cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13110292
title: Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

description: The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation profiling. Fifteen tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulphite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.
DOI: 10.6084/m9.figshare.13110292.v1
title: Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

description: The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation profiling. Fifteen tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulphite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.
DOI: 10.6084/m9.figshare.14561196
title: Angelobacter genomes

description: Genomes of candidatus Angelobacter from this study<br>
DOI: 10.6084/m9.figshare.14561196.v1
title: Angelobacter genomes

description: Genomes of candidatus Angelobacter from this study<br>
DOI: 10.6084/m9.figshare.14561199.v1
title: Acidobacteria Genomes

description: All high quality dereplicated Acidobacteria genomes obtained from a vernal pool sediments in Lake County, CA.<br>
DOI: 10.6084/m9.figshare.14561199
title: Acidobacteria Genomes

description: All high quality dereplicated Acidobacteria genomes obtained from a vernal pool sediments in Lake County, CA.<br>
DOI: 10.6084/m9.figshare.14561205
title: Angelobacter Biosynthetic Gene Clusters

description: All biosynthetic gene clusters predicted with antiSMASH for Angelobacter genomes in this study.<br>
DOI: 10.6084/m9.figshare.12851612.v3
title: Expression of microRNAs in human platelet-poor plasma: analysis of the factors affecting their expression and association with proximal genetic variants

description: To translate circulating microRNAs (miRNAs) into the clinic, a deeper understanding of the factors affecting their expression is needed. In this study, we explored the features affecting the expression of miRNAs and their genetic regulation using the expression data of 103 miRNAs obtained by qPCR in the platelet-poor plasma of 104 subjects. The principal components (PCs) of the expression of the miRNAs were associated with technical and biological features (e.g., synthetic controls or sex) and with blood cell counts. Also, the associations with proximal genetics variants were analysed. We found that haemolysis marker (dCt hsa-miR-23a-3p-hsa-miR-451a) was correlated strongly (β = 0.84, p = 2.07x10<sup>−29</sup>) with the second PC, which explained 10.1% of the overall variability. Thus, we identified haemolysis as a source of variability for miRNA expression even in mild hemolyzed samples (haemolysis marker dCt &lt;5). In addition to hsa-miR-23a-3p and hsa-miR-451a, the miRNAs most stable and most susceptible to haemolysis were identified. Then, we discovered that the expression of miRNAs in platelet-poor plasma was not biased by any blood cell count, and thus, our results supported their role as biomarkers of tissue-specific conditions. Finally, we identified 1,323 genetic variants that corresponded to 158 miRNA expression quantitative trait loci for 14 miRNAs (FDR &lt;0.2), which were enriched in promoter regions (p = 0.03). This enrichment corresponded to a range of specific tissues (e.g., breast or fat) although not to blood tissue, supporting the concept that the expression of circulating miRNAs is under the genetic control of different tissues.
DOI: 10.6084/m9.figshare.12851597
title: Estrogen-induced epigenetic silencing of <i>FTH1</i> and <i>TFRC</i> genes reduces liver cancer cell growth and survival

description: Estrogen (E2) regulates hundreds of genes involved in cell metabolism and disrupts iron homoeostasis in various cell types. Herein, we addressed whether E2-induced epigenetic modifications are involved in modulating the expression of iron-regulatory genes. Epigenetic status of <i>FTH1</i> and <i>TFRC</i> genes was assessed in E2-treated cancer cells. E2-induced DNA methylation was associated with decreased <i>FTH1</i> and <i>TFRC</i> expression in Hep-G2 and Huh7 cells, but not in AGS or MCF7 cells. Demethylation with 5-Aza-2-deoxycytidine upregulated the expression of both these genes in Hep-G2 cells. The expression of DNMT3B, PRMT5, and H4R3me2s increased in E2-treated cells. Chromatin immunoprecipitation showed that E2 treatment recruited PRMT5 and H4R3me2s on <i>FTH1</i> but not on <i>TFRC</i>. Knockdown of PRMT5, DNMT3B, and Estrogen-receptor alpha rescued <i>FTH1</i> from E2-induced silencing. However, knockdown of DNMT3B alone blocked the inhibitory effects of E2 on <i>TFRC</i>. Analysis of human liver tissues in publicly available datasets showed that <i>FTH1</i> and <i>TFRC</i> are highly expressed in primary liver tumours, but a lower expression is associated with better survival. Interestingly, we showed that the silencing of <i>FTH1</i> and/or <i>TFRC</i> inhibited carcinogenesis in Hep-G2 cells. For the first time, our findings uncovered the novel signalling pathway involved in the protective effects of E2 against liver cancer.
DOI: 10.6084/m9.figshare.12851612
title: Expression of microRNAs in human platelet-poor plasma: analysis of the factors affecting their expression and association with proximal genetic variants

