Participants included patients with schizophrenia (84 males and 38 females) and healthy controls (96 males and 48 females). Blood samples were collected from all of the subjects in treated tubes for DNA extraction. The determination of the methylation pattern of the NGF gene CpG island-2 was based on the principle that bisulfite treatment of DNA results in the conversion of unmethylated bases of cytosine into uracil bases. The results showed no significant difference in the DNA methylation status for the NGF gene CpG island-2 in patients with schizophrenia and healthy individuals. Also, no significant difference was observed in the methylated and unmethylated status for the NGF gene CpG island-2 region when patients were compared with clinical parameters. In addition, relative NGF mRNA expression was significantly lower in patients with schizophrenia compared to healthy controls. However, no significant difference was observed in methylated and unmethylated status in the NGF mRNA expression. Although clinical evidence indicates a decrease in serum NGF levels in patients with schizophrenia, in the present study, there was no difference in the methylation status of the NGF gene promoter CpG island-2 between patients with schizophrenia and healthy individuals.

In Cis Effect of DMPK Expanded Alleles in Myotonic Dystrophy Type 1 Patients Carrying Variant Repeats at 5' and 3' Ends of the CTG Array.

Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disease caused by a CTG repeat expansion in the 3'-untranslated region (UTR) of DMPK gene. DM1 alleles containing non-CTG variant repeats (VRs) have been described, with uncertain molecular and clinical consequences. The expanded trinucleotide array is flanked by two CpG islands, and the presence of VRs could confer an additional level of epigenetic variability. This study aims to investigate the association between VR-containing DMPK alleles, parental inheritance and methylation pattern of the DM1 locus. The DM1 mutation has been characterized in 20 patients using a combination of SR-PCR, TP-PCR, modified TP-PCR and LR-PCR. Non-CTG motifs have been confirmed by Sanger sequencing. The methylation pattern of the DM1 locus was determined by bisulfite pyrosequencing. We characterized 7 patients with VRs within the CTG tract at 5' end and 13 patients carrying non-CTG sequences at 3' end of the DM1 expansion. DMPK alleles with VRs at 5' end or 3' end were invariably unmethylated upstream of the CTG expansion. Interestingly, DM1 patients with VRs at the 3' end showed higher methylation levels in the downstream island of the CTG repeat tract, preferentially when the disease allele was maternally inherited. Our results suggest a potential correlation between VRs, parental origin of the mutation and methylation pattern of the DMPK expanded alleles. A differential CpG methylation status could play a role in the phenotypic variability of DM1 patients, representing a potentially useful diagnostic tool.

Assessment of MGP gene expression in cancer and contribution to prognosis

Matrix Gla protein (MGP) was first identified as a calcification physiological inhibitor and the causal agent of the Keutel syndrome. MGP has been suggested to play a role in development, cell differentiation, and tumorigenesis. This study aimed to compare MGP expression and methylation status in different tumors and adjacent tissues, using The Cancer Genome Atlas (TCGA) data repository. We investigated if changes in MGP mRNA expression were correlated to cancer progression and whether the correlation coefficients could be used for prognosis. Strong correlations were observed between altered MGP levels and disease progression in breast, kidney, liver, and thyroid cancers, suggesting that it could be used to complement current clinical biomarker assays, for early cancer diagnosis.We have also analyzed MGP methylation and identified CpG sites in its promoter and first intron with clear differences in methylation status between healthy and tumoral tissue providing evidence for epigenetic regulation of MGP transcription. Furthermore, we demonstrate that these alterations correlate with the overall survival of the patients suggesting that its assessment can serve as an independent prognostic indicator of patients’ survival.

Identification of a novel PARP4 gene promoter CpG locus associated with cisplatin chemoresistance

The protein family of poly (ADP-ribose) polymerases (PARPs) is comprised of multifunctional nuclear enzymes. Several PARP inhibitors have been developed as new anticancer drugs to combat resistance to chemotherapy. Herein, we characterized PARP4 mRNA expression profiles in cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. PARP4 mRNA expression was significantly upregulated in cisplatin-resistant ovarian cancer cell lines, and this upregulation was associated with hypomethylation of specific cytosine-phosphate-guanine (CpG) sites (cg18582260 and cg17117459) on its promoter. Reduced PARP4 expression was restored by treating cisplatin-sensitive cell lines with a demethylation agent, implicating epigenetic regulation of PARP4 expression by promoter methylation. Depletion of PARP4 expression in cisplatin-resistant cell lines reduced cisplatin chemoresistance and promoted cisplatin-induced DNA fragmentation. The differential mRNA expression and DNA methylation status at specific PARP4 promoter CpG sites (cg18582260 and cg17117459) according to cisplatin responses, were further validated in primary ovarian tumor tissues. The results showed significantly increased PARP4 mRNA expressions and decreased DNA methylation levels at specific PARP4 promoter CpG sites (cg18582260 and cg17117459) in cisplatin-resistant patients. Additionally, the DNA methylation status at cg18582260 CpG sites in ovarian tumor tissues showed fairly clear discrimination between cisplatin-resistant patients and cisplatin-sensitive patients, with high accuracy (area under the curve = 0.86, p = 0.003845). Our findings suggested that the DNA methylation status of PARP4 at the specific promoter site (cg18582260) may be a useful diagnostic biomarker for predicting the response to cisplatin in ovarian cancer patients.

