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Møller MW, Andersen MS, Halle B, Pedersen CB, Boldt HB, Tan Q, Jurmeister PS, Herrgott GA, Castro AV, Petersen JK, Poulsen FR. Genome-Wide DNA Methylation Profiling as a Prognostic Marker in Pituitary Adenomas-A Pilot Study. Cancers (Basel) 2024; 16:2210. [PMID: 38927917 PMCID: PMC11201450 DOI: 10.3390/cancers16122210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The prediction of the regrowth potential of pituitary adenomas after surgery is challenging. The genome-wide DNA methylation profiling of pituitary adenomas may separate adenomas into distinct methylation classes corresponding to histology-based subtypes. Specific genes and differentially methylated probes involving regrowth have been proposed, but no study has linked this epigenetic variance with regrowth potential and the clinical heterogeneity of nonfunctioning pituitary adenomas. This study aimed to investigate whether DNA methylation profiling can be useful as a clinical prognostic marker. METHODS A DNA methylation analysis by Illumina's MethylationEPIC array was performed on 54 pituitary macroadenomas from patients who underwent transsphenoidal surgery during 2007-2017. Twelve patients were excluded due to an incomplete postoperative follow-up, degenerated biobank-stored tissue, or low DNA methylation quality. For the quantitative measurement of the tumor regrowth rate, we conducted a 3D volumetric analysis of tumor remnant volume via annual magnetic resonance imaging. A linear mixed effects model was used to examine whether different DNA methylation clusters had different regrowth patterns. RESULTS The DNA methylation profiling of 42 tissue samples showed robust DNA methylation clusters, comparable with previous findings. The subgroup of 33 nonfunctioning pituitary adenomas of an SF1-lineage showed five subclusters with an approximately unbiased score of 86%. There were no overall statistically significant differences when comparing hazard ratios for regrowth of 100%, 50%, or 0%. Despite this, plots of correlated survival estimates suggested higher regrowth rates for some clusters. The mixed effects model of accumulated regrowth similarly showed tendencies toward an association between specific DNA methylation clusters and regrowth potential. CONCLUSION The DNA methylation profiling of nonfunctioning pituitary adenomas may potentially identify adenomas with increased growth and recurrence potential. Larger validation studies are needed to confirm the findings from this explorative pilot study.
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Affiliation(s)
- Morten Winkler Møller
- Department of Neurosurgery, Odense University Hospital, 5000 Odense, Denmark; (B.H.); (C.B.P.); (F.R.P.)
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
| | - Marianne Skovsager Andersen
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
- Department of Endocrinology, Odense University Hospital, 5000 Odense, Denmark
| | - Bo Halle
- Department of Neurosurgery, Odense University Hospital, 5000 Odense, Denmark; (B.H.); (C.B.P.); (F.R.P.)
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
| | - Christian Bonde Pedersen
- Department of Neurosurgery, Odense University Hospital, 5000 Odense, Denmark; (B.H.); (C.B.P.); (F.R.P.)
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
| | - Henning Bünsow Boldt
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
- Department of Pathology, Odense University Hospital, 5000 Odense, Denmark
| | - Qihua Tan
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
- Department of Public Health, Odense University Hospital, 5000 Odense, Denmark
| | - Philipp Sebastian Jurmeister
- Institute of Pathology, Ludwig Maximilians University Hospital Munich, 80336 Munich, Germany;
- German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Grayson A. Herrgott
- Omics Laboratory, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Health, Detroit, MI 48202, USA; (G.A.H.); (A.V.C.)
| | - Ana Valeria Castro
- Omics Laboratory, Hermelin Brain Tumor Center, Department of Neurosurgery, Henry Ford Health, Detroit, MI 48202, USA; (G.A.H.); (A.V.C.)
- Department of Physiology, College of Human Medicine, Michigan State University, E. Lansing, MI 48824, USA
| | - Jeanette K. Petersen
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
- Department of Pathology, Odense University Hospital, 5000 Odense, Denmark
| | - Frantz Rom Poulsen
- Department of Neurosurgery, Odense University Hospital, 5000 Odense, Denmark; (B.H.); (C.B.P.); (F.R.P.)