description: To translate circulating microRNAs (miRNAs) into the clinic, a deeper understanding of the factors affecting their expression is needed. In this study, we explored the features affecting the expression of miRNAs and their genetic regulation using the expression data of 103 miRNAs obtained by qPCR in the platelet-poor plasma of 104 subjects. The principal components (PCs) of the expression of the miRNAs were associated with technical and biological features (e.g., synthetic controls or sex) and with blood cell counts. Also, the associations with proximal genetics variants were analysed. We found that haemolysis marker (dCt hsa-miR-23a-3p-hsa-miR-451a) was correlated strongly (β = 0.84, p = 2.07x10<sup>−29</sup>) with the second PC, which explained 10.1% of the overall variability. Thus, we identified haemolysis as a source of variability for miRNA expression even in mild hemolyzed samples (haemolysis marker dCt &lt;5). In addition to hsa-miR-23a-3p and hsa-miR-451a, the miRNAs most stable and most susceptible to haemolysis were identified. Then, we discovered that the expression of miRNAs in platelet-poor plasma was not biased by any blood cell count, and thus, our results supported their role as biomarkers of tissue-specific conditions. Finally, we identified 1,323 genetic variants that corresponded to 158 miRNA expression quantitative trait loci for 14 miRNAs (FDR &lt;0.2), which were enriched in promoter regions (p = 0.03). This enrichment corresponded to a range of specific tissues (e.g., breast or fat) although not to blood tissue, supporting the concept that the expression of circulating miRNAs is under the genetic control of different tissues.
DOI: 10.6084/m9.figshare.12851597.v1
title: Estrogen-induced epigenetic silencing of <i>FTH1</i> and <i>TFRC</i> genes reduces liver cancer cell growth and survival

description: Estrogen (E2) regulates hundreds of genes involved in cell metabolism and disrupts iron homoeostasis in various cell types. Herein, we addressed whether E2-induced epigenetic modifications are involved in modulating the expression of iron-regulatory genes. Epigenetic status of <i>FTH1</i> and <i>TFRC</i> genes was assessed in E2-treated cancer cells. E2-induced DNA methylation was associated with decreased <i>FTH1</i> and <i>TFRC</i> expression in Hep-G2 and Huh7 cells, but not in AGS or MCF7 cells. Demethylation with 5-Aza-2-deoxycytidine upregulated the expression of both these genes in Hep-G2 cells. The expression of DNMT3B, PRMT5, and H4R3me2s increased in E2-treated cells. Chromatin immunoprecipitation showed that E2 treatment recruited PRMT5 and H4R3me2s on <i>FTH1</i> but not on <i>TFRC</i>. Knockdown of PRMT5, DNMT3B, and Estrogen-receptor alpha rescued <i>FTH1</i> from E2-induced silencing. However, knockdown of DNMT3B alone blocked the inhibitory effects of E2 on <i>TFRC</i>. Analysis of human liver tissues in publicly available datasets showed that <i>FTH1</i> and <i>TFRC</i> are highly expressed in primary liver tumours, but a lower expression is associated with better survival. Interestingly, we showed that the silencing of <i>FTH1</i> and/or <i>TFRC</i> inhibited carcinogenesis in Hep-G2 cells. For the first time, our findings uncovered the novel signalling pathway involved in the protective effects of E2 against liver cancer.
DOI: 10.6084/m9.figshare.12851612.v2
title: Expression of microRNAs in human platelet-poor plasma: analysis of the factors affecting their expression and association with proximal genetic variants.

description: To translate circulating microRNAs (miRNAs) into the clinic, a deeper understanding of the factors affecting their expression is needed. In this study, we explored the features affecting the expression of miRNAs and their genetic regulation using the expression data of 103 miRNAs obtained by qPCR in the platelet-poor plasma of 104 subjects. The principal components (PCs) of the expression of the miRNAs were associated with technical and biological features (e.g., synthetic controls or sex) and with blood cell counts. Also, the associations with proximal genetics variants were analyzed. We found that hemolysis marker (dCt hsa-miR-23a-3p-hsa-miR-451a) was correlated strongly (β =0.84, p =2.07x10<sup>−29</sup>) with the second PC, which explained 10.1% of the overall variability. Thus, we identified hemolysis as a source of variability for miRNA expression even in mild hemolyzed samples (hemolysis marker dCt &lt;5). In addition to hsa-miR-23a-3p and hsa-miR-451a, the miRNAs that are most stable and most susceptible to hemolysis in platelet-poor plasma were identified. Then, we discovered that the expression of miRNAs in platelet-poor plasma was not biased by any blood cell count, and thus, our results supported their role as biomarkers of tissue-specific conditions. Finally, we identified 1,323 genetic variants that corresponded to 158 miRNA expression quantitative trait loci for 14 miRNAs (FDR &lt;0.2), which were enriched in promoter regions (p =0.03). This enrichment corresponded to a range of specific tissues (e.g., breast or fat) although not to blood tissue, supporting the concept that the expression of circulating miRNAs is under the genetic control of different tissues.
DOI: 10.6084/m9.figshare.12851639
title: Mitochondrial DNA methylation in placental tissue: a proof of concept study by means of prenatal environmental stressors

