20 Works

Additional file 2 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 2: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 3 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 3: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 6 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 6: Fig. S4. Differential gene expression of IL6 between T-LGL and healthy donor-derived CD8+ memory T cells. Differential gene expression for IL6 was measured by qPCR. Bulk CD8+ cells from two healthy donors were used for comparison. In line with previous publications, the T-LGLL cohort analyzed exhibits a higher IL6 expression compared to healthy donor-derived C8+ cells. HD Healthy donor.

Additional file 9 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 9: Fig. S1. Correlation of bisulfite Pyrosequencing (BPS) and methylation Array DNA methylation levels. The correlation matrix shows the Pearson correlation coefficient (r: 1 (red) to − 1 (blue) among all CpG loci analyzed by BPS. The candidate genes LINC01550 and BCL11B contained multiple CpG sites. Columns and rows represent one CpG loci of the listed candidate gene.

Additional file 9 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 9: Fig. S1. Correlation of bisulfite Pyrosequencing (BPS) and methylation Array DNA methylation levels. The correlation matrix shows the Pearson correlation coefficient (r: 1 (red) to − 1 (blue) among all CpG loci analyzed by BPS. The candidate genes LINC01550 and BCL11B contained multiple CpG sites. Columns and rows represent one CpG loci of the listed candidate gene.

Additional file 4 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 4: Fig. S3A. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. A Gene Ontology analysis of hypermethylated genes in T-LGL.

Additional file 6 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 6: Fig. S4. Differential gene expression of IL6 between T-LGL and healthy donor-derived CD8+ memory T cells. Differential gene expression for IL6 was measured by qPCR. Bulk CD8+ cells from two healthy donors were used for comparison. In line with previous publications, the T-LGLL cohort analyzed exhibits a higher IL6 expression compared to healthy donor-derived C8+ cells. HD Healthy donor.

Additional file 7 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 7: Fig. S5A. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). A Significant differentially methylated CpGs in BCL11B (T-LGLL compared to CD8+. memory T cells) were located in the gene body and assigned as enhancers by ENCODE, which match as enhancers in CD8-positive memory cells.

Additional file 8 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 8: Fig. S5B. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). B Significant differentially methylated CpGs in C14orf64 (LINC01550) (T-LGL compared to CD8 pos. memory T cells).

Additional file 10 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 10: Fig. S6. Expression correlation between BCL11B & C14ORF64 (LINC01550). Expression correlation between BCL11B & C14ORF64 (LINC01550) in 426 human datasets with 42563 samples from R2: Genomics analysis and visualization platform (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi).

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

Additional file 2 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 2: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 4 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 4: Fig. S3A. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. A Gene Ontology analysis of hypermethylated genes in T-LGL.

Additional file 5 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Additional file 7 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 7: Fig. S5A. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). A Significant differentially methylated CpGs in BCL11B (T-LGLL compared to CD8+. memory T cells) were located in the gene body and assigned as enhancers by ENCODE, which match as enhancers in CD8-positive memory cells.

Additional file 8 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 8: Fig. S5B. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). B Significant differentially methylated CpGs in C14orf64 (LINC01550) (T-LGL compared to CD8 pos. memory T cells).

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

Additional file 3 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 3: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 5 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Additional file 10 of Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker

Patricia Johansson, Teresa Laguna, Julio Ossowski, Vera Pancaldi, Martina Brauser, Ulrich Dührsen, Lara Keuneke, Ana Queiros, Julia Richter, José I. Martín-Subero, Reiner Siebert, Brigitte Schlegelberger, Ralf Küppers, Jan Dürig, Eva M. Murga Penas, Enrique Carillo-de Santa Pau & Anke K. Bergmann
Additional file 10: Fig. S6. Expression correlation between BCL11B & C14ORF64 (LINC01550). Expression correlation between BCL11B & C14ORF64 (LINC01550) in 426 human datasets with 42563 samples from R2: Genomics analysis and visualization platform (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi).

Registration Year

  • 2022
    18
  • 2020
    2

Resource Types

  • Image
    20

Affiliations

  • Institució Catalana de Recerca i Estudis Avançats
    20
  • Cancer Research Center of Toulouse
    18
  • Hannover Medical School
    18
  • University Hospital Schleswig-Holstein
    18
  • University of Barcelona
    18
  • Essen University Hospital
    18
  • St. Josef Krankenhaus
    18
  • University of Ulm
    18
  • IMDEA Food
    18
  • University of Duisburg-Essen
    18