- Department of Clinical Research and BRIDGE (Brain Research—Inter Disciplinary Guided Excellence), University of Southern Denmark, 5000 Odense, Denmark; (M.S.A.); (H.B.B.); (Q.T.); (J.K.P.)
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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3
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Zhang L, Liu Y, Lu Y, Wang G. Targeting epigenetics as a promising therapeutic strategy for treatment of neurodegenerative diseases. Biochem Pharmacol 2022; 206:115295. [DOI: 10.1016/j.bcp.2022.115295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
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Abstract
Modern epigenetics emerged about 40 years ago. Since then, the field has rapidly grown. Unfortunately, this development has been accompanied by certain misconceptions and methodological shortcomings. A profound misconception is that chromatin modifications are a distinct layer of gene regulation that is directly responsive to the environment and potentially heritable between generations. This view ignores the fact that environmental factors affect gene expression mainly through signaling cascades and the activation or repression of transcription factors, which recruit chromatin regulators. The epigenome is mainly shaped by the DNA sequence and by transcription. Methodological shortcomings include the insufficient consideration of genetic variation and cell mixture distribution. Mis- and overinterpretation of epigenetic data foster genetic denialism ("We can control our genes") and epigenetic determinism ("You are what your parents ate"). These erroneous beliefs can be overcome by using precise definitions, by raising the awareness about methodological pitfalls and by returning to the basic facts in molecular and cellular biology.
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Rabaneda-Bueno R, Mena-Montes B, Torres-Castro S, Torres-Carrillo N, Torres-Carrillo NM. Advances in Genetics and Epigenetic Alterations in Alzheimer's Disease: A Notion for Therapeutic Treatment. Genes (Basel) 2021; 12:1959. [PMID: 34946908 PMCID: PMC8700838 DOI: 10.3390/genes12121959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is a disabling neurodegenerative disorder that leads to long-term functional and cognitive impairment and greatly reduces life expectancy. Early genetic studies focused on tracking variations in genome-wide DNA sequences discovered several polymorphisms and novel susceptibility genes associated with AD. However, despite the numerous risk factors already identified, there is still no fully satisfactory explanation for the mechanisms underlying the onset of the disease. Also, as with other complex human diseases, the causes of low heritability are unclear. Epigenetic mechanisms, in which changes in gene expression do not depend on changes in genotype, have attracted considerable attention in recent years and are key to understanding the processes that influence age-related changes and various neurological diseases. With the recent use of massive sequencing techniques, methods for studying epigenome variations in AD have also evolved tremendously, allowing the discovery of differentially expressed disease traits under different conditions and experimental settings. This is important for understanding disease development and for unlocking new potential AD therapies. In this work, we outline the genomic and epigenomic components involved in the initiation and development of AD and identify potentially effective therapeutic targets for disease control.
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Affiliation(s)
- Rubén Rabaneda-Bueno
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic
- School of Biological Sciences, James Clerk Maxwell Building, The King’s Buildings Campus, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Beatriz Mena-Montes
- Laboratorio de Biología del Envejecimiento, Departamento de Investigación Básica, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Sara Torres-Castro
- Departamento de Epidemiología Demográfica y Determinantes Sociales, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
| | - Nora Magdalena Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
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Kawai T, Richards JS, Shimada M. Large-scale DNA demethylation occurs in proliferating ovarian granulosa cells during mouse follicular development. Commun Biol 2021; 4:1334. [PMID: 34824385 PMCID: PMC8617273 DOI: 10.1038/s42003-021-02849-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
During ovarian follicular development, granulosa cells proliferate and progressively differentiate to support oocyte maturation and ovulation. To determine the underlying links between proliferation and differentiation in granulosa cells, we determined changes in 1) the expression of genes regulating DNA methylation and 2) DNA methylation patterns, histone acetylation levels and genomic DNA structure. In response to equine chorionic gonadotropin (eCG), granulosa cell proliferation increased, DNA methyltransferase (DNMT1) significantly decreased and Tet methylcytosine dioxygenase 2 (TET2) significantly increased in S-phase granulosa cells. Comprehensive MeDIP-seq analyses documented that eCG treatment decreased methylation of promoter regions in approximately 40% of the genes in granulosa cells. The expression of specific demethylated genes was significantly increased in association with specific histone modifications and changes in DNA structure. These epigenetic processes were suppressed by a cell cycle inhibitor. Based on these results, we propose that the timing of sequential epigenetic events is essential for progressive, stepwise changes in granulosa cell differentiation.
