Methylation-specific PCR Analysis Research Articles

Abstract 455: Identification of hsa-miR-6794-3p as a key regulatory factor in human pancreatic cancer metastasis

Abstract Metastasis is a major factor in treatment failure in patients with pancreatic cancer, but the underlying mechanisms remain unclear, and new, effective treatment strategies are needed. Here, we sought to identify novel microRNAs (miRNAs) with a key role in pancreatic cancer metastasis. Using a microarray analysis to evaluate miRNA expression in metastatic and non-metastatic pancreatic cancer, we found that expression of the miRNA, hsa-miR-6794-3p, was significantly lower in metastatic pancreatic cancer tissues than in non-metastatic pancreatic cancer tissues. Methylation-specific polymerase chain reaction analyses revealed that hsa-miR-6794-3p expression was downregulated in metastatic pancreatic cancer cells by hypermethylation of CpG islands within the hsa-miR-6794-3p promoter. Gain- and loss-of-function approaches using the human pancreatic cancer cell lines, MIA-PaCa-2 and HPAF-II, expressing low and high levels of hsa-miR-6794-3p, respectively, suggested a role for hsa-miR-6794-3p in decreasing cell invasion, migration, and epithelial-mesenchymal transition (EMT) signaling. Notably, we found that hsa-miR-6794-3p exerts its effects by inhibiting expression of the chromatin remodeling factor, RBBP4, through direct binding to the 3’-untranslated region of its mRNA. The resulting suppression of RBBP4 expression increases levels of the transcription factor GRHL2, which is involved in regulating invasion, migration, and EMT signaling in metastatic pancreatic cancer cells. Thus, lower levels of hsa-miR-6794-3p disrupt GRHL2-mediated regulation of these pathways by disinhibiting expression of the GRHL2 negative regulator, RBBP4. Consistent with these findings, an investigation of the relationship between hsa-miR-6794-3p and clinicopathological features in pancreatic cancer patients using publicly available datasets and immunohistochemistry showed that low levels of hsa-miR-6794-3p are correlated with a poorer prognosis in pancreatic cancer patients. Additional preclinical experiments in nude mice clearly demonstrated that hsa-miR-6794-3p is capable of suppressing pancreatic cancer cell metastasis. Taken together, these results suggest that hsa-miR-6794-3p suppresses tumor metastasis and thus represents a promising prognostic biomarker and therapeutic target in pancreatic cancer. Citation Format: Ha Gyeong Kim, Eun-Taex Oh, Yunmi Cho, Heon Joo Park. Identification of hsa-miR-6794-3p as a key regulatory factor in human pancreatic cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 455.

Pathophysiology Crossroads: Examining the Role of Adiponectin (ADIPOQ) in the Intersection of Type II Diabetes and Dementia

Background: Type II Diabetes Mellitus (Type II DM) is intricately linked with an increased risk of cognitive impairment and dementia. The ADIPOQ gene encodes adiponectin, a hormone that plays a critical role in glucose regulation and fatty acid oxidation and may be implicated in the pathophysiology of both diabetes and dementia. Understanding the expression of ADIPOQ in diabetic patients with dementia could offer insights into the mechanisms at play and aid in the development of potential therapeutic targets. Objective: This study aims to analyze the expression of the ADIPOQ gene in diabetic patients diagnosed with dementia and to correlate these findings with cognitive impairment as assessed by Mini-Mental State Examination (MMSE) scores. Methods: We collected 5ml EDTA blood samples from 88 diabetic dementia patients and 12 healthy controls after obtaining written informed consent. The study adhered to the Declaration of Helsinki guidelines. Serum adiponectin levels were measured via Chemiluminescent immunoassay (CLIA), and genomic DNA was isolated for methylation-specific PCR and expression analysis. ADIPOQ gene expression was quantified using real-time PCR, and data were analyzed using SPSS version 25, employing descriptive and inferential statistics. Results: The diabetic dementia patient group demonstrated significantly lower adiponectin levels (5.62 ± 1.08 µg/mL) and MMSE scores (10.68 ± 4.56) compared to healthy controls (adiponectin: 15.68 ± 4.64 µg/mL, MMSE: 25.9 ± 3.12). Real-time PCR results indicated a relative fold decrease of 4.9 in ADIPOQ gene expression in the dementia cohort. Conclusion: The ADIPOQ gene expression is inversely associated with cognitive function in diabetic patients, highlighting its potential as a biomarker for early detection and targeted therapeutic interventions in dementia associated with diabetes.

EN1 promotes lung metastasis of salivary adenoid cystic carcinoma by regulating the PI3K-AKT pathway and epithelial-mesenchymal transition

BackgroundEngrailed homeobox 1 (EN1) is a candidate oncogene that is epigenetically modified in salivary adenoid cystic carcinoma (SACC). We investigated the expression of EN1 in SACC tissues and cells, EN1 promoter methylation, and the role of EN1 in tumour progression in SACC.MethodsThirty-five SACC samples were screened for key transcription factors that affect tumour progression. In vitro and in vivo assays were performed to determine the viability, tumorigenicity, and metastatic ability of SACC cells with modulated EN1 expression. Quantitative methylation-specific polymerase chain reaction analysis was performed on SACC samples.ResultsEN1 was identified as a transcription factor that was highly overexpressed in SACC tissues, regardless of clinical stage and histology subtype, and its level of expression correlated with distant metastasis. EN1 promoted cell invasion and migration through epithelial-mesenchymal transition in vitro and enhanced SACC metastasis to the lung in vivo. RNA-seq combined with in vitro assays indicated that EN1 might play an oncogenic role in SACC through the PI3K-AKT pathway. EN1 mRNA levels were negatively correlated with promoter hypermethylation, and inhibition of DNA methylation by 5-aza-dC increased EN1 expression.ConclusionsThe transcription factor EN1 is overexpressed in SACC under methylation regulation and plays a pivotal role in SACC progression through the PI3K-AKT pathway. These results suggest that EN1 may be a diagnostic biomarker and a potential therapeutic target for SACC.

