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  1. Article: my experience of the pandemic. 2 years of COVID-19 from the perspective of a young scientist

    Lukassen, Sören

    Gesundhyte.de

    2021  Volume 14, Issue Dez., Page(s) 11

    Language German
    Document type Article
    ZDB-ID 3044168-7
    ISSN 2702-2544
    Database Current Contents Medicine

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  2. Article ; Online: Conserved host-pathogen interactions identify novel treatment options in betacoronavirus infections.

    Lukassen, Soeren / Eils, Roland

    Signal transduction and targeted therapy

    2021  Volume 6, Issue 1, Page(s) 57

    MeSH term(s) COVID-19 ; Host-Pathogen Interactions ; Humans
    Language English
    Publishing date 2021-02-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2886872-9
    ISSN 2059-3635 ; 2095-9907
    ISSN (online) 2059-3635
    ISSN 2095-9907
    DOI 10.1038/s41392-021-00480-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Conserved host-pathogen interactions identify novel treatment options in betacoronavirus infections

    Soeren Lukassen / Roland Eils

    Signal Transduction and Targeted Therapy, Vol 6, Iss 1, Pp 1-

    2021  Volume 3

    Keywords Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  4. Article: resVAE ensemble: Unsupervised identification of gene sets in multi-modal single-cell sequencing data using deep ensembles.

    Ten, Foo Wei / Yuan, Dongsheng / Jabareen, Nabil / Phua, Yin Jun / Eils, Roland / Lukassen, Sören / Conrad, Christian

    Frontiers in cell and developmental biology

    2023  Volume 11, Page(s) 1091047

    Abstract: Feature identification and manual inspection is currently still an integral part of biological data analysis in single-cell sequencing. Features such as expressed genes and open chromatin status are selectively studied in specific contexts, cell states ... ...

    Abstract Feature identification and manual inspection is currently still an integral part of biological data analysis in single-cell sequencing. Features such as expressed genes and open chromatin status are selectively studied in specific contexts, cell states or experimental conditions. While conventional analysis methods construct a relatively static view on gene candidates, artificial neural networks have been used to model their interactions after hierarchical gene regulatory networks. However, it is challenging to identify consistent features in this modeling process due to the inherently stochastic nature of these methods. Therefore, we propose using ensembles of autoencoders and subsequent rank aggregation to extract consensus features in a less biased manner. Here, we performed sequencing data analyses of different modalities either independently or simultaneously as well as with other analysis tools. Our resVAE ensemble method can successfully complement and find additional unbiased biological insights with minimal data processing or feature selection steps while giving a measurement of confidence, especially for models using stochastic or approximation algorithms. In addition, our method can also work with overlapping clustering identity assignment suitable for transitionary cell types or cell fates in comparison to most conventional tools.
    Language English
    Publishing date 2023-02-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2023.1091047
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: CD3 downregulation identifies high-avidity, multipotent SARS-CoV-2 vaccine- and recall antigen-specific Th cells with distinct metabolism.

    Sattler, Arne / Gamradt, Stefanie / Proß, Vanessa / Thole, Linda Marie Laura / He, An / Schrezenmeier, Eva Vanessa / Jechow, Katharina / Gold, Stefan M / Lukassen, Sören / Conrad, Christian / Kotsch, Katja

    JCI insight

    2024  Volume 9, Issue 4

    Abstract: Functional avidity is supposed to critically shape the quality of immune responses, thereby influencing host protection against infectious agents including SARS-CoV-2. Here we show that after human SARS-CoV-2 vaccination, a large portion of high-avidity ... ...

    Abstract Functional avidity is supposed to critically shape the quality of immune responses, thereby influencing host protection against infectious agents including SARS-CoV-2. Here we show that after human SARS-CoV-2 vaccination, a large portion of high-avidity spike-specific CD4+ T cells lost CD3 expression after in vitro activation. The CD3- subset was enriched for cytokine-positive cells, including elevated per-cell expression levels, and showed increased polyfunctionality. Assessment of key metabolic pathways by flow cytometry revealed that superior functionality was accompanied by a shift toward fatty acid synthesis at the expense of their oxidation, whereas glucose transport and glycolysis were similarly regulated in SARS-CoV-2-specific CD3- and CD3+ subsets. As opposed to their CD3+ counterparts, frequencies of vaccine-specific CD3- T cells positively correlated with both the size of the naive CD4+ T cell pool and vaccine-specific IgG levels. Moreover, their frequencies negatively correlated with advancing age and were impaired in patients under immunosuppressive therapy. Typical recall antigen-reactive T cells showed a comparable segregation into functionally and metabolically distinct CD3+ and CD3- subsets but were quantitatively maintained upon aging, likely due to earlier recruitment in life. In summary, our data identify CD3- T helper cells as correlates of high-quality immune responses that are impaired in at-risk populations.
    MeSH term(s) Humans ; Down-Regulation ; COVID-19 Vaccines ; COVID-19/prevention & control ; SARS-CoV-2 ; T-Lymphocytes, Helper-Inducer
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2024-01-11
    Publishing country United States
    Document type Journal Article
    ISSN 2379-3708
    ISSN (online) 2379-3708
    DOI 10.1172/jci.insight.166833
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: resVAE ensemble