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Affiliation(s)
- Tomoko Kawai
- Laboratory of Reproductive Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - JoAnne S Richards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Masayuki Shimada
- Laboratory of Reproductive Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
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Neri de Souza Reis V, Tahira AC, Daguano Gastaldi V, Mari P, Portolese J, Feio dos Santos AC, Lisboa B, Mari J, Caetano SC, Brunoni D, Bordini D, Silvestre de Paula C, Vêncio RZN, Quackenbush J, Brentani H. Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity. Genes (Basel) 2021; 12:genes12091433. [PMID: 34573415 PMCID: PMC8467464 DOI: 10.3390/genes12091433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Although Autism Spectrum Disorders (ASD) is recognized as being heavily influenced by genetic factors, the role of epigenetic and environmental factors is still being established. This study aimed to identify ASD vulnerability components based on familial history and intrauterine environmental stress exposure, explore possible vulnerability subgroups, access DNA methylation age acceleration (AA) as a proxy of stress exposure during life, and evaluate the association of ASD vulnerability components and AA to phenotypic severity measures. Principal Component Analysis (PCA) was used to search the vulnerability components from 67 mothers of autistic children. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 had a higher correlation with biological factors (psychiatric family history and gestational complications). Comparing the methylome between above and below PC1 average subgroups we found 11,879 statistically significant differentially methylated probes (DMPs, p < 0.05). DMPs CpG sites were enriched in variably methylated regions (VMRs), most showing environmental and genetic influences. Hypermethylated probes presented higher rates in different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability components score moderated by epigenetic clock AA was associated with Vineland Total score (p = 0.0036, adjR2 = 0.31), suggesting risk factors with stress burden can influence ASD phenotype.
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Affiliation(s)
- Viviane Neri de Souza Reis
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Ana Carolina Tahira
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
- Instituto Butantan, São Paulo 05503-900, SP, Brazil
| | - Vinícius Daguano Gastaldi
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Paula Mari
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Joana Portolese
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Ana Cecilia Feio dos Santos
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
- Laboratório de Pesquisas Básicas em Malária—Entomologia, Seção de Parasitologia—Instituto Evandro Chagas/SVS/MS, Ananindeua 66093-020, PA, Brazil
| | - Bianca Lisboa
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Jair Mari
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
| | - Sheila C. Caetano
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
| | - Décio Brunoni
- Centro de Ciências Biológicas e da Saúde, Universidade Presbiteriana Mackenzie (UPM), São Paulo 01302-907, SP, Brazil;
| | - Daniela Bordini
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
| | - Cristiane Silvestre de Paula
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
- Centro de Ciências Biológicas e da Saúde, Universidade Presbiteriana Mackenzie (UPM), São Paulo 01302-907, SP, Brazil;
| | - Ricardo Z. N. Vêncio
- Departamento de Computação e Matemática FFCLRP-USP, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil;
| | - John Quackenbush
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; or
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Helena Brentani
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
- Correspondence: ; Tel.: +55-(11)-99-931-4349
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Di Persio S, Leitão E, Wöste M, Tekath T, Cremers JF, Dugas M, Li X, Meyer Zu Hörste G, Kliesch S, Laurentino S, Neuhaus N, Horsthemke B. Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes. Clin Epigenetics 2021; 13:160. [PMID: 34419158 PMCID: PMC8379757 DOI: 10.1186/s13148-021-01144-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/01/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Several studies have reported an association between male infertility and aberrant sperm DNA methylation patterns, in particular in imprinted genes. In a recent investigation based on whole methylome and deep bisulfite sequencing, we have not found any evidence for such an association, but have demonstrated that somatic DNA contamination and genetic variation confound methylation studies in sperm of severely oligozoospermic men. To find out whether testicular germ cells (TGCs) of such patients might carry aberrant DNA methylation, we compared the TGC methylomes of four men with cryptozoospermia (CZ) and four men with obstructive azoospermia, who had normal spermatogenesis and served as controls (CTR). RESULTS There was no difference in DNA methylation at the whole genome level or at imprinted regions between CZ and CTR samples. However, using stringent filters to identify group-specific methylation differences, we detected 271 differentially methylated regions (DMRs), 238 of which were hypermethylated in CZ (binominal test, p < 2.2 × 10-16). The DMRs were enriched for distal regulatory elements (p = 1.0 × 10-6) and associated with 132 genes, 61 of which are differentially expressed at various stages of spermatogenesis. Almost all of the 67 DMRs associated with the 61 genes (94%) are hypermethylated in CZ (63/67, p = 1.107 × 10-14). As judged by single-cell RNA sequencing, 13 DMR-associated genes, which are mainly expressed during meiosis and spermiogenesis, show a significantly different pattern of expression in CZ patients. In four of these genes, the promoter is hypermethylated in CZ men, which correlates with a lower expression level in these patients. In the other nine genes, eight of which downregulated in CZ, germ cell-specific enhancers may be affected. CONCLUSIONS We found that impaired spermatogenesis is associated with DNA methylation changes in testicular germ cells at functionally relevant regions of the genome. We hypothesize that the described DNA methylation changes may reflect or contribute to premature abortion of spermatogenesis and therefore not appear in the mature, motile sperm.
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Affiliation(s)
- Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Tobias Tekath
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Jann-Frederik Cremers
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Xiaolin Li
- Department of Neurology, Institute of Translational Neurology, University Hospital of Münster, 48149, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology, Institute of Translational Neurology, University Hospital of Münster, 48149, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany.
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
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Moser DA, Müller S, Hummel EM, Limberg AS, Dieckmann L, Frach L, Pakusch J, Flasbeck V, Brüne M, Beygo J, Klein-Hitpass L, Kumsta R. Targeted bisulfite sequencing: A novel tool for the assessment of DNA methylation with high sensitivity and increased coverage. Psychoneuroendocrinology 2020; 120:104784. [PMID: 32673938 DOI: 10.1016/j.psyneuen.2020.104784] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023]
Abstract
DNA methylation analysis is increasingly used in stress research. Available methods are expensive, laborious and often limited by either the analysis of short CpG stretches or low assay sensitivity. Here, we present a cost-efficient next generation sequencing-based strategy for the simultaneous investigation of multiple candidate genes in large cohorts. To illustrate the method, we present analysis of four candidate genes commonly assessed in psychoneuroendocrine research: Glucocorticoid receptor (NR3C1), Serotonin transporter (SLC6A4), FKBP Prolyl isomerase 5 (FKBP5), and the Oxytocin receptor (OXTR). DNA methylation standards (100 %; 75 %; 50 %; 25 % and 0 %) and DNA of a female and male donor were bisulfite treated in three independent trials and were used to generate sequencing libraries for 42 CpGs from the NR3C1 1 F promoter region, 84 CpGs of the SLC6A4 5' regulatory region, 5 CpGs located in FKBP5 intron 7, and additional 12 CpGs located in a potential enhancer element in intron 3 of the OXTR. In addition, DNA of 45 patients with borderline personality disorder (BPD) and 45 healthy controls was assayed. Multiplex libraries of all samples were sequenced on a MiSeq system and analyzed for mean methylation values of all CpG sites using amplikyzer2 software. Results indicated excellent accuracy of the assays when investigating replicates generated from the same bisulfite converted DNA, and very high linearity (R2 > 0.9) of the assays shown by the analysis of differentially methylated DNA standards. Comparing DNA methylation between BPD and healthy controls revealed no biologically relevant differences. The technical approach as described here facilitates targeted DNA methylation analysis and represents a highly sensitive, cost-efficient and high throughput tool to close the gap between coverage and precision in epigenetic research of stress-associated phenotypes.