The interplay mechanism between IDH mutation, MGMT-promoter methylation, and PRMT5 activity in the progression of grade 4 astrocytoma: unraveling the complex triad theory.

The dysregulation of Isocitrate dehydrogenase (IDH) and the subsequent production of 2-Hydroxyglutrate (2HG) may alter the expression of epigenetic proteins in Grade 4 astrocytoma. The interplay mechanism between IDH, O-6-methylguanine-DNA methyltransferase (MGMT)-promoter methylation, and protein methyltransferase proteins-5 (PRMT5) activity, with tumor progression has never been described. A retrospective cohort of 34 patients with G4 astrocytoma is classified into IDH-mutant and IDH-wildtype tumors. Both groups were tested for MGMT-promoter methylation and PRMT5 through methylation-specific and gene expression PCR analysis. Inter-cohort statistical significance was evaluated. Both IDH-mutant WHO grade 4 astrocytomas (n = 22, 64.7%) and IDH-wildtype glioblastomas (n = 12, 35.3%) had upregulated PRMT5 gene expression except in one case. Out of the 22 IDH-mutant tumors, 10 (45.5%) tumors showed MGMT-promoter methylation and 12 (54.5%) tumors had unmethylated MGMT. All IDH-wildtype tumors had unmethylated MGMT. There was a statistically significant relationship between MGMT-promoter methylation and IDH in G4 astrocytoma (p-value = 0.006). Statistically significant differences in progression-free survival (PFS) were also observed among all G4 astrocytomas that expressed PRMT5 and received either temozolomide (TMZ) or TMZ plus other chemotherapies, regardless of their IDH or MGMT-methylation status (p-value=0.0014). Specifically, IDH-mutant tumors that had upregulated PRMT5 activity and MGMT-promoter methylation, who received only TMZ, have exhibited longer PFS. The relationship between PRMT5, MGMT-promoter, and IDH is not tri-directional. However, accumulation of D2-hydroxyglutarate (2-HG), which partially activates 2-OG-dependent deoxygenase, may not affect their activities. In IDH-wildtype glioblastomas, the 2HG-2OG pathway is typically inactive, leading to PRMT5 upregulation. TMZ alone, compared to TMZ-plus, can increase PFS in upregulated PRMT5 tumors. Thus, using a PRMT5 inhibitor in G4 astrocytomas may help in tumor regression.

Effect of Aerobic/Strength Training on RANKL Gene DNA Methylation Levels.

The osteoclastogenesis RANKL gene plays a key role in bone remodeling. The hypomethylation of its promoter region may cause osteoporosis. The present study aimed to elucidate the influence of physical activity on DNA methylation changes of RANKL promoter cytosine-phosphate-guanine (CpG)-rich region in active and sedentary adults and to assess the effect of aerobic and strength training on RANKL DNA methylation changes among Tunisian-North African adults. A total of 104 participants including 52 adults (58% males and 42% females) and 52 adults (31% males and 69% females) were recruited for the observational and interventional part of the study, respectively. The intervention consisted of 12weeks of aerobic training (30min/session) followed by 10minutes of strengthening exercises. All participants completed the International Physical Activity Questionnaire and provided blood samples for quantitative methylation-specific polymerase chain reaction (PCR) analysis. The study revealed a significant difference (P = 6 × 10-10) in the methylation level of the RANKL promoter region between active and sedentary adults, with a 6.68-fold increase observed in the active group. After the intervention, both the trained (P = 41 × 10-5) and untrained (P = .002) groups displayed high methylation levels in the RANKL promoter region. In addition, the trained group exhibited significant improvements in heart rate (P = 2.2 × 10-16), blood pressure (P = 39 × 10-3), maximal oxygen uptake (P = 1.5 × 10-7), and fat mass (P = 7 × 10-4). Exploring epigenetic modifications in the RANKL promoter region may contribute to a more comprehensive understanding of the complexity of osteoporosis. This suggests that aerobic/strength training could potentially improve the bone system, reducing its vulnerability to osteoporosis by increasing RANKL DNA methylation.

Lack of Methylation Changes in GJB2 and RB1 Non-coding Regions of Cochlear Implant Patients with Sensorineural Hearing Loss.

