Molecular and immune correlates of TIM-3 (HAVCR2) and galectin 9 (LGALS9) mRNA expression and DNA methylation in melanoma

Abstract Background The T cell immunoglobulin and mucin-domain containing-3 receptor TIM-3 (also known as hepatitis A virus cellular receptor 2, encoded by HAVCR2) and its ligand galectin 9 (LGALS9) are promising targets for immune checkpoint inhibition immunotherapies. However, little is known about epigenetic regulation of the encoding genes. This study aimed to investigate the association of TIM-3 and LGALS9 DNA methylation with gene expression, patients’ survival, as well as molecular and immune correlates in malignant melanoma. Results Methylation of all six TIM-3 CpGs correlated significantly with TIM-3 mRNA levels (P ≤ 0.05). A strong inverse correlation (Spearman’s ρ = − 0.49) was found in promoter regions, while a strong positive correlation (ρ = 0.63) was present in the gene body of TIM-3. High TIM-3 mRNA expression (hazard ratio (HR) = 0.88, 95% confidence interval (CI) [0.81–0.97], P = 0.007) was significantly associated with better overall survival. Seven of the eight LGALS9 CpG sites correlated significantly with LGALS9 mRNA levels (P ≤ 0.003). Methylation at five CpG sites showed a strong inverse correlation (Spearman’s ρ = − 0.67) and at two sites a weak positive correlation (Spearman’s ρ = 0.15). High LGALS9 mRNA expression was significantly associated with increased overall survival (HR = 0.83, 95%CI [0.75–0.93], P = 0.001). In addition, we found significant correlations between TIM-3 and LGALS9 methylation and mRNA expression with immune cell infiltrates and significant differences among distinct immune cell subsets. Conclusions Our study points toward an epigenetic regulation of TIM-3 and LGALS9 via DNA methylation and might provide an avenue for the development of a predictive biomarker for response to immune checkpoint blockade.

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PD-1, CTLA4, PD-L1 and PD-L2 DNA methylation in papillary thyroid carcinoma

Immunotherapy ◽

10.2217/imt-2020-0037 ◽

2020 ◽

Vol 12 (12) ◽

pp. 903-920

Author(s):

Luka de Vos ◽

Jörn Dietrich ◽

Sebastian Strieth ◽

Friedrich Bootz ◽

Dimo Dietrich ◽

...

Keyword(s):

Dna Methylation ◽

Papillary Thyroid Carcinoma ◽

Thyroid Carcinoma ◽

Mrna Expression ◽

Immune Checkpoint ◽

Noncoding Rna ◽

Immune Cell ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Papillary Thyroid

Aim: We investigated DNA methylation patterns of immune checkpoint genes PD-1, PD-L1, PD-L2, CTLA4 and an adjacent long noncoding RNA in papillary thyroid carcinoma (PTC). Materials & methods: DNA methylation and mRNA expression were examined in PTCs. DNA methylation was correlated with mRNA expression, BRAF and RAS mutational status, and immune cell infiltration. Results: Inverse correlations between DNA methylation and mRNA expression were observed. Immune checkpoint expression correlated positively, and DNA methylation negatively, with immune cell infiltration. Higher DNA methylation levels accompanied by lower immune checkpoint expression were observed in RAS-mutated tumors. Conclusion: We suggest epigenetic regulation of immune checkpoints in PTC. Methylation was associated with BRAF and RAS mutation status. DNA methylation might be a promising biomarker candidate in the context of immunotherapies in PTC.

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Postnatal Smoke Exposure Further Increases the Hepatic Nicotine Metabolism in Prenatally Smoke Exposed Male Offspring and Is Linked with Aberrant Cyp2a5 Methylation

International Journal of Molecular Sciences ◽

10.3390/ijms22010164 ◽

2020 ◽

Vol 22 (1) ◽

pp. 164

Author(s):

Khosbayar Lkhagvadorj ◽

Zhijun Zeng ◽

Karolin F. Meyer ◽

Laura P. Verweij ◽

Wierd Kooistra ◽

...