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Affiliation(s)
- D A Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
| | - S Müller
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - E M Hummel
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - A S Limberg
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - L Dieckmann
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - L Frach
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - J Pakusch
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - V Flasbeck
- LWL University Hospital Department of Psychiatry, Psychotherapy and Preventive Medicine, Division of Social Neuropsychiatry and Evolutionary Medicine, Ruhr-University Bochum, Bochum, Germany
| | - M Brüne
- LWL University Hospital Department of Psychiatry, Psychotherapy and Preventive Medicine, Division of Social Neuropsychiatry and Evolutionary Medicine, Ruhr-University Bochum, Bochum, Germany
| | - J Beygo
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - L Klein-Hitpass
- Institute of Cell Biology (Tumor Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - R Kumsta
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
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10
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Wöste M, Leitão E, Laurentino S, Horsthemke B, Rahmann S, Schröder C. wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. BMC Bioinformatics 2020; 21:169. [PMID: 32357829 PMCID: PMC7195798 DOI: 10.1186/s12859-020-3470-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/24/2020] [Indexed: 11/20/2022] Open
Abstract
Background Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tasks such as alignment, comprehensive end-to-end pipelines are still sparse. Furthermore, previous pipelines lack features or show technical deficiencies, thus impeding analyses. Results We developed wg-blimp (whole genome bisulfite sequencing methylation analysis pipeline) as an end-to-end pipeline to ease whole genome bisulfite sequencing data analysis. It integrates established algorithms for alignment, quality control, methylation calling, detection of differentially methylated regions, and methylome segmentation, requiring only a reference genome and raw sequencing data as input. Comparing wg-blimp to previous end-to-end pipelines reveals similar setups for common sequence processing tasks, but shows differences for post-alignment analyses. We improve on previous pipelines by providing a more comprehensive analysis workflow as well as an interactive user interface. To demonstrate wg-blimp’s ability to produce correct results we used it to call differentially methylated regions for two publicly available datasets. We were able to replicate 112 of 114 previously published regions, and found results to be consistent with previous findings. We further applied wg-blimp to a publicly available sample of embryonic stem cells to showcase methylome segmentation. As expected, unmethylated regions were in close proximity of transcription start sites. Segmentation results were consistent with previous analyses, despite different reference genomes and sequencing techniques. Conclusions wg-blimp provides a comprehensive analysis pipeline for whole genome bisulfite sequencing data as well as a user interface for simplified result inspection. We demonstrated its applicability by analysing multiple publicly available datasets. Thus, wg-blimp is a relevant alternative to previous analysis pipelines and may facilitate future epigenetic research.
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Affiliation(s)
- Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Münster, 48149, Germany.
| | - Elsa Leitão
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University Hospital Münster, Albert-Schweitzer-Campus 1, Münster, 48149, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.,Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, Münster, 48149, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.,Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany
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11
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Identification of Novel Human Monocyte Subsets and Evidence for Phenotypic Groups Defined by Interindividual Variations of Expression of Adhesion Molecules. Sci Rep 2020; 10:4397. [PMID: 32157175 PMCID: PMC7064612 DOI: 10.1038/s41598-020-61022-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
Monocytes contribute to immune responses as a source for subsets of dendritic cells and macrophages. Human blood monocytes are classified as classical, non-classical and intermediate cells. However, the particular functions of these subsets have been hard to define, with conflicting results and significant overlaps. One likely reason for these ambiguities is in the heterogeneity of these monocyte subsets regrouping cells with divergent functions. To better define monocyte populations, we have analysed expression of 17 markers by multicolour flow cytometry in samples obtained from 28 control donors. Data acquisition was tailored to detect populations present at low frequencies. Our results reveal the existence of novel monocyte subsets detected as larger CD14+ cells that were CD16+ or CD16neg. These large monocytes differed from regular, smaller monocytes with respect to expression of various cell surface molecules, such as FcR, chemokine receptors, and adhesion molecules. Unsupervised multidimensional analysis confirmed the existence of large monocytes and revealed interindividual variations that were grouped according to unique patterns of expression of adhesion molecules CD62L, CD49d, and CD43. Distinct inflammatory responses to TLR agonists were found in small and large monocytes. Overall, refining the definition of monocyte subsets should lead to the identification of populations with specific functions.