Recent advances in epigenetic studies continue to reveal novel mechanisms of gene regulation and control, however little is known on the role of epigenetics in sensorineural hearing loss (SNHL) in humans. We aimed to investigate the methylation patterns of two regions, one in RB1 and another in GJB2 in Filipino patients with SNHL compared to hearing control individuals. We investigated an RB1 promoter region that was previously identified as differentially methylated in children with SNHL and lead exposure. Additionally, we investigated a sequence in an enhancer-like region within GJB2 that contains four CpGs in close proximity. Bisulfite conversion was performed on salivary DNA samples from 15 children with SNHL and 45 unrelated ethnically-matched individuals. We then performed methylation-specific real-time PCR analysis (qMSP) using TaqMan® probes to determine percentage methylation of the two regions. Using qMSP, both our cases and controls had zero methylation at the targeted GJB2 and RB1 regions. Our study showed no changes in methylation at the selected CpG regions in RB1 and GJB2 in the two comparison groups with or without SNHL. This may be due to a lack of environmental exposures to these target regions. Other epigenetic marks may be present around these regions as well as those of other HL-associated genes.

Quantitative Investigation of Methylation Heterogeneity by Digital Melting Curve Analysis on a SlipChip for Atrial Fibrillation.

Methylation is an essential epigenetic modification involved in regulating gene expression and maintaining genome stability. Methylation patterns can be heterogeneous, exhibiting variations in both level and density. However, current methods of methylation analysis, including sequencing, methylation-specific PCR, and high-resolution melting curve analysis (HRM), face limitations of high cost, time-consuming workflows, and the difficulty of both accurate heterogeneity analysis and precise quantification. Here, a droplet array SlipChip-based (da-SlipChip-based) digital melting curve analysis (MCA) method was developed for the accurate quantification of both methylation level (ratio of methylated molecules to total molecules) and methylation density (ratio of methylated CpG sites to total CpG sites). The SlipChip-based digital MCA system supplements an in situ thermal cycler with a fluorescence imaging module for real-time MCA. The da-SlipChip can generate 10,656 droplets of 1 nL each, which can be separated into four lanes, enabling the simultaneous analysis of four samples. This method's clinical application was demonstrated by analyzing samples from ten healthy individuals and twenty patients with atrial fibrillation (AF), the most common arrhythmia. This method can distinguish healthy individuals from those with AF of both the paroxysmal and persistent types. It also holds potential for broader application in various research and clinical settings requiring methylation analysis.

Demethylation in promoter region of severely damaged hepatocytes enhances chemokine receptor CXCR4 gene expression.

The liver is known to possess remarkable regenerative potential, but persistent inflammation or severe acute injury can lead to liver fibrosis and incomplete regeneration, ultimately resulting in liver failure. Recent studies have shown that the axis of two types of CXCL12 receptors, CXCR4 and CXCR7, plays a crucial role in liver fibrosis and regeneration. The present study aimed to investigate the regulatory factors involved in CXCR4 expression in injured liver. Immunohistochemical screening of liver tissue samples collected during liver transplantation revealed a reciprocal expression pattern between CXCR4 and MeCP2. An in vitro system involving cultured cell lines and H2O2 treatment was established to study the impact of oxidative stress on signaling pathways and epigenetic alterations that affect CXCR4 mRNA expression. Operating through distinct signaling pathways, H2O2 treatment induced a dose-dependent increase in CXCR4 expression in both hepatocyte- and intrahepatic cholangiocyte-derived cells. Treatment of the cells with trichostatin and azacytidine modulated CXCR4 expression in hepatocytes by modifying the methylation status of CpG dinucleotides located in a pair of TA repeats adjacent to the TATA box of the CXCR4 gene promoter. Only MeCP2 bound to oligonucleotides representing the TATA box region when the cytosine residues within the sequence were methylated, as revealed by electrophoretic mobility shift assay (EMSA). Methylation-specific PCR analysis of microdissected samples revealed a correlation between the loss of CpG methylation and the upregulation of CXCR4 in injured hepatocytes, replicating the findings from the in vitro study. Besides the conventional MEK/ERK and NF-κB signaling pathways that activate CXCR4 in intrahepatic cholangiocytes, the unique epigenetic modifications observed in hepatocytes might also contribute to a shift in the CXCR4-CXCR7 balance towards CXCR4, leading to irreversible liver injury and fibrosis. This study highlights the importance of epigenetic modifications in regulating CXCR4 expression in liver injury and fibrosis.

Poster 113: Epigenetic Regulation of PPARγ Rescues Articular Chondrocytes from Catabolic State Suggesting PPARγ as a Potential Target to Slow Down Progression of OA in Hip FAI