Keyword(s):

Dna Methylation ◽

Mrna Expression ◽

Nicotine Dependence ◽

Susceptibility Gene ◽

Smoke Exposure ◽

Adverse Outcomes ◽

Male Offspring ◽

Adult Offspring ◽

Mrna Levels ◽

Nicotine Metabolism

Prenatal smoke exposure (PreSE) is a risk factor for nicotine dependence, which is further enhanced by postnatal smoke exposure (PostSE). One susceptibility gene to nicotine dependence is Cytochrome P450 (CYP) 2A6, an enzyme responsible for the conversion of nicotine to cotinine in the liver. Higher CYP2A6 activity is associated with nicotine dependence and could be regulated through DNA methylation. In this study we investigated whether PostSE further impaired PreSE-induced effects on nicotine metabolism, along with Cyp2a5, orthologue of CYP2A6, mRNA expression and DNA methylation. Using a mouse model where prenatally smoke-exposed adult offspring were exposed to cigarette smoke for 3 months, enzyme activity, mRNA levels, and promoter methylation of hepatic Cyp2a5 were evaluated. We found that in male offspring, PostSE increased PreSE-induced cotinine levels and Cyp2a5 mRNA expression. In addition, both PostSE and PreSE changed Cyp2a5 DNA methylation in male groups. PreSE however decreased cotinine levels whereas it had no effect on Cyp2a5 mRNA expression or methylation. These adverse outcomes of PreSE and PostSE were most prominent in males. When considered in the context of the human health aspects, the combined effect of prenatal and adolescent smoke exposure could lead to an accelerated risk for nicotine dependence later in life.

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DDR1 methylation is associated with bipolar disorder and the isoform expression and methylation of myelin genes

Epigenomics ◽

10.2217/epi-2021-0006 ◽

2021 ◽

Author(s):

Beatriz Garcia-Ruiz ◽

Manuel Castro de Moura ◽

Gerard Muntané ◽

Lourdes Martorell ◽

Elena Bosch ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Bipolar Disorder ◽

Mrna Expression ◽

Gene Expression Analysis ◽

Mrna Levels ◽

Healthy Controls ◽

Genome Wide ◽

Isoform Expression

Aim: To investigate DDR1 methylation in the brains of bipolar disorder (BD) patients and its association with DDR1 mRNA levels and comethylation with myelin genes. Materials & methods: Genome-wide profiling of DNA methylation (Infinium MethylationEPIC BeadChip) corrected for glial composition and DDR1 gene expression analysis in the occipital cortices of individuals with BD (n = 15) and healthy controls (n = 15) were conducted. Results: DDR1 5-methylcytosine levels were increased and directly associated with DDR1b mRNA expression in the brains of BD patients. We also observed that DDR1 was comethylated with a group of myelin genes. Conclusion: DDR1 is hypermethylated in BD brain tissue and is associated with isoform expression. Additionally, DDR1 comethylation with myelin genes supports the role of this receptor in myelination.

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Sini Decoction Improves Adrenal Function and the Short-Term Outcome of Septic Rats through Downregulation of Adrenal Toll-Like Receptor 4 Expression

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2018/5186158 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Fang Lai ◽

Gengbiao Zhou ◽

Shutao Mai ◽

Xiaolian Qin ◽

Wenting Liu ◽

...

Keyword(s):