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12
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Next-Generation-Sequencing in der Epigenetik. MED GENET-BERLIN 2019. [DOI: 10.1007/s11825-019-0245-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Zusammenfassung
Molekulare Epigenetik bezieht sich auf die chemische und physikalische Modifikation von DNA und Chromatin. Transkriptionsfaktoren bestimmen die Chromatinzustände ihrer Zielgene, während Chromatinzustände andererseits die Bindung von Transkriptionsfaktoren an die DNA beeinflussen. Chromatinzustände sind gekennzeichnet durch spezifische Muster der DNA-Methylierung, Histonmodifikation, den Abstand der Nukleosomen und die 3‑D-Faltung von Chromatin. Seit dem Aufkommen des Next-Generation-Sequencing (NGS) ist es möglich, diese Muster im genomweiten Maßstab mit einer beispiellosen Auflösung zu analysieren. Solche epigenetischen Karten sind wertvoll, um regulatorische Elemente zu identifizieren, normale und gestörte Entwicklungsvorgänge zu verstehen und Epimutationen zu entdecken.
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13
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Kumsta R. The role of epigenetics for understanding mental health difficulties and its implications for psychotherapy research. Psychol Psychother 2019; 92:190-207. [PMID: 30924323 DOI: 10.1111/papt.12227] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Indexed: 12/14/2022]
Abstract
Many mental health difficulties have developmental origins. Understanding the mechanisms for how psychosocial experiences are biologically embedded and influence lifelong development is a key challenge for the mental health disciplines. In recent years, epigenetic processes have emerged as a potential mechanism mediating the long-lasting vulnerability following the experience of adversity. Animal models provide evidence that early-life adversity can produce enduring epigenetic modifications in the brain, which mediate disorder-like behaviours, and there is emerging evidence to support that environmental factors influence epigenetic processes in humans. The investigation of DNA methylation, a chemical modification of the DNA with a role in gene regulatory processes, is becoming increasingly popular in psychological studies. A particular interest for the psychotherapy field lies in the potential for psychological interventions to influence epigenetic processes. Hence, the focus of this review will be on studies that have investigated intervention-associated changes in DNA methylation. Results of the first few studies will be critically reviewed, and a model of how therapy-associated changes of DNA methylation in peripheral, non-brain tissue might be useful as epigenetic biomarkers of treatment outcome will be presented. PRACTITIONER POINTS: Many mental health difficulties have substantial developmental origin. Epigenetic processes have emerged as a potential mechanism mediating the long-term effects of early adversity Epigenetic refers to cellular mechanisms that control gene expression states, independent of changes to the underlying DNA sequence. The epigenome can be highly dynamic and potentially influenced by external factors A particular interest for the psychotherapy field lies in the potential for psychological interventions to influence epigenetic processes.
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Affiliation(s)
- Robert Kumsta
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
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14
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Fan S, Tang J, Li N, Zhao Y, Ai R, Zhang K, Wang M, Du W, Wang W. Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers. NPJ Genom Med 2019; 4:2. [PMID: 30729033 PMCID: PMC6358616 DOI: 10.1038/s41525-019-0077-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/02/2019] [Indexed: 11/09/2022] Open
Abstract
The integration of genomic and DNA methylation data has been demonstrated as a powerful strategy in understanding cancer mechanisms and identifying therapeutic targets. The TCGA consortium has mapped DNA methylation in thousands of cancer samples using Illumina Infinium Human Methylation 450 K BeadChip (Illumina 450 K array) that only covers about 1.5% of CpGs in the human genome. Therefore, increasing the coverage of the DNA methylome would significantly leverage the usage of the TCGA data. Here, we present a new model called EAGLING that can expand the Illumina 450 K array data 18 times to cover about 30% of the CpGs in the human genome. We applied it to analyze 13 cancers in TCGA. By integrating the expanded methylation, gene expression, and somatic mutation data, we identified the genes showing differential patterns in each of the 13 cancers. Many of the triple-evidenced genes identified in majority of the cancers are biomarkers or potential biomarkers. Pan-cancer analysis also revealed the pathways in which the triple-evidenced genes are enriched, which include well known ones as well as new ones, such as axonal guidance signaling pathway and pathways related to inflammatory processing or inflammation response. Triple-evidenced genes, particularly TNXB, RRM2, CELSR3, SLC16A3, FANCI, MMP9, MMP11, SIK1, and TRIM59 showed superior predictive power in both tumor diagnosis and prognosis. These results have demonstrated that the integrative analysis using the expanded methylation data is powerful in identifying critical genes/pathways that may serve as new therapeutic targets.