Objectives: Hip Femoroacetabular impingement (FAI) has a high prevalence of chondral lesions, and the severity of chondral damage is associated with an increased risk of postoperative OA progression, but the mechanisms of cartilage degeneration in OA progression remains unclear. Peroxisome proliferator- activated receptor-gamma (PPARγ) is widely expressed in healthy articular chondrocytes (ACs) and plays an essential role in cartilage homeostasis. Recent investigations into OA pathogenesis have revealed that hyper or hypomethylation (by DNMTs) of OA susceptibility genes are involved in OA progression, especially downregulation of PPARγ has been linked to OA progression. This study aimed to investigate the expression of PPARγ and DNA methyltransferases enzymes (DNMT1 and DNMT3A) during progression of hip disease and 2) methylation changes in the PPARγ promoter area during progression of hip disease. Methods: Full-thickness cartilage samples were collected from the impingement zone. Twelve patients underwent hip preservation surgery for cam FAI (early FAI) and twelve patients underwent total hip replacement for advanced OA secondary to cam FAI (late FAI-OA) were included. As a non-disease (ND) group, six healthy samples were procured from hip joint cadavers. Cartilage explants were cultured in unstimulated conditions or catabolic stimulus (IL1β) with or without DNA demethylating agent 5-Aza-2’- deoxycytidine (5Aza). Histological analysis was performed with safranin O/fast green. Gene expression was analyzed via qPCR for GAPDH, DNMT1, DNMT3A, PPARγ, MMP13, and COL10A1. Methylation specific PCR (MSP) was performed to assess the methylation status at PPARγ promoter site. Chromatin immunoprecipitation (ChIP) assay was performed to confirm an interaction between DNMT3A and the PPAR promoter region. Results: The early FAI group included younger subjects than the late FAI OA group. Cartilage samples in early and late FAI-OA displayed a histological OA phenotype (Figure 1A). ACs in early and late FAI-OA displayed increased expression of catabolism and chondrocyte hypertrophy markers ( MMP13: ND vs early p<0.001, ND vs late p<0.001, COL10A1: ND vs early p<0.001, ND vs late p<0.001, Figure. 1B). Contrary, expression of PPARγ gradually declined as the disease progressed (ND vs early p=0.001, early vs late p=0.003, Figure. 1B). IF analysis also displayed a gradual decrease of the PPARγ expression during disease progression (ND vs early p=0.001, early vs late p=0.041, Figure 1C). In the assessment of the epigenetic mechanisms of aberrant DNA methylation in OA progression, overexpression of DNMT1 and DNMT3A levels was observed with disease progression in RT-PCR ( DNMT1: ND vs early p<0.001, early vs late p=0.041, DNMT3A: ND vs early p=0.015, early vs late p=0.053,Figure 2A) and IF analysis ( DNMT1: ND vs early p<0.001, early vs late p<0.001, DNMT3A: ND vs early <0.001, early vs late p=0.008, Figure 2B). Next, in MSP analysis, human PPARγ promoter was featured by typical CpG islands (Figure 3A). As the OA progresses, hypermethylation at PPARγ promoter (ND: 9%, Early-FAI: 34%, Late FAI-OA: 48%) was observed (Figure 3B), and ChIP assay confirmed DNMT3A interaction with the CpG PPARγ promoter area (Figure 3C). IL1β stimulus increased PPARγ promoter methylation for early (34% to 57%, p=0.016, Figure 3D) and late stages (48% to 79%, p=0.001, Figure 3D) resulting in suppression of PPARγ expression (P=0.073, Figure 3F). Contrary, treatment with 5Aza (a DNA demethylator) brought the level of methylation back to 37% for early FAI ( p=0.033, Figure 3D) and 46% for late FAI-OA (p<0.001, Figure 3D), reversed the PPARγ suppression induced by IL1β (early- FAI p=0.009, and late FAI-OA ACs p<0.001 Figure 3F) and decreased expression of MMP-13 and COL10A1 induced by IL1β (early-FAI p=0.009, Figure 4C and late FAI-OA ACs p<0.001 Figure 3F). PPARγ inhibitor rescued cells from the catabolic phenotype. (Fig.3E, F), suggesting that restoration of PPARγ by 5Aza contributes significantly to the cartilage protective effect. Conclusions: This current study demonstrates that PPARγ expression was gradually suppressed via promoter hypermethylation during OA progression in hip FAI. Moreover, the inflammatory stimulus with IL1β further increased catabolic markers and enhanced PPARγ suppression via promoter excessive hypermethylation in human hip ACs. Notably, DNA demethylating agent (5 aza) prevents the IL1β induced PPARγ promoter hypermethylation rescuing PPARγ and alleviating cartilage degenerative damage. Certainly, for patients with symptomatic hip FAI, surgical correction should be prioritized to suppress inflammation, but our observations suggests that critical epigenetic dysregulation occurs during the progression of hip OA. Future investigations will be needed to confirm if regulation of these epigenetic changes could potentially complement surgical treatment to minimize OA progression in hip FAI.

Helicobacter pylori-induced aberrant demethylation and expression of GNB4 promotes gastric carcinogenesis via the Hippo–YAP1 pathway