Overall Survival ◽

Survival Rate ◽

Mrna Expression ◽

Adrenal Insufficiency ◽

Adrenal Glands ◽

Group Versus ◽

Mrna Levels ◽

Toll Like Receptor ◽

Adrenal Tissue ◽

The Impact

Background. Sini Decoction (SND) is composed of Aconitum carmichaelii Debeaux, Zingiber officinale Roscoe, and Glycyrrhiza uralensis Fisch, having been used in China for centuries for collapsing phrase of disease. Studies reported that SND could alleviate inflammatory response, ameliorate microcirculatory disturbances, and improve shock reversal and adrenal gland glucocorticoid stress response during sepsis shock, yet the underlying mechanism is still elusive. Toll-like receptor (TLR) 4 is demonstrated to be crucially correlated with the corticosterone secretion and the impaired adrenal glucocorticoid responses in sepsis. Materials and Methods. SND at dose of 10 g/kg (in low-dose SND group, LD-SND) and 20 g/kg (in high-dose SND group, HD-SND) was administered to CLP rats. Four days later, overall survival rates of rats were calculated; rat serum and adrenal glands were collected. Basic serum corticosterone levels were determined, and the increase of corticosterone after 0.8 ug/kg ACTH injection was checked to detect the adrenocortical sensitivity to ACTH. The protein and mRNA expression of TLR4 in adrenal glands were measured to study the impact of SND on TLR4 expression. mRNA levels of IL-10 and TNF-a in adrenal glands and IL-10 and TNF-a levels in serum were also determined to study the cytokines profile. Results. SND improved the cumulative survival rate of CLP rats up to 4 days (P < 0.05 with HD-SND) and adrenocortical sensitivity to 0.8 ug/kg ACTH stimulation (P < 0.05 at 60 mins, 31.02 ± 19.23 ng/ml in LD-SND group and 32.18 ± 14.88 ng/ml in HD-SND group versus 5.03 ± 13.34 ng/ml in CLP group), with a significant decrease of protein (P < 0.05, 29.6% in LD-SND group and 27.8% in HD-SND group), mRNA expression of TLR4 (P < 0.05, 32.9% in LD-SND group and 36.1% in HD-SND group), mRNA expression of IL-10 (P < 0.05, 32.0% in LD-SND group and 29.6% in HD-SND group), TNF-a in adrenal glands (P < 0.05, 26.0% in LD-SND group and 25.3% in HD-SND group), and TNF-a level in serum (P < 0.05, 100.20 ± 19.41 pg/ml in LD-SND group and 92.40 ± 11.66 pg/ml in HD-SND group versus 134.40 ± 27.87 pg/ml in CLP group). Conclusion. SND increased overall survival rate within 4 days and attenuated adrenal insufficiency in septic rats by downregulating TLR4 mRNA and protein expression in adrenal tissue, inhibiting adrenal production of TNF-α and IL-10, and improving adrenal responsiveness. Our results suggest that SND is able to ameliorate adrenal stress responses in a local immune-adrenal crosstalk way involving downregulated expression of TLR4 in adrenal tissue. SND might be a promising treatment for adrenal insufficiency prevention in prolonged sepsis.

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Signature Based on Immune-Related LncRNA Can Predict Overall Survival of Osteosarcoma Patients

10.21203/rs.3.rs-45370/v1 ◽

2020 ◽

Author(s):

Longqing Li ◽

Lianghao Zhang ◽

Manhas Adbul Khader ◽

Yan Zhang ◽

Xinchang Lu ◽

...

Keyword(s):

Gene Expression ◽

Overall Survival ◽

Immune Checkpoint ◽

High Throughput Sequencing ◽

Immune Cell ◽

Cox Regression ◽

Risk Group ◽

Low Risk ◽

Checkpoint Gene ◽

Cox Regression Analysis

Abstract Background: Osteosarcoma is a malignant bone tumor common in children and adolescents. Metastatic status remains the most important guideline for classifying patients and making clinical decisions. Despite many efforts, newly diagnosed patients receive the same therapy that patients have received over the last 4 decades. With the development of high-throughput sequencing technology and the rise of immunotherapy, it is necessary to deeply explore the immune molecular mechanism of osteosarcoma.Methods: We obtained RNA-seq data and clinical information of osteosarcoma patients from TCGA database and TARGET database. With the help of co-expression analysis we identified immune-related lncRNA and then by means of univariate Cox regression analysis prognostic-related lncRNA was screened out. And also by using least absolute shrinkage and selection operator regression method a model based on immune-related lncRNA was constructed. The differences in overall survival, immune infiltration, immune checkpoint gene expression, and tumor microenvironmental immunity type between the two groups were evaluated.Results: We constructed a signature consisting of 13 lncRNA. Our results show that signatures can reliably predict the overall survival of patients with osteosarcoma and can bring net clinical benefits. Further more, the signatures can be used for further risk stratification of the metastasis patients. Patients in the low-risk group had higher immune cell infiltration and immune checkpoint gene expression. The results from gene set variation analysis show that patients in low-risk group are closely related to immune-related pathways when compared with patients in high-risk group. Finally, patients in the low-risk group are more likely to be classified as TMIT I and hence more likely to benefit from immunotherapy.Conclusion: Our signature may be a reliable marker for predicting the overall survival of patients with osteosarcoma.