The promoters of OsGLP genes exhibited differentially methylated sites under drought and salt stress in rice cultivars

DNA methylation at cytosine residues governs the regulation of stress responsive genes in plant for self-protection against various environmental abiotic stresses. Here, we analyzed the epigenetic consequences of drought and salinity on cytosine methylation dynamics of promoter regions of stress responsive Germin-like protein genes in rice (Oryza sativa). The bisulfite sequencing technique was employed to identify differential methylation status at cytosine residues in selected promoter regions of three OsGLP genes (OsGLP4-1, OsGLP8-10 and OsGLP8-12) in leaves and roots of two elite Indica rice cultivars (tolerant KS282 and sensitive Super Basmati) under drought and salt stress. Our results identified cultivar, tissue and stress-dependent differentially methylated cytosine residues, however, the extent of methylation was found to be different depending upon CGN, CHG and CHH sequence contexts. Among all three OsGLP genes, the promoter region of OsGLP8-12 was detected with the most heavily methylated and significantly differential methylated sites depending upon types of variety, tissue or stress conditions. However, no methylated site was detected in the promoter region of OsGLP4-1. Moreover, in the promoter regions of OsGLP8-10 and OsGLP8-12, several differentially methylated sites in response to stress treatments were identified either near or within cis-regulatory elements (CREs) related to abiotic stress. This indicated the association between methylation in the promoter regions and regulation of OsGLP genes which might be a key mechanism associated with their regulation under abiotic stresses in contrasting rice cultivars.

A low-protein maternal diet during gestation affects the expression of key pancreatic β-cell genes and the methylation status of the regulatory region of the MafA gene in the offspring of Wistar rats.

Maternal nutrition during gestation has important effects on gene expression-mediated metabolic programming in offspring. To evaluate the effect of a protein-restricted maternal diet during gestation, pancreatic islets from male progeny of Wistar rats were studied at postnatal days (PND) 36 (juveniles) and 90 (young adults). The expression of key genes involved in β-cell function and the DNA methylation pattern of the regulatory regions of two such genes, Pdx1 (pancreatic and duodenal homeobox 1) and MafA (musculoaponeurotic fibrosarcoma oncogene family, protein A), were investigated. Gene expression analysis in the pancreatic islets of restricted offspring showed significant differences compared with the control group at PND 36 (P < 0.05). The insulin 1 and 2 (Ins1 and Ins2), Glut2 (glucose transporter 2), Pdx1, MafA, and Atf2 (activating transcription factor 2), genes were upregulated, while glucokinase (Gck) and NeuroD1 (neuronal differentiation 1) were downregulated. Additionally, we studied whether the gene expression differences in Pdx1 and MafA between control and restricted offspring were associated with differential DNA methylation status in their regulatory regions. A decrease in the DNA methylation levels was found in the 5' flanking region between nucleotides -8118 to -7750 of the MafA regulatory region in restricted offspring compared with control pancreatic islets. In conclusion, low protein availability during gestation causes the upregulation of MafA gene expression in pancreatic β-cells in the male juvenile offspring at least in part through DNA hypomethylation. This process may contribute to developmental dysregulation of β-cell function and influence the long-term health of the offspring.

CeDAR: incorporating cell type hierarchy improves cell type-specific differential analyses in bulk omics data

Bulk high-throughput omics data contain signals from a mixture of cell types. Recent developments of deconvolution methods facilitate cell type-specific inferences from bulk data. Our real data exploration suggests that differential expression or methylation status is often correlated among cell types. Based on this observation, we develop a novel statistical method named CeDAR to incorporate the cell type hierarchy in cell type-specific differential analyses of bulk data. Extensive simulation and real data analyses demonstrate that this approach significantly improves the accuracy and power in detecting cell type-specific differential signals compared with existing methods, especially in low-abundance cell types.

Association of promoter methylation status of NRF2 and PNPLA3 genes in alcoholic liver disease.