BackgroundHelicobacterpylori (H. pylori) infection causes aberrant DNA methylation and contributes to the risk of gastric cancer (GC). Guanine nucleotide-binding protein subunit beta-4 (GNB4) is involved in various tumorigenic processes. We found an aberrant methylation level of GNB4 in H. pylori-induced GC in our previous bioinformatic analysis; however, its expression and underlying molecular mechanisms are poorly understood.MethodsThe expression, underlying signaling pathways, and clinical significance of GNB4 were analyzed in a local cohort of 107 patients with GC and several public databases. H. pylori infection was induced in in vitro and in vivo models. Methylation-specific PCR, pyrosequencing, and mass spectrometry analysis were used to detect changes in methylation levels. GNB4, TET1, and YAP1 were overexpressed or knocked down in GC cell lines. We performed gain- and loss-of-function experiments, including CCK-8, EdU, colony formation, transwell migration, and invasion assays. Nude mice were injected with genetically manipulated GC cells, and the growth of xenograft tumors and metastases was measured. Real-time quantitative PCR, western blotting, immunofluorescence, immunohistochemistry, chromatin immunoprecipitation, and co-immunoprecipitation experiments were performed to elucidate the underlying molecular mechanisms.ResultsGNB4 expression was significantly upregulated in GC and correlated with aggressive clinical characteristics and poor prognosis. Increased levels of GNB4 were associated with shorter survival times. Infection with H. pylori strains 26695 and SS1 induced GNB4 mRNA and protein expression in GC cell lines and mice. Additionally, silencing of GNB4 blocked the pro-proliferative, metastatic, and invasive ability of H. pylori in GC cells. H. pylori infection remarkably decreased the methylation level of the GNB4 promoter region, particularly at the CpG#5 site (chr3:179451746–179451745). H. pylori infection upregulated TET1 expression via activation of the NF-κB. TET binds to the GNB4 promoter region which undergoes demethylation modification. Functionally, we identified that GNB4 induced oncogenic behaviors of tumors via the Hippo–YAP1 pathway in both in vitro and in vivo models.ConclusionsOur findings demonstrate that H. pylori infection activates the NF-κB-TET1-GNB4 demethylation-YAP1 axis, which may be a potential therapeutic target for GC.

LncRNA PMS2L2 Is Downregulated in Sepsis-Induced Acute Kidney Injury and Inhibits LPS-Induced Apoptosis of Podocytes

Introduction: Long noncoding RNA PMS2L2 can inhibit inflammation induced by LPS, while LPS plays an important role in sepsis, indicating the possible involvement of PMS2L2 in sepsis. Methods: Expressions of miR-21 and PMS2L2 in patients with acute kidney injury (AKI), sepsis patients without induced AKI, and healthy controls were determined by performing RT-qPCR. Overexpression assay was performed to explore the crosstalk between miR-21 and PMS2L2. Methylation-specific PCR (MSP) was performed to explore the role of PMS2L2 in regulating the methylation of miR-21 gene. The role of miR-21 and PMS2L2 in the apoptosis of CIHP-1 cells induced by LPS was assessed by cell apoptosis assay. Results: PMS2L2 was downregulated in AKI patients induced by sepsis compared to sepsis patients without AKI and healthy controls. MiR-21 was also downregulated in AKI induced by sepsis and positively correlated with PMS2L2. In addition, in cells of human podocyte cell line (CIHP-1), overexpression of PMS2L2 promoted the expression of miR-21, while miR-21 did not affect the expression of PMS2L2. MSP analysis showed that overexpression of PMS2L2 decreased methylation of miR-21. LPS treatment downregulated PMS2L2 and miR-21 in a time-dependent manner. PMS2L2 and miR-21 decreased the apoptosis of CIHP-1 cells induced by LPS, and co-overexpression of PMS2L2 and miR-21 showed stronger inhibitory effect. Conclusion: PMS2L2 is downregulated in AKI induced by sepsis and inhibits LPS-induced apoptosis of podocytes.

Abstract B047: Promoter hypermethylation of SFRP1 as a prognostic and predictive blood-based biomarker in patients with stage IV pancreatic ductal adenocarcinoma

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is a disease with an abysmal prognosis. Unfortunately, no reliable prognostic or predictive blood-based biomarkers are currently available. An increasingly promising prognostic and predictive tool in cancer is the analysis of genetic and epigenetic alterations in cell-free DNA. One such alteration, promoter hypermethylation (ph) of SFRP1, has recently been linked to poor prognosis in gemcitabine-treated patients with stage IV PDAC. This study aimed to further examine phSFRP1 as a clinically relevant prognostic and predictive biomarker in FOLFIRINOX-treated patients with stage IV PDAC. Methods: Serum samples from patients with stage IV PDAC, treated with first-line FOLFIRINOX, were obtained from two danish biobanks. All blood samples were drawn before the initiation of palliative treatment. Based on a bisulfite treatment, we conducted a methylation-specific polymerase chain reaction analysis of the promoter region of the gene SFRP1. Methylation status was dichotomized based on the measured Cycle threshold. Survival according to SFRP1 promoter methylation status was assessed with Kaplan-Meier curves, log-rank tests, and Cox proportional hazard regression models. The adjusted Cox regression model included SFRP1 promoter methylation status, WHO performance status, age > 65 years, and sex. Results: Fifty-two FOLFIRINOX-treated patients with stage IV PDAC were included in the study. Patients with phSFRP1 (n = 23) had a median overall survival (mOS) of 6.8 months, significantly shorter than patients with unmethylated (um) SFRP1 (n = 29) who had a mOS of 15.7 months (log-rank test, p < 0.01). Likewise, in both crude and adjusted Cox-regression analysis, patients with phSFRP1 had an hazard ratio for death of 2.78 (95% CI 1.55-4.99) and 2.82 (95% CI 1.55-5.14) respectively, compared to patients with umSFRP1. Conclusions: Results indicate that FOLFIRINOX-treated stage IV PDAC patients with phSFRP1 have significantly shorter survival than patients with umSFRP1. Combined with previous literature, this indicates the value of phSFRP1 as a blood-based prognostic biomarker in patients with stage IV PDAC, regardless of the given first-line palliative chemotherapy. In addition, it indicates that phSFRP1 may also have predictive value for chemotherapy sensitivity in patients with stage IV PDAC. This knowledge may facilitate individualized treatment of patients with stage IV PDAC. Additionally, SFRP1 could be a valuable target for treatment with hypomethylating drugs to improve treatment response. Citation Format: Benjamin E. Stubbe, Stine D. Henriksen, Poul H. Madsen, Anders C. Larsen, Henrik B. Krarup, Inge S. Pedersen, Julia S. Johansen, Carsten P. Hansen, Ole Thorlacius-Ussing. Promoter hypermethylation of SFRP1 as a prognostic and predictive blood-based biomarker in patients with stage IV pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B047.