description: While previous studies have demonstrated that prenatal exposure to environmental stressors is associated with mitochondrial DNA (mtDNA) methylation, more recent investigations are questioning the accuracy of the methylation assessment and its biological relevance. In this study, we investigated placental mtDNA methylation while accounting for methodological issues such as nuclear contamination, bisulphite conversion, and PCR bias. From the ENVIR<i>ON</i>AGE birth cohort, we selected three groups of participants (n = 20/group). One group with mothers who smoked during pregnancy (average 13.2 cig/day), one group with high air pollutant exposure (PM<sub>2.5</sub>: 16.0 ± 1.4 µg/m<sup>3</sup>, black carbon: 1.8 ± 0.3 µg/m<sup>3</sup>) and one control group (non-smokers, PM<sub>2.5</sub>: 10.6 ± 1.7 µg/m<sup>3</sup>, black carbon: 0.9 ± 0.1 µg/m<sup>3</sup>) with low air pollutant exposure. DNA methylation levels were quantified in two regions of the displacement loop control region (<i>D-loop</i> and <i>LDLR2</i>) by bisulphite pyrosequencing. Additionally, we measured DNA methylation on nuclear genes involved in mitochondrial maintenance (<i>PINK1, DNA2</i>, and <i>POLG1</i>) and assessed mtDNA content using qPCR. Absolute <i>D-loop</i> methylation levels were higher for mothers that smoked extensively (+0.36%, 95% CI: 0.06% to 0.66%), and for mothers that were highly exposed to air pollutants (+0.47%, 95% CI: 0.20% to 0.73%). The relevance of our findings is further supported, as <i>D-loop</i> methylation levels were correlated with placental mtDNA content (r = −0.40, p = 0.002) and associated with birth weight (−106.98 g, 95% CI: −209.60 g to −4.36 g for an IQR increase in <i>D-loop</i> methylation). Most notably, our data demonstrates relevant levels of mtDNA methylation in placenta tissue, with significant associations between prenatal exposure to environmental stressors and <i>D-loop</i> methylation.
DOI: 10.6084/m9.figshare.12851639.v1
title: Mitochondrial DNA methylation in placental tissue: a proof of concept study by means of prenatal environmental stressors

description: While previous studies have demonstrated that prenatal exposure to environmental stressors is associated with mitochondrial DNA (mtDNA) methylation, more recent investigations are questioning the accuracy of the methylation assessment and its biological relevance. In this study, we investigated placental mtDNA methylation while accounting for methodological issues such as nuclear contamination, bisulphite conversion, and PCR bias. From the ENVIR<i>ON</i>AGE birth cohort, we selected three groups of participants (n = 20/group). One group with mothers who smoked during pregnancy (average 13.2 cig/day), one group with high air pollutant exposure (PM<sub>2.5</sub>: 16.0 ± 1.4 µg/m<sup>3</sup>, black carbon: 1.8 ± 0.3 µg/m<sup>3</sup>) and one control group (non-smokers, PM<sub>2.5</sub>: 10.6 ± 1.7 µg/m<sup>3</sup>, black carbon: 0.9 ± 0.1 µg/m<sup>3</sup>) with low air pollutant exposure. DNA methylation levels were quantified in two regions of the displacement loop control region (<i>D-loop</i> and <i>LDLR2</i>) by bisulphite pyrosequencing. Additionally, we measured DNA methylation on nuclear genes involved in mitochondrial maintenance (<i>PINK1, DNA2</i>, and <i>POLG1</i>) and assessed mtDNA content using qPCR. Absolute <i>D-loop</i> methylation levels were higher for mothers that smoked extensively (+0.36%, 95% CI: 0.06% to 0.66%), and for mothers that were highly exposed to air pollutants (+0.47%, 95% CI: 0.20% to 0.73%). The relevance of our findings is further supported, as <i>D-loop</i> methylation levels were correlated with placental mtDNA content (r = −0.40, p = 0.002) and associated with birth weight (−106.98 g, 95% CI: −209.60 g to −4.36 g for an IQR increase in <i>D-loop</i> methylation). Most notably, our data demonstrates relevant levels of mtDNA methylation in placenta tissue, with significant associations between prenatal exposure to environmental stressors and <i>D-loop</i> methylation.
DOI: 10.6084/m9.figshare.12851645
title: Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study