Alcoholic liver disease (ALD) is the leading cause of chronic liver disease. In the liver, metabolism of alcohol occurs through multiple mechanisms and it results in the generation of various toxic products. Multiple genetic causes have been identified that are associated with the development and progression of ALD. The present study assessed the promoter site methylation status ofnuclear factor erythroid 2-related factor 2 (NRF2) and patatin-like phospholipase domain-containing protein-3 (PNPLA3) genes in different subgroups of ALD. The patients recruited were cases of alcohol dependence syndrome with hepatic dysfunction, compensated cirrhosis, decompensated cirrhosis, and acute-on-chronicliver failure due to alcohol as an etiology along with healthy control subjects. Routine biochemical investigations were performed along with methylation-specific polymerase chain reaction (MS-PCR) to qualitatively assess the promoter methylation status of NRF2 and PNPLA3 in all these cases. There was significant difference in methylation status of NRF2 gene in ALD when compared to healthy controls but there was no such difference in PNPLA3. All biochemical and clinical parameters studied were significantly different in subgroups of ALD except the serum aspartate aminotransferase (AST) level. Subgroups of ALD did not show any significant association with NRF2 or PNPLA3 methylation status. Gamma-glutamyl transferase (GGT) and creatinine levels in serum were significantly associated with the methylation status of NRF2 gene while no such association was seen with PNPLA3 gene. Model for end-stage liver disease (MELD) score varied differentially with NRF2 methylation and PNPLA3 methylation but there was no statistical significance. The present study showed that methylation status of NRF2 and PNPLA3 genes could not differentiate between subgroups of alcoholic liver diseases. However, the unmethylation of NRF2 promoter is associated with higher serum levels of GGT.

Identification and validation of DNA methylation markers to predict axillary lymph node metastasis of breast cancer.

Axillary lymph node metastasis (ALNM) is one of the most important prognostic factors for breast cancer patients, and DNA methylation is involved in ALNM of breast cancer. However, the methylation profile of breast cancer ALNM remains unknown. Breast cancer tissues were collected from patients with and without ALNM. We investigated the genome-wide DNA methylation profile in breast cancer with and without ALNM using reduced representation bisulfite sequencing (RRBS). Then, differentially methylated regions (DMRs) were verified by targeted bisulfite sequencing. A total of 21491 DMRs were identified between the lymph node positive group and negative group. Compared to the LN-negative breast cancer, LN-positive breast cancer had 10,920 hypermethylated DMRs and 10,571 hypomethylated DMRs. Then, 10 DMRs in the gene promoter region were detected by targeted bisulfite sequencing, these gene included HOXA5, PTOV1-AS1, RHOF, PAX6, GSTP1, RASGRF2, AKR1B1, BNIP3, CRMP1, ING5. Compared with negative lymph node, the promoter methylation levels of RASGRF2, AKR1B1 and CRMP1 increased in positive lymph node, while the promoter methylation level of RHOF decreased in positive lymph node. In addition, Cancer Genome Atlas (TCGA) data showed that RASGRF2, AKR1B1 and CRMP1 were low expressed in breast Cancer tissues, while RHOF was high expressed in breast Cancer tissues. Furthermore, in addition to highly methylated AKR1B1, RASGRF2 and CRMP1 gene promoters, BNIP3, GSTP1, HOXA5 and PAX6 gene promoters were also methylated in ER-positive and HER2-negative breast cancer with ALNM. When compared to negative lymph node breast cancer, the positive lymph node breast cancer has a differential methylation status. Promoter methylation of RASGRF2, AKR1B1, CRMP1 and RHOF in lymph node positive breast cancer tissues was significantly different from that in lymph node negative breast cancer tissues. AKR1B1, RASGRF2, CRMP1, BNIP3, GSTP1, HOXA5 and PAX6 genes were methylated in ER-positive and HER2-negative breast cancer with ALNM. The study provides an important biological base for understanding breast cancer with ALNM and developing therapeutic targets for breast cancer with ALNM.

Salivary DNA methylation markers for cancer of oral cavity.