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Affiliation(s)
- Shicai Fan
- 1School of Automation Engineering, University of Electronic Science and Technology of China, 611731 Chengdu, Sichuan China.,2Center for Informational Biology, University of Electronic Science and Technology of China, 611731 Chengdu, Sichuan China.,3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA.,4Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, 130012 Changchun, China
| | - Jianxiong Tang
- 1School of Automation Engineering, University of Electronic Science and Technology of China, 611731 Chengdu, Sichuan China
| | - Nan Li
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Ying Zhao
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Rizi Ai
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Kai Zhang
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Mengchi Wang
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Wei Du
- 4Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, 130012 Changchun, China
| | - Wei Wang
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA.,5Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093-0359 USA
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15
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Hernandez I, Dhiman H, Klanert G, Jadhav V, Auer N, Hanscho M, Baumann M, Esteve-Codina A, Dabad M, Gómez J, Alioto T, Merkel A, Raineri E, Heath S, Rico D, Borth N. Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture. Biotechnol Bioeng 2019; 116:677-692. [PMID: 30512195 PMCID: PMC6492168 DOI: 10.1002/bit.26891] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/18/2018] [Accepted: 11/21/2018] [Indexed: 12/31/2022]
Abstract
The existence of dynamic cellular phenotypes in changing environmental conditions is of major interest for cell biologists who aim to understand the mechanism and sequence of regulation of gene expression. In the context of therapeutic protein production by Chinese Hamster Ovary (CHO) cells, a detailed temporal understanding of cell‐line behavior and control is necessary to achieve a more predictable and reliable process performance. Of particular interest are data on dynamic, temporally resolved transcriptional regulation of genes in response to altered substrate availability and culture conditions. In this study, the gene transcription dynamics throughout a 9‐day batch culture of CHO cells was examined by analyzing histone modifications and gene expression profiles in regular 12‐ and 24‐hr intervals, respectively. Three levels of regulation were observed: (a) the presence or absence of DNA methylation in the promoter region provides an ON/OFF switch; (b) a temporally resolved correlation is observed between the presence of active transcription‐ and promoter‐specific histone marks and the expression level of the respective genes; and (c) a major mechanism of gene regulation is identified by interaction of coding genes with long non‐coding RNA (lncRNA), as observed in the regulation of the expression level of both neighboring coding/lnc gene pairs and of gene pairs where the lncRNA is able to form RNA–DNA–DNA triplexes. Such triplex‐forming regions were predominantly found in the promoter or enhancer region of the targeted coding gene. Significantly, the coding genes with the highest degree of variation in expression during the batch culture are characterized by a larger number of possible triplex‐forming interactions with differentially expressed lncRNAs. This indicates a specific role of lncRNA‐triplexes in enabling rapid and large changes in transcription. A more comprehensive understanding of these regulatory mechanisms will provide an opportunity for new tools to control cellular behavior and to engineer enhanced phenotypes.
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Affiliation(s)
- Inmaculada Hernandez
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Heena Dhiman
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Gerald Klanert
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Vaibhav Jadhav
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Norbert Auer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Michael Hanscho
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Anna Esteve-Codina
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jessica Gómez
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Angelika Merkel
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Emanuele Raineri
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Simon Heath
- CNAG-CRG National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, Vienna, Austria
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