description: In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in paediatric oncology in a cost-effective and minimally invasive manner.
DOI: 10.6084/m9.figshare.12851645.v1
title: Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study

description: In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in paediatric oncology in a cost-effective and minimally invasive manner.
DOI: 10.6084/m9.figshare.12115584
title: The landscape of <i>CD28, CD80, CD86, CTLA4</i>, and <i>ICOS</i> DNA methylation in head and neck squamous cell carcinomas

description: CTLA-4 blocking therapeutic antibodies are currently under investigation in head and neck squamous cell carcinoma (HNSCC). A better understanding of the epigenetic regulation of the CD28 superfamily members CD28, CTLA-4, and ICOS and their B7 ligands, CD80 and CD86, could support the development of biomarkers for response prediction to anti-CTLA-4 immunotherapy. We investigated methylation of the encoding genes <i>CD28, CTLA4, ICOS, CD80</i>, and <i>CD86</i> at single CpG resolution (51 CpG sites) in a cohort of HNSCC (<i>N = </i>528) and normal adjacent tissue samples (<i>N = </i>50) provided by The Cancer Genome Research Atlas, in isolated blood leukocytes from healthy individuals (<i>N = </i>28), and HNSCC cell lines (<i>N</i> = 39). We analysed methylation levels with regard to mRNA expression, overall survival, mutational load, interferon-γ signature, and signatures of immune cell infiltrates. Depending on the location of the CpG sites (promoter, promoter flank, gene body, and intergenic sites), we found significant differences in methylation levels among isolated leukocytes, between leukocytes and HNSCC cell lines, and among HNSCCs. Methylation of all analysed genes correlated inversely or positively with mRNA expression, depending on the CpG site. <i>CD28, CTLA4</i>, and <i>ICOS</i> revealed almost identical correlation patterns. Furthermore, we found significant correlations with survival and features of response to immunotherapy, i.e. interferon-γ signature, signatures of tumour infiltrating immune cells, and mutational load. Our results suggest <i>CD28, CTLA4, ICOS, CD80</i>, and <i>CD86</i> expression levels are epigenetically co-regulated by DNA methylation. This study provides rationale to test their DNA methylation as potential biomarker for prediction of response to CTLA-4 immune checkpoint inhibitors.
DOI: 10.6084/m9.figshare.12115584.v2
title: The landscape of <i>CD28, CD80, CD86, CTLA4</i>, and <i>ICOS</i> DNA methylation in head and neck squamous cell carcinomas

description: CTLA-4 blocking therapeutic antibodies are currently under investigation in head and neck squamous cell carcinoma (HNSCC). A better understanding of the epigenetic regulation of the CD28 superfamily members CD28, CTLA-4, and ICOS and their B7 ligands, CD80 and CD86, could support the development of biomarkers for response prediction to anti-CTLA-4 immunotherapy. We investigated methylation of the encoding genes <i>CD28, CTLA4, ICOS, CD80</i>, and <i>CD86</i> at single CpG resolution (51 CpG sites) in a cohort of HNSCC (<i>N = </i>528) and normal adjacent tissue samples (<i>N = </i>50) provided by The Cancer Genome Research Atlas, in isolated blood leukocytes from healthy individuals (<i>N = </i>28), and HNSCC cell lines (<i>N</i> = 39). We analysed methylation levels with regard to mRNA expression, overall survival, mutational load, interferon-γ signature, and signatures of immune cell infiltrates. Depending on the location of the CpG sites (promoter, promoter flank, gene body, and intergenic sites), we found significant differences in methylation levels among isolated leukocytes, between leukocytes and HNSCC cell lines, and among HNSCCs. Methylation of all analysed genes correlated inversely or positively with mRNA expression, depending on the CpG site. <i>CD28, CTLA4</i>, and <i>ICOS</i> revealed almost identical correlation patterns. Furthermore, we found significant correlations with survival and features of response to immunotherapy, i.e. interferon-γ signature, signatures of tumour infiltrating immune cells, and mutational load. Our results suggest <i>CD28, CTLA4, ICOS, CD80</i>, and <i>CD86</i> expression levels are epigenetically co-regulated by DNA methylation. This study provides rationale to test their DNA methylation as potential biomarker for prediction of response to CTLA-4 immune checkpoint inhibitors.