Aberrant DNA methylation plays a crucial role in oral carcinogenesis. Our previous study demonstrated hypermethylation of DAPK1, LRPPRC, RAB6C, and ZNF471 promoters in patients with tongue squamous cell carcinoma compared with normal samples. Methylation profiling using salivary DNA is considered a non-invasive alternative to tissue samples. Hence, the present study tested the DNA methylation status of these four promoters as indicators of oral cancer progression. We performed the bisulfite-based targeted next-generation sequencing of four candidate genes in saliva and tissue DNA from normal, premalignant, and squamous cell carcinoma subjects. The clinicopathological association, diagnostic, and prognostic utility of aberrant DNA methylation were evaluated using the TCGA-HNSCC dataset. Using the Xgboost algorithm and logistic regression, CpG sites were prioritized, and Receiver Operating Characteristic was generated. By Log-rank test and Kaplan-Meier (KM) curves, an association between methylation and overall survival (OS), disease-free interval (DFI), and progression-free interval (PFI) were computed. We identified all four genes as significantly hypermethylated in premalignant and malignant samples compared with normal samples. The methylation levels were comparable between saliva and tissue samples with an r-value of 0.6297 to 0.8023 and 0.7823 to 0.9419 between premalignant tissue vs. saliva and OC vs. saliva, respectively. We identified an inverse correlation between DAPK1, LRPPRC, RAB6C, and ZNF471 promoter methylation with their expression. A classifier of 8 differentially methylated CpG sites belonging to DAPK1, RAB6C, and ZNF471 promoters was constructed, showing an AUC of 0.984 to differentiate tumors from normal samples. The differential methylation status of DAPK1, LRPPRC, and ZNF71 promoters was prognostically important. Abnormal expression of all four genes was associated with immune infiltration. Thus, methylation analysis of these candidate CpG sites from saliva can be helpful as a non-invasive tool for the clinical management of OC.

Molecular, Epigenetic, and Immune Landscape of TP53-mutated (TP53-M) Acute Myeloid Leukemia (AML) and Higher Risk Myelodysplastic Syndromes (HR-MDS)

Introduction: Mutations in TP53 confer an adverse prognosis in patients (pts) with AML and HR-MDS. Comprehensive analyses of the genetic, epigenetic, and immunologic landscape of TP53-M AML and HR-MDS are lacking, especially associations of allelic status of TP53 with immune and epigenetic disease phenotype. Methods: Using a large, randomized study with extensive and prospective clinical, histopathological, cytogenetic, molecular, epigenetic, and immunologic annotations, we compared data from 61 TP53-M (37 AML, 24 HR-MDS) and 144 TP53 wild-type (TP53-WT; 89 AML, 55 HR-MDS) pts. Pts were randomized to azacitidine (AZA) monotherapy or AZA + anti-PDL1 antibody durvalumab, which did not improve clinical outcomes (Zeidan et al. Blood Advances 2022). A 38 gene-targeted myeloid mutation analysis from screening bone marrow (BM) was performed at Munich Leukemia Laboratory. Only pathogenic TP53 variants with variant allele frequency (VAF) ≥2% were included. Pts with a common SNP or VUS in the TP53 gene were classified as TP53-WT. Multi-hit TP53 mutations were defined as previously published by Grob et al. (Blood 2022) which confirmed that TP53-M AML and HR-MDS can be grouped as one entity. BM aspirates from screening and cycle 3 day 22 (C3D22) were used to study gene expression profiles by RNA-sequencing and immune phenotyping by flow cytometry. Gene set enrichment analysis (GSEA) using the MSigDB and H (Hallmark) gene sets as provided by the msigdbr R package were performed. Flow cytometry data were analyzed into a collection of 170 reportable subpopulations in the immune cell and immune checkpoint panel and 68 reportables in the tumor/blast panel. DNA methylation of peripheral blood samples was assessed using Illumina's Infinium Human Methylation EPIC methylation array pre-treatment and at C2D1. Global DNA methylation scores (GDMS) and focal DNA demethylation in PD-1, PD-L1 and PD-L2 regulatory regions were analyzed. Results: Of the 61 TP53-M and 144 TP53-WT pts, 85.4% and 10.4% had complex karyotype, respectively. TP53-M pts had fewer co-occurring mutations compared with TP53-WT (mean number of mutations: 1.8 [SD: 0.77] vs 2.9 [SD: 1.4]; P <0.001). Distinct mutational patterns by TP53 mutational status were noted (Figure 1). The median VAF for TP53 mutations was 40%, and 90% had a VAF ≥10%. 22 (11.0%) and 41 (20.5%) pts were mono-hit and multi-hit, respectively. Global DNA methylation was independent of TP53 mutation status at baseline when comparing mono-hit, multi-hit and wild-type. AZA therapy led to statistically significant decrease in GDMS independent of TP53 mutation status (Figure 2). Various loci of PD-1, PD-L1 and PD-L2 genes showed differences in methylation status by TP53 mutation status, which were reversed on treatment. However, methylation of 2 PD-L2 gene loci (cg07211259 and cg11299543) remained significantly lower for multi-hit TP53-M compared to TP53-W at C2D1. Patterns of differentially expressed genes were similar for multi-hit TP53-M vs wild-type and for all TP53-M vs wild-type. The number of differentially expressed genes was higher in the AML cohort compared to MDS pts both at baseline (1887 vs 78) and after C3 (116 vs 0) with TP53-M samples having more differentially expressed genes. ZNF560 was the gene with the strongest differential expression by TP53 mutation status. TP53-M pts had higher expression of T-cell genes (e.g., IL7R), markers of proliferation (MKI67), and PD-L1 (CD274) expression compared to TP53-W at baseline. Genes in hallmark clusters of heme metabolism, inflammatory response, cell cycle regulation, and TGF-β signaling pathways were enriched in TP53-M pts in GSEA. TP53-M pts had higher median levels of PD-L1-positive progenitors (5.6% vs 2.4%; p=0.006) and less myeloid progenitor cells (58% vs 75%; p=0.005) than TP53-WT at baseline. However, there was no shift towards a more exhausted T-cell phenotype among TP53-M pts (CD3+CD4+ PD1+ TIM3+ T-cells and CD3+CD8+PD1+TIM3+ T-cells as % of CD3+CD4+ T-cells and CD3+CD8+ T-cells, respectively). Conclusion: Although an increased population of cytotoxic T-cells suggest an activated immune system, we also found the upregulation of inhibitory immune checkpoints such as PD-L1 in TP53-mut pts suggesting an immunosuppressive microenvironment as a potential contributor to the poor prognosis of TP53-M AML and MDS with similar findings across disease type (HR-MDS vs AML) and mono- vs multi-hit TP53 mutation status. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Biomarkers of Clinical Resistance to Decitabine and Venetoclax Therapy Inferred By Transcriptome and Methylation Analyses