LncRNA PCED1B-AS1 knockdown inhibits osteosarcoma via methylation-mediated miR-10a downregulation

BackgroundLncRNA PCED1B-AS1 (PCED1B-AS1) promotes glioma. This study aimed to investigate its role in osteosarcoma (OS).MethodsThe study included 60 OS patients. Accumulation of miR-10a and PCED1B-AS1 in tissues from OS patients and cell lines was determined by RT-qPCR. Cell transfections were performed for interaction analysis. Participation of PCED1B-AS1 siRNA silencing and miR-10a overexpression in proliferation, invasion, and migration of U2OS and MG-63 cells was analyzed by cell proliferation assay and Transwell assay.ResultsPCED1B-AS1 level was increased in OS and positively correlated with miR-10a level. In OS cells, PCED1B-AS1 siRNA silencing downregulated miR-10a. Methylation-specific PCR analysis showed that PCED1B-AS1 siRNA silencing decreased the methylation of miR-10a gene promoter. Moreover, PCED1B-AS1 siRNA silencing suppressed OS cell proliferation, invasion, and migration. In addition, miR-10a overexpression attenuated the effects of PCED1B-AS1 siRNA silencing.ConclusionPCED1B-AS1 knockdown may inhibit OS cell proliferation and movement by regulating miR-10 gene methylation.

The reversion of DNA methylation-induced miRNA silence via biomimetic nanoparticles-mediated gene delivery for efficient lung adenocarcinoma therapy

BackgroundLung cancer is one of the fatal cancers worldwide, and over 60% of patients are lung adenocarcinoma (LUAD). Our clinical data demonstrated that DNA methylation of the promoter region of miR-126-3p was upregulated, which led to the decreased expression of miR-126-3p in 67 cases of lung cancer tissues, implying that miR-126-3p acted as a tumor suppressor. Transduction of miR-126-3p is a potential therapeutic strategy for treating LUAD, yet the physiological environment and properties of miRNA challenge current transduction approaches.MethodsWe evaluated the expression of miR-126-3p in 67 pairs of lung cancer tissues and the corresponding adjacent non-tumorous tissues by Reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The relationship between the overall survival of lung cancer patients and miR-126-3p was analyzed by the Cancer Genome Atlas cohort database (Oncolnc, http://www.oncolnc.org). We analyzed DNA methylation Methylation-specific PCR (MSP) analysis. To determine whether ADAM9 is the direct target of miR-126-3p, we performed the 3′-UTR luciferase reporter assay. The protein levels in the cells or tissues were evaluated with western blotting (WB) analysis. The biodistribution of nanoparticles were monitored by in vivo tracking system.ResultsWe describe the development of novel stealth and matrix metalloproteinase 2 (MMP2)-activated biomimetic nanoparticles, which are constructed using MMP2-responsive peptides to bind the miR-126-3p (known as MAIN), and further camouflaged with red blood cell (RBC) membranes (hence named REMAIN). REMAIN was able to effectively transduce miRNA into lung cancer cells and release them via MMP2 responsiveness. Additionally, REMAIN possessed the advantages of the natural RBC membrane, including extended circulation time, lower toxicity, better biocompatibility, and immune escape. Moreover, in vitro and in vivo results demonstrated that REMAIN effectively induced apoptosis of lung cancer cells and inhibited LUAD development and progression by targeting ADAM9.ConclusionThe novel style of stealth and MMP2-activated biomimetic nanoparticles show great potential in miRNA delivery.

Impact of Deletion on Angelman Syndrome Phenotype Variability: Phenotype-Genotype Correlation in 97 Patients with Motor Developmental Delay.

Angelman syndrome (AS) is a rare neurodevelopmental disorder due to genetic defects involving chromosome 15, known by intellectual disability, cognitive and behavioral disorders, ataxia, delayed motor development, and seizures. This study highlights the clinical spectrum and molecular research to establish the genotype-phenotype correlation in the pediatric Moroccan population. Methylation-specific-polymerase chain reaction (MS-PCR) is a primordial technique not only to identify the genetic mechanism of AS but also to characterize the different molecular classes induced in the appearance of the clinical symptoms. Patients with positive methylation profile were additionally studied by fluorescent in situ hybridization. Sequencing analysis of the UBE3A gene was performed for patients with negative MS-PCR. We used Fisher's test to assess differences in the distribution of features frequencies among the deletional and the nondeletional group. Statistical analysis was performed using R project. We identified from 97 patients diagnosed with AS, 14 (2.06%) had a classical AS phenotype, while 70 (84.5%) patients displayed a subset of consistent and frequent criteria. Development delay was shown severe in 63% and moderate in 37%. Nineteen out of 97 of them had MS-PCR positive in which 17 (89.47%) had 15q11-q13 deletion. Deletion patients presented a higher incidence of epileptic seizures ( p = 0.04), ataxia ( p = 0.0008), and abnormal electroencephalogram (EEG) profile ( p = 0.003). We further found out a frameshift deletion located at exon 9 of the UBE3A gene discovered in a 5 years old patient. We report in this study the genotype-phenotype correlation using different molecular testing. Correlation analysis did not reveal any statistical differences in phenotypic dissimilarity between deletion and nondeletion groups for most clinical features, except the correlation was highly significant in the abnormal EEG. According to our findings, we recommend offering MS-PCR analysis to all patients with severe intellectual disability, developmental delay, speech impairment, happy demeanor, and hypopigmentation.