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Discovery and Validation of Circulating EVL mRNA as a Prognostic Biomarker in Pancreatic Cancer

Journal of Oncology ◽

10.1155/2021/6656337 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Yan Du ◽

Kai Yao ◽

Qingbo Feng ◽

Feiyu Mao ◽

Zechang Xin ◽

...

Keyword(s):

Pancreatic Cancer ◽

Overall Survival ◽

Mrna Expression ◽

Cox Regression ◽

Expression Profiles ◽

Differentially Expressed ◽

Cancer Type ◽

Mrna Levels ◽

Plasma Samples ◽

Patient Prognosis

Background. Circulating plasma mRNAs can be analyzed to identify putative cancer biomarkers. This study was conducted in an effort to detect plasma mRNA biomarkers capable of predicting pancreatic cancer (PACA) patient prognosis. Material and Methods. First, prognostic mRNAs that were differentially expressed in PACA in The Cancer Genome Atlas (TCGA) were established, after which microarray expression profiles from PACA patient plasma samples were utilized to specifically identify potential prognostic plasma mRNA biomarkers associated with this cancer type. In total, plasma samples were then collected from 79 PACA patients and 19 healthy controls to confirm differential mRNA expression via qPCR, while Kaplan–Meier analyses were used to examine the link between mRNA expression and patient overall survival. Results. In total, three prognostic differentially expressed genes were identified in PACA patient plasma samples, including SMAP2, PTPN6, and EVL (Ena/VASP-like). Plasma EVL levels were confirmed via qPCR to be correlated with tumor pathology p < 0.01 , while the overall survival of patients with low plasma EVL levels was poor p < 0.01 . Multivariate Cox regression analyses further confirmed that plasma EVL levels were independent predictors of PACA patient prognosis. Conclusion. We found that PACA is associated with the downregulation of plasma EVL mRNA levels, indicating that this mRNA may be a viable biomarker associated with patient prognosis.

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Epigenome-wide association study identifies Behçet’s disease-associated methylation loci in Han Chinese

Rheumatology ◽

10.1093/rheumatology/kez043 ◽

2019 ◽

Vol 58 (9) ◽

pp. 1574-1584 ◽

Cited By ~ 5

Author(s):

Hongsong Yu ◽

Liping Du ◽

Shenglan Yi ◽

Qingfeng Wang ◽

Yunyun Zhu ◽

...

Keyword(s):