The combination of the selective BCL-2 inhibitor venetoclax (VEN) with the hypomethylating agent (HMA) decitabine (DEC) is highly effective in treating older ineligible for intensive chemotherapy AML patients. However, approximately 15-34% of newly diagnosed (ND) and 60% of relapsed/refractory (R/R) patients fail to achieve complete remission (CR) (DiNardo et al. New Engl J Med. 2020, DiNardo et al. Lancet Haematol. 2020). Factors that reduce efficacy remain to be elucidated. To dissect underlying mechanisms of HMA-VEN resistance, we performed RNA-seq utilizing primary samples from patients treated on a prospective clinical trial of 10-day DEC with VEN (NCT03404193). Previously, we reported that alterations of transcriptome signatures of energy-metabolism and cell migration/adhesion pathways were upregulated in primary resistant ND group, and immune-system-associated genes were downregulated in R/R group (Yamatani et al. ASH 2021). This study investigated transcriptomic and DNA methylation signatures associated with DEC10-VEN response or resistance in ND and R/R AML. Because DEC was reported to strongly induce interferon-stimulated genes (ISGs) through gene methylation modifications, we focused on 116 ISGs. An integrated analysis of DNA methylation status around the transcription start site (TSS) was performed using the Infinium methylated EPIC array (Illumina). Forty-four pre-treatment samples from 32 patients with AML from DEC-VEN clinical trial, ND patient group (CR/CRi 14; non-responder, NR 11) and R/R patient group (CR/CRi 6; NR 13), were analyzed. First, we performed the comparative analysis of NR vs CRs. In the ND group, NR cases showed significantly higher gene expression and lower TSS methylation of an urea cycle enzyme, ASS1 (Argininosuccinate Synthase 1) with RNA-seq Log2 fold-change (FC) 3.6 and methylation array Δβ (differential methylation β-value) -0.11, p < 0.05, and of an actin-based molecular motor, MYO1C (Myosin 1C), Log2FC 2.5, Δβ = -0.18, p< 0.05, than in CR cases. In the R/R group, gene expression levels of seven ISGs, including CCL3 (C-C motif chemokine 3), were significantly lower in NR than in CRs, with no difference in methylation status. Next, changes in gene expression levels and TSS methylation status after DEC-VEN treatment were investigated in non-responders in ND group (pre 19, post 12) and R/R group (pre 16, post 4). After DEC-VEN treatment, PPARG (Peroxisome Proliferator-Activated Receptor γ), a transcription factor that activates fatty acid metabolism and negatively regulates subsets of IFN-γ target genes, was significantly upregulated along with its TSS demethylation both in ND (Log2FC 4.9, Δβ = -0.14, p < 0.05), and R/R groups (Log2FC 3.7, Δβ = -0.06, p < 0.05). CDC42EP4, an effector protein of CDC42 involved in the organization of the actin cytoskeleton, was upregulated after the treatment in the R/R group (Log2FC 2.7, Δβ = -0.14, p < 0.05). Based on these findings, we validated transcriptional and methylation changes of ASS1, PPARG, MYO1C and CDC42EP4 by RT-qPCR and bisulfite pyrosequencing using HL60 and MV4-11 AML cell lines in which DEC (IC50, HL60, 249 nM; MV4-11, 2090 nM) and VEN (IC50, HL60, 18 nM; MV4-11, 64 nM) produced additive or synergistic combination effect. Cells were treated by DEC and/or VEN under BM-derived mesenchymal stem cells (MSCs) co-culture conditions to mimic the BM microenvironment. DEC upregulated gene expression levels with TSS demethylation of PPARG, MYO1C and CDC42EP4 both in HL60 and MV4-11, and of ASS1 only in HL-60. VEN treatment alone or in combination with DEC did not induce significant changes in the expression of these tested genes. Of note, PPARG expression was further upregulated under MSCs co-culture condition without TSS methylation status change in AML cells. DEC treatment induced no significant changes of PPARG in MSC. These findings suggest that not only TSS demethylation but also interaction with BM stromal cells may be involved in PPARG upregulation associated with energy production in AML cells. Taken together, DEC-VEN treatment stimulates two key factors, energy metabolism and interaction with the BM microenvironment, which may reduce therapeutic efficacy by increasing gene expression of PPARG,MYO1C,ASS1, and CDC42EP4 through TSS demethylation and/or interaction with BM stromal cells. Experimentally, the consequences of overexpression / knockdown of these genes will be further validated.