Promoter methylation analysis of DKK2 may be a potential biomarker for early detection of cervical cancer.

Dickkopf 2 (DKK2) plays an important role in multiple cancers. Its potential value in the clinical diagnosis of cervical cancer has remained unclear. To investigate the expression and promoter methylation levels of DKK2 in cervical cancer and their clinicopathological associations. We used the Gene Expression Omnibus, Oncomine, Cancer Genome Atlas, and University of ALabama at Birmingham CANcer data analysis databases, reverse transcription-PCR, and methylation-specific PCR analysis to predict and examine the expression of DKK2 mRNA and DKK2 methylation levels in cell lines and cervical cancer tissues from 79 patients with cervical cancer and 63 with cervical precancerous lesions including 25 with low-grade squamous intraepithelial lesions (LSIL) and 38 patients with high-grade squamous intraepithelial lesions (HSIL). DKK2 mRNA expression was downregulated in all cancer cell lines and cervical cancer tissues, whereas hypermethylation of DKK2 was higher in cervical cancer tissue samples. DKK2 methylation in cervical cancer was significantly higher than that in HSIL (χ2 = 8.346, P = 0.004), whereas DKK2 methylation in HSIL was significantly higher than that in normal cervical samples (χ2 = 7.934, P = 0.005) and in LSIL samples (χ2 = 4.375, P = 0.037). DKK2 silencing caused by its promoter hypermethylation was confirmed by treatment with the methyltransferase inhibitor 5-Aza-dC in cell lines. Patients with lymph node metastasis exhibited increased promoter methylation frequency (χ2 = 5.239, P = 0.022) and low DKK2 mRNA expression (χ2 = 3.958, P = 0.047) compared with patients with no lymph node metastasis. Patients with high-risk human papillomavirus infection exhibited increased promoter methylation frequency (χ2 = 6.279, P = 0.015). DKK2 epigenetic changes of DKK2 may play a key role in the development of cervical cancer, suggesting that DKK2 hypermethylation could be used as a triage test for screening, early diagnosis, or risk prediction of cervical cancer.

Detection of non-metastatic non-small-cell lung cancer in urine by methylation-specific PCR analysis: A feasibility study

BackgroundLung cancer has the highest cancer-related mortality worldwide and earlier detection could improve outcomes. Urine circulating tumor DNA (ctDNA) represents a true non-invasive means for ambulant sample collection. In this prospective study, the potential of urine for perioperative detection of non-metastatic non-small cell lung cancer (NSCLC) using ctDNA methylation analysis is evaluated. MethodsPreoperative urine samples of 46 surgical NSCLC patients and 50 sex and age-matched controls were analyzed for DNA methylation of NSCLC-associated methylation markers CDO1, SOX17, and TAC1, using quantitative methylation-specific PCR (qMSP). The accuracy for NSCLC detection was determined by univariable and multivariable logistic regression analysis, followed by leave-one-out cross-validation. Fourteen additional urine samples were collected postoperatively to evaluate whether DNA methylation levels alter after surgery with curative intent. ResultsMethylation levels of CDO1 and SOX17 were significantly elevated in patients compared to controls (P =.016 and P <.001, respectively). This marker combination yielded an area under the receiver operating curve (AUC) value of 0.71 upon leave-one-out cross-validation for non-metastatic NSCLC detection in urine. Stage I patients tended to have higher methylation levels of SOX17 as compared to stage III patients. Similar methylation levels were found across the different histological subtypes of NSCLC. In some patients with preoperative elevated methylation levels, reduced methylation levels were found in post-operative urine samples. ConclusionsUrine CDO1 and SOX17 showed increased methylation levels in NSCLC patients as compared to sex- and age-matched controls. This demonstrates that urine ctDNA methylation analysis may provide an interesting non-invasive means to detect non-metastatic NSCLC. Further studies are needed to validate the clinical usefulness of this approach and to assess the potential of post-operative monitoring.

5‑Aza‑dC suppresses melanoma progression by inhibiting GAS5 hypermethylation.