Dna Methylation ◽

Association Study ◽

Mrna Expression ◽

Behcet’S Disease ◽

Behçet's Disease ◽

Han Chinese ◽

Healthy Controls ◽

Behcet's Disease ◽

Cpg Sites ◽

Aberrant Dna Methylation

Abstract Objective The aetiology of Behçet’s disease (BD), known as a systemic vasculitis, is not completely understood. Increasing evidence suggests that aberrant DNA methylation may contribute to the pathogenesis of BD. The aim of this epigenome-wide association study was to identify BD-associated methylation loci in Han Chinese. Methods Genome-wide DNA methylation profiles were compared between 60 BD patients and 60 healthy controls using the Infinium Human Methylation 450 K Beadchip. BD-associated methylation loci were validated in 100 BD patients and 100 healthy controls by pyrosequencing. Gene expression and cytokine production was quantified by real-time PCR and ELISA. Results A total of 4332 differentially methylated CpG sites were associated with BD. Five differentially methylated CpG sites (cg03546163, cg25114611, cg20228731, cg23261343 and cg14290576) revealed a significant hypomethylation status across four different genes (FKBP5, FLJ43663, RUNX2 and NFIL3) and were validated by pyrosequencing. Validation results showed that the most significant locus was located in the 5’UTR of FKBP5 (cg03546163, P = 3.81E-13). Four CpG sites with an aberrant methylation status, including cg03546163, cg25114611, cg23261343 and cg14290576, may serve as a diagnostic marker for BD (area under the receiver operating curve curve = 83.95%, 95% CI 78.20, 89.70%). A significantly inverse correlation was found between the degree of methylation at cg03546163 as well as cg25114611 and FKBP5 mRNA expression. Treatment with a demethylation agent, 5-Aza-2’-deoxycytidine resulted in an increase of FKBP5 mRNA expression and a stimulated IL-1β production. Conclusion Our findings suggest that aberrant DNA methylation, independently of previously known genetic variants, plays a vital role in the pathogenesis of BD. Trial registration Chinese Clinical Trial Registry, chictr.org.cn, ChiCTR-CCC-12002184.

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Exploring DNA Methylation for Prognosis and Analyzing the Tumor Microenvironment in Pleomorphic Xanthoastrocytoma

Journal of Neuropathology & Experimental Neurology ◽

10.1093/jnen/nlaa051 ◽

2020 ◽

Vol 79 (8) ◽

pp. 880-890

Author(s):

Karen Tang ◽

David Kurland ◽

Varshini Vasudevaraja ◽

Jonathan Serrano ◽

Michael Delorenzo ◽

...

Keyword(s):

Dna Methylation ◽

Overall Survival ◽

Tumor Microenvironment ◽

Immune Cell ◽

Progression Free Survival ◽

Cell Types ◽

Homozygous Deletion ◽

Pleomorphic Xanthoastrocytoma ◽

Braf V600e ◽

Rare Type

Abstract Pleomorphic xanthoastrocytoma (PXA) is a rare type of brain tumor that affects children and young adults. Molecular prognostic markers of PXAs remain poorly established. Similar to gangliogliomas, PXAs show prominent immune cell infiltrate, but its composition also remains unknown. In this study, we correlated DNA methylation and BRAF status with clinical outcome and explored the tumor microenvironment. We performed DNA methylation in 21 tumor samples from 18 subjects with a histological diagnosis of PXA. MethylCIBERSORT was used to deconvolute the PXA microenvironment by analyzing the associated immune cell-types. Median age at diagnosis was 16 years (range 7–32). At median follow-up of 30 months, 3-year and 5-year overall survival was 73% and 71%, respectively. Overall survival ranged from 1 to 139 months. Eleven out of 18 subjects (61%) showed disease progression. Progression-free survival ranged from 1 to 89 months. Trisomy 7 and CDKN2A/B (p16) homozygous deletion did not show any association with overall survival (p = 0.67 and p = 0.74, respectively). Decreased overall survival was observed for subjects with tumors lacking the BRAF V600E mutation (p = 0.02). PXAs had significantly increased CD8 T-cell epigenetic signatures compared with previously profiled gangliogliomas (p = 0.0019). The characterization of immune cell-types in PXAs may have implications for future development of immunotherapy.

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ERCC1 mRNA levels as a useful prognostic biomarker for extrahepatic cholangiocarcinoma with R0 resection.

Journal of Clinical Oncology ◽

10.1200/jco.2014.32.3_suppl.239 ◽

2014 ◽

Vol 32 (3_suppl) ◽

pp. 239-239

Author(s):

Shuichiro Uemura ◽

Hidekazu Kuramochi ◽

Go Nakajima ◽

Yasuto Sato ◽

Ryota Higuchi ◽

...