Evaluation of genetic and epigenetic changes of Tumor Necrosis Factor-Alpha gene in larynx cancer

BackgroundTumor Necrosis Factor-Alpha (TNF-α) is a proinflammatory cytokine that plays a role in inflammation, which is one of the hallmarks of cancer, and its polymorphic variants have been associated with disease risk in many cancers in the literature. The aim of this study was to investigate four different polymorphic variants, differential methylation and expression status of the TNF-α gene and to determine the associations between these variants and disease risk, and to evaluate the relationship between the results and clinical parameters. We purposed to investigate the genetic and epigenetic alterations of the TNF-α gene in larynx cancer (LC). Material and MethodsAfter isolation of DNA/RNA from whole blood, tumor and normal tissue, polymorphic variant alleles differrential expression and methylation levels were analyzed by RFLP, semiquantitative RT-PCR, and restriction enzyme digestion, respectively. TNF-α expression and methylation levels were calculated using BIO1D software. The frequencies of the variants c.–238 G>A (rs361525), c.–857 C>T (rs1799724), c.–863 C>A (rs1800630), and c.–1031 T > C (rs1799964) in the promoter region of TNF-α in LC Turkish patients and healthy individuals were examined using the De-Finetti case-control program. Haplotype frequencies and linkage disequilibrium were analyzed using the SNPStats program. ResultsThe frequency of genotype c.–1031 T > C was significantly lower in patients than in healthy individuals [TT vs TC: OR (%95CI) = 7.00 (1.75–27.93), p = 0.003, χ2 = 8.76]. The heterozygous variant of − 857 was associated with recurrence [T vs G: OR (%95CI) = 0.15 (0.02–0.95), p = 0.02, χ2 = 4.86]. For c.–238 G>A, c.–857 C>T, and c.–863 C>A, there was no statistically significant difference between the patient and healthy group in terms of disease risk. A significant association was found between c.–1031 T > C and disease risk of LC. Decreased expression was detected in 46% (23/50) and increased expression in 54% (27/50) of tumor tissue samples compared to the matched normal tissues of patients. Methylation-related loss of expression was detected in 53.3% (16/30) of patients. ConclusionOur study is the first investigating four different polymorphic regions of the TNF-α promoter region and the expression/methylation status of TNF-α in the same LC patient and healthy cohort. According to our results, the c.–1031 T > C variant was reported to be significantly associated with a reduced risk of LC. In addition, the TNF-α variant c. –857 C>T suggests that it may be a potential biomarker for predicting the recurrence of LC. An association between c. –857 C>T variant and methylation-based expression status was observed.

Expanding the clinico-molecular spectrum of Angelman syndrome phenotype with the GABRG3 gene: Evidence from methylation and sequencing studies.