The in-depth study of melanoma pathogenesis has revealed that epigenetic modifications, particularly DNA methylation, is a universal inherent feature of the development and progression of melanoma. In the present study, the analysis of the tumor suppressor gene growth arrest-specific transcript 5 (GAS5) demonstrated that its expression was downregulated in melanoma, and its expression level had a certain negative association with its methylation modification level. The promoter of GAS5 presented with detectable CpG islands, and methylation-specific polymerase chain reaction analysis demonstrated that GAS5 was actually modified by methylation in melanoma tissues and cells; however, no methylation modification of GAS5 was detected in normal tissues. Following the treatment of melanoma cells with 5-Aza-2′-deoxycytidine (5-Aza-dC), GAS5 methylation was significantly reversed. The analysis of melanoma cell proliferation revealed that 5-Aza-dC inhibited A375 and SK-MEL-110 cell proliferation in a time-dependent manner. Further analysis of apoptosis demonstrated that 5-Aza-dC significantly increased the apoptosis level of the two cell lines. Moreover, migration analysis of melanoma cells revealed that 5-Aza-dC significantly reduced cell migration. Furthermore, 5-Aza-dC significantly decreased the invasive ability of the two cell lines. However, when the expression of GAS5 was silenced, the effects of 5-Aza-dC on cell proliferation, apoptosis, invasion and migration were not significant. Furthermore, the subcutaneous injection of A375 cells in nude mice successfully resulted in xenograft tumor formation. However, following an intraperitoneal injection of 5-Aza-dC, the volume and weight of xenograft tumors and Ki-67 expression were significantly reduced, and caspase-3 activity and GAS5 expression were enhanced; following the silencing of GAS5, the antitumor effect of 5-Aza-dC was significantly blocked. On the whole, the present study demonstrates that 5-Aza-dC inhibits the growth of melanoma, and its function may be related to the methylation modification of GAS5.

DNMT3a negatively regulates PTEN to activate the PI3K/AKT pathway to aggravate renal fibrosis

BackgroundRenal fibrosis has become one of the major diseases threatening global public health and harming human life and health. PTEN methylation plays an important role in fibrotic diseases of many organs. However, the relationship between PTEN methylation and renal fibrosis is still elusive. MethodsIn the present study, we established a unilateral ureteral obstruction (UUO) mouse model in vivo and a transforming growth factor β1 (TGF-β1)-stimulated renal tubular epithelial cell (HK−2) model in vitro. The degree of renal interstitial fibrosis was detected by haematoxylin-eosin (HE) staining and Masson's trichrome staining. Western blot (WB), qRT–PCR, immunohistochemistry (IHC) and methylation-specific PCR (MSP) analyses were used to determine the mechanism by which PTEN methylation regulates renal fibrosis. The α-SMA fibrosis marker was detected by immunofluorescence (IF). Additionally, the relationship of PTEN and DNMT3a in UUO was determined by ChIP-qRT–PCR. ResultsOur results showed that the promoter region of PTEN was methylated in UUO. Compared to the sham group, the expression of PTEN was significantly reduced in the UUO group. However, the demethylation reagent significantly inhibited epithelial-mesenchymal transition (EMT), which showed increased expression of E-cadherin and decreased expression of α-SMA and fibronectin. Moreover, treatment of HK-2 cells with 5-aza-dc reversed the activation of the TGF-β1-induced PI3K/AKT signalling pathway, which inhibited renal fibrosis. WB analysis demonstrated that TGF-β1 inhibited the PTEN protein expression level and DNMT3a knockdown reversed the inhibitory effect of TGF-β1 on PTEN expression. Furthermore, ChIP-qRT–PCR showed that DNMT3a interacted with PTEN. Finally, we found that DNMT3a negatively regulated PTEN to activate the PI3K/AKT signalling pathway and aggravate renal fibrosis in vitro and in vivo. ConclusionIn summary, these results indicated that renal fibrosis is related to the downregulation of PTEN. Additionally, DNMT3a negatively regulates PTEN to activate the PI3K/AKT signalling pathway and induce EMT in renal tubular epithelial cells, thereby aggravating renal fibrosis.

LncRNA SNHG10 suppresses the development of doxorubicin resistance by downregulating miR-302b in triple-negative breast cancer

ABSTRACT Unlike other types of breast cancer, triple negative breast cancer (TNBC) does not respond to therapies targeting human epidermal growth factor receptor-2 (HER2) or hormone therapy, and the prognosis of patients with TNBC is usually poor. The role of long non-coding RNA (lncRNA) small nucleolar RNA host gene 10 (SNHG10) has been investigated in many types of cancer, but its role in TNBC is unknown. This study aimed to explore the role of SNHG10 in TNBC in the context of doxorubicin treatment, a common therapy for TNBC. Analysis of the TCGA dataset revealed the downregulation of SNHG10 in TNBC. The downregulation of SNHG10 of TNBC in TNBC was further confirmed by detecting its expression in 60 patients with TNBC by qPCR. The expression of SNHG10 was further downregulated after doxorubicin treatment. In TNBC, microRNA-302b (miR-302b) was downregulated and was positively correlated with SNHG10. In TNBC cells, overexpression of SNHG10 resulted in upregulation of miR-302b, and methylation-specific PCR analysis showed that SNHG10 negatively regulates the methylation of miR-302b. In addition, doxorubicin treatment resulted in the downregulation of SNHG10 in TNBC cells, and overexpression of SNHG10 and miR-302b promoted apoptosis of doxorubicin-treated TNBC cells. Furthermore, overexpression of both SNHG10 and miR-302b had a stronger effect on apoptosis than that of overexpression of SNHG10 alone. Our study showed that SNHG10 could inhibit the development of resistance to doxorubicin by upregulating miR-302b in TNBC through methylation. Our findings suggested that SNHG10 might serve as a molecular target for intervening in TBNC metastasis.