Keyword(s):

Overall Survival ◽

Survival Rate ◽

Mrna Expression ◽

Biliary Tract ◽

Prognostic Biomarker ◽

Biliary Tract Carcinoma ◽

R0 Resection ◽

Cancer Type ◽

Mrna Levels ◽

Extrahepatic Cholangiocarcinoma

239 Background: To date, no prognostic biomarker for biliary tract carcinoma has been identified. In previous studies of biliary tract carcinoma, no reliable data was found due to the varying composition of the cancer type (gallbladder, cholangiocarcinoma, and ampullary carcinoma), differences in tumor location, a mixture of curative and non-curative operations, and differences in operative methods. Methods: Fifty extrahepatic cholangiocarcinoma patients who underwent a pancreatoduodenectomy with R0 resection at the Tokyo Women’s Medical University Hospital were examined. All patients were pathologically diagnosed as having papillary or tubular adenocarcinoma. T-RNA was extracted from FFPE samples, and mRNA expression levels were measured by real-time RT-PCR. Results: In the preliminary analysis, 10 patients who have survived more than 5 years (LS group) and 10 patients who had a relapse within 2 years (SS group) were selected. EGFR, AREG, EREG, MMP-9, CDH-1, PARP1, and ERCC1 mRNA expression were examined; only the ERCC1 mRNA levels showed a significant difference between the LS and SS groups (median ERCC1: LS 26.5 vs. SS 9.7, p=0.0073). The median survival time (MST) of the patients with high ERCC1 levels was significantly higher than that in patients with a low ERCC1 level (MST: not reached vs. 16M). Then, 30 more patients with the same backgrounds were added to the study, and ERCC1 mRNA levels were measured in all 50 patients. The patients with high ERCC1 mRNA levels had a significantly greater overall survival rate compared with those with low ERCC1 levels (MST: not reached vs. 12.5M, 5-year survival rate: 92% vs 51%; p=0.04). In multivariate analysis, no lymph node metastases or high ERCC1 expression were significantly associated with better overall survival. Conclusions: ERCC1 mRNA expression seemed to be a useful prognostic biomarker for extrahepatic cholangiocarcinoma with R0 resection.

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Prenatal smoke effect on mouse offspring Igf1 promoter methylation from fetal stage to adulthood is organ and sex specific

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00293.2019 ◽

2020 ◽

Vol 318 (3) ◽

pp. L549-L561

Author(s):

Zhijun Zeng ◽

Karolin F. Meyer ◽

Khosbayar Lkhagvadorj ◽

Wierd Kooistra ◽

Marjan Reinders-Luinge ◽

...

Keyword(s):

Dna Methylation ◽

Promoter Methylation ◽

Large Scale ◽

Developmental Stages ◽

Association Studies ◽

Inverse Correlation ◽

Cpg Sites ◽

Increased Risk ◽

Organ Specific ◽

Health And Disease

Prenatal smoke exposure (PSE) is associated with reduced birth weight, impaired fetal development, and increased risk for diseases later in life. Changes in DNA methylation may be involved, as multiple large-scale epigenome-wide association studies showed that PSE is robustly associated with DNA methylation changes in blood among offspring in early life. Insulin-like growth factor-1 (IGF1) is important in growth, differentiation, and repair processes after injury. However, no studies investigated the organ-specific persistence of PSE-induced methylation change of Igf1 into adulthood. Based on our previous studies on the PSE effect on Igf1 promoter methylation in fetal and neonatal mouse offspring, we now have extended our studies to adulthood. Our data show that basal Igf1 promoter methylation generally increased in the lung but decreased in the liver (except for 2 persistent CpG sites in both organs) across three different developmental stages. PSE changed Igf1 promoter methylation in all three developmental stages, which was organ and sex specific. The PSE effect was less pronounced in adult offspring compared with the fetal and neonatal stages. In addition, the PSE effect in the adult stage was more pronounced in the lung compared with the liver. For most CpG sites, an inverse correlation was found for promoter methylation and mRNA expression when the data of all three stages were combined. This was more prominent in the liver. Our findings provide additional evidence for sex- and organ-dependent prenatal programming, which supports the developmental origins of health and disease (DOHaD) hypothesis.

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