Angelman syndrome (AS) (OMIM#105830) is an imprinting disorder caused due to alterations in the maternal chr 15q11-13 region. Majority of cases can be diagnosed by methylation-specific polymerase chain reaction (MS-PCR) of SNRPN gene and by UBE3A sequencing, however, about 10% of cases with AS phenotype remain undiagnosed. Differential diagnoses of AS can be detected by chromosomal microarray (CMA) and clinical exome sequencing (CES). In this study, 30 cases with AS features were evaluated by MS-PCR, CMA, and CES. SNRPN MS-PCR confirmed AS in eight (26%), CMA and CES diagnosed nine (30%) cases. One case was identified with a novel variant c.1125C>T in GABRG3, located at 15q12 region, which is currently not associated with any syndrome. The GABRG3 gene is also speculated to be imprinted, a MS-PCR assay was designed to confirm its differential parental methylation status. This assay identified another case with altered GABRG3 methylation. The two cases with GABRG3 alteration-sequence change and methylation indicate that GABRG3 may be associated with a subtype of AS or a new related syndrome. Performing GABRG3 MS-PCR and sequencing of a larger group of patients with AS phenotype and normal SNPRN and UBE3A status will help in establishing exact genotype-phenotype correlation.

The ERK1/2 Regulator WNK2 Shows Differential Expression and Isoform Usage, Primarily Driven By Aberrant Methylation, in MYD88 Mutated Waldenström's Macroglobulinemia

MYD88 mutations (MYD88 MUT) are present in 95-97% of patients with Waldenström's Macroglobulinemia (WM). Transgenic mouse studies show that MYD88 MUT alone is insufficient to drive oncogenesis. We previously reported the occurrence of non-overlapping somatic mutations in either CXCR4 (CXCR4 MUT) or deletions in 6q (del6q) in MYD88 mutated (MYD88 MUT) WM patients, suggesting either event may serve as a secondary driver of WM oncogenesis. Intersecting the lists of genes differentially modulated by either CXCR4 MUT or del6q revealed WNK2 as a top hit (Guerrera ML et al, Haematologica 2018). WNK2 is a serine/threonine protein kinase that negatively regulates ERK1/2 activation and has known tumor suppressor function in several solid tumors, wherein its expression is primarily silenced by aberrant promoter methylation. ERK1/2 pathway plays an important pro-survival role, its activation is accompanied by the release of inflammatory cytokines and can mediate ibrutinib resistance in WM (Chen et al, Blood 2018). We therefore sought to investigate the expression of WNK2, and clarify the mechanisms underlying its aberrant expression by genomic subtypes in WM.To study the regulation of WNK2 gene expression, we analyzed our previously published RNA-Seq data (Hunter ZH et al, Blood 2016) and validated findings in 47 WM patients by RT-qPCR. Compared to healthy donor (HD) B and plasma cells (PC), we observed marked upregulation of WNK2 expression in bone marrow (BM) CD19-selected tumor cells from MYD88 MUTCXCR4 WT patients (p<0.0001). Conversely, WNK2 expression was silenced in tumor cells from MYD88 MUTCXCR4 MUT and MYD88 WTCXCR4 WT (p<0.001 vs HD PC) patients, with less pronounced suppression of WNK2 also observed in MYD88 MUTdel6q cases. Immunohistochemistry analysis on patient BM biopsies confirmed the findings observed at the mRNA level per patient genotype.To assess the impact of alternative splice variants on overall gene expression, we then studied the relative composition of the 16 documented isoforms (Figure 1). RNA-Seq showed a prevalence of protein-coding transcripts, particularly those coding for isoforms missing the ERK regulatory kinase domain, in MYD88 MUT vs MYD88 WT WM. By RT-PCR, we validated the preferential use of the protein-coding WNK2-208, WNK2-203 and WNK2-205 transcripts in 32 of 47 WM samples with detectable total WNK2 levels. Of those, WNK2-208 and WNK2-203 lack the region coding for the functional kinase domain. Analysis of known post-translational modification (PTM) sites annotated for the canonical isoform WNK2-201 in the 3 isoforms of interest demonstrated that C-terminal PTM sites are highly conserved across all isoforms even in the absence of the kinase domain, alluding to novel protein regulatory sites yet to be characterized.Analysis of CpG methylation using enhanced reduced representation bisulfite sequencing from 62 WM patients identified 3 clusters of differentially methylated CpG islands (CpGs) between MYD88 MUTCXCR4 WT and MYD88 MUTCXCR4 MUT patients. Three CpGs in the WNK2 promoter, four in intron 1 and one in intron 11 constituted clusters 1, 2 and 3, respectively (Figure 1). Compared to healthy donor memory B-cell and PC, we observed aberrant hypermethylation in cluster 1 in MYD88 MUTCXCR4 MUT and hypomethylation at a putative enhancer in cluster 2 in MYD88 MUTCXCR4 WT patients, while del6q cases showed a mixed methylation pattern. A higher degree of methylation, particularly in cluster 2, significantly correlated with reduction in total and transcript-specific WNK2 mRNA levels that affected expression of transcripts encoding for kinase domain-containing isoforms. Furthermore, we validated the differential methylation status of 3 of 4 methylated CpGs in cluster 2 in 10 patients, including MYD88 MUTCXCR4 WT, MYD88 MUTCXCR4 MUT and MYD88 MUTdel6q, and 3 MYD88 MUT (BCWM.1, TMD-8) and MYD88 WT (Ramos) cell lines by means of bisulfite PCR followed by Sanger sequencing. Taken together, our findings reveal that the ERK1/2 regulator WNK2 shows differential expression and isoform usage in distinct genomic subsets of MYD88 MUT WM; is primarily driven by aberrant methylation; and may serve as a key driver of disease progression in WM. [Display omitted] DisclosuresYang: Blueprint Medicines Corporations: Current Employment, Current holder of individual stocks in a privately-held company. Castillo: Abbvie: Consultancy, Research Funding; BeiGene: Consultancy, Research Funding; Pharmacyclics: Consultancy, Research Funding; Janssen: Consultancy; Roche: Consultancy; TG Therapeutics: Research Funding. Treon: BeiGene: Consultancy, Research Funding; Eli Lily: Research Funding; Abbvie/Pharmacyclics: Consultancy, Research Funding.

DNA Methylation Patterns in the HLA-DPB1 and PDCD1LG2 Gene Regions in Patients with Autoimmune Thyroiditis from Different Water Iodine Areas.

Background: Epigenetic disorders play an important role in the pathogenesis of autoimmune thyroiditis (AIT). Therefore, the study of the possible role of DNA methylation in AIT is of great significance to explore the pathogenesis of AIT. Methods: From May 2019 to June 2019, whole blood samples were collected from 176 AIT patients and 176 controls from different water iodine levels in Shandong Province, China. We used the Illumina Methylation 850K BeadChip to determine significant differences in methylation status of genes and used the MethylTarget™ assay to verify the methylation level in 176 cases and 176 controls. The relative mRNA levels of genes were detected by quantitative real-time-polymerase chain reaction. Results: There were multiple differential methylation sites in the HLA-DPB1 and PDCD1LG2 genes between the case and control population with different water iodine levels. Some target regions of HLA-DPB1 and PDCD1LG2 genes were negatively correlated with relative mRNA expression in the case and control populations and with different water iodine levels. Conclusions: There is differential methylation status in genomic DNA in patients with AIT. The methylation patterns of HLA-DPB1 and PDCD1LG2 genes related to cell adhesion molecule pathway may be different based on different water iodine levels. HLA-DPB1 and PDCD1LG2 genes related to the cell adhesion molecules pathway may play a role in the development of AIT. This study is registered with Chinese Clinical Trial Registry, www.chictr.org.cn, number ChiCTR2000039105.

Long Noncoding RNA DICER1-AS1 Functions in Methylation Regulation on the Multi-Drugresistance of Osteosarcoma Cells via miR-34a-5p and GADD45A.

Osteosarcoma (OS) is a common malignant bone tumor that commonly occurs in children and adolescents. Long noncoding RNAs (lncRNAs) are recognized as a novel class of regulators of gene expression associated with tumorigenesis. However, the effect and mechanism of lncRNAs in OS tumorigenesis and drug resistance have not been characterized. The purpose of the study is to screen potential biomarker and therapeutic target against OS. We compared the lncRNA expression profiles between OS cell lines with different drug resistance levels using RNA-seq analysis and found that lncRNA DICER1-AS1 was significantly differentially expressed in multi-drugresistant OS cells SJSA-1 versus multi-drugsensitive OS cells G-292. Bisulfite Sequencing PCR (BSP) assay was performed to analyze the differential methylation status of the promoter region of DICER1-AS1 in four OS cells. Subsequently, in vitro gain- and loss-of-function experiments demonstrated the roles of DICER1-AS1 and miR-34a-5p in the multi-drugresistance of OS cells. The main findings is that DICER1-AS1 directly binds to miR-34a-5p, and their expression has a negative correlation with each other. The hypermethylation of the promoter region of DICER1-AS1 silenced its expression in the drugresistant cells SJSA-1 and MNNG/HOS. Moreover, we found that growth arrest and DNA damage-inducible alpha (GADD45A) participates in the DICER1-AS1/miR-34a-5p-regulated drug resistance of OS cells, probably via the cell cycle/pRb-E2F pathway. Our results revealed DICER1-AS1/miR-34a-5p-regulated drug resistance of OS cells, a new lncRNA-regulated network in OS tumorigenesis, suggested that DICER1-AS1 can be considered as a potential biomarker and therapeutic target against OS cells.