    Foo Wei Ten / Dongsheng Yuan / Nabil Jabareen / Yin Jun Phua / Roland Eils / Sören Lukassen / Christian Conrad

    Frontiers in Cell and Developmental Biology, Vol

    Unsupervised identification of gene sets in multi-modal single-cell sequencing data using deep ensembles

    2023  Volume 11

    Abstract: Feature identification and manual inspection is currently still an integral part of biological data analysis in single-cell sequencing. Features such as expressed genes and open chromatin status are selectively studied in specific contexts, cell states ... ...

    Abstract Feature identification and manual inspection is currently still an integral part of biological data analysis in single-cell sequencing. Features such as expressed genes and open chromatin status are selectively studied in specific contexts, cell states or experimental conditions. While conventional analysis methods construct a relatively static view on gene candidates, artificial neural networks have been used to model their interactions after hierarchical gene regulatory networks. However, it is challenging to identify consistent features in this modeling process due to the inherently stochastic nature of these methods. Therefore, we propose using ensembles of autoencoders and subsequent rank aggregation to extract consensus features in a less biased manner. Here, we performed sequencing data analyses of different modalities either independently or simultaneously as well as with other analysis tools. Our resVAE ensemble method can successfully complement and find additional unbiased biological insights with minimal data processing or feature selection steps while giving a measurement of confidence, especially for models using stochastic or approximation algorithms. In addition, our method can also work with overlapping clustering identity assignment suitable for transitionary cell types or cell fates in comparison to most conventional tools.
    Keywords bioinformatics ; single-cell sequencing ; deep learning ; gene set analysis ; rank aggregation ; ensemble ; Biology (General) ; QH301-705.5
    Subject code 612 ; 004
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article: The glycolytic enzyme ALDOA and the exon junction complex protein RBM8A are regulators of ribosomal biogenesis.

    Schwarz, Jessica Denise / Lukassen, Sören / Bhandare, Pranjali / Eing, Lorenz / Snaebjörnsson, Marteinn Thor / García, Yiliam Cruz / Kisker, Jan Philipp / Schulze, Almut / Wolf, Elmar

    Frontiers in cell and developmental biology

    2022  Volume 10, Page(s) 954358

    Abstract: Cellular growth is a fundamental process of life and must be precisely controlled in multicellular organisms. Growth is crucially controlled by the number of functional ribosomes available in cells. The production of new ribosomes depends critically on ... ...

    Abstract Cellular growth is a fundamental process of life and must be precisely controlled in multicellular organisms. Growth is crucially controlled by the number of functional ribosomes available in cells. The production of new ribosomes depends critically on the activity of RNA polymerase (RNAP) II in addition to the activity of RNAP I and III, which produce ribosomal RNAs. Indeed, the expression of both, ribosomal proteins and proteins required for ribosome assembly (ribosomal biogenesis factors), is considered rate-limiting for ribosome synthesis. Here, we used genetic screening to identify novel transcriptional regulators of cell growth genes by fusing promoters from a ribosomal protein gene (
    Language English
    Publishing date 2022-09-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2022.954358
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Pharmacological Improvement of CFTR Function Rescues Airway Epithelial Homeostasis and Host Defense in Children with Cystic Fibrosis.

    Loske, Jennifer / Völler, Mirjam / Lukassen, Sören / Stahl, Mirjam / Thürmann, Loreen / Seegebarth, Anke / Röhmel, Jobst / Wisniewski, Sebastian / Messingschlager, Marey / Lorenz, Stephan / Klages, Sven / Eils, Roland / Lehmann, Irina / Mall, Marcus A / Graeber, Simon Y / Trump, Saskia

    American journal of respiratory and critical care medicine

    2024  

    Abstract: Rationale: Pharmacological improvement of CFTR function with elexacaftor/tezacaftor/ivacaftor (ETI) provides unprecedented improvements in lung function and other clinical outcomes to patients with cystic fibrosis (CF). However, ETI effects on impaired ... ...

    Abstract Rationale: Pharmacological improvement of CFTR function with elexacaftor/tezacaftor/ivacaftor (ETI) provides unprecedented improvements in lung function and other clinical outcomes to patients with cystic fibrosis (CF). However, ETI effects on impaired mucosal homeostasis and host defense at the molecular and cellular level in the airways of CF patients remain unknown.
    Objectives: To investigate effects of ETI on the transcriptiome of nasal epithelial and immune cells from children with CF at the single cell level.
    Methods: Nasal swabs from 13 children with CF and at least one
    Measurements and main results: Proportions of
    Conclusions: Pharmacological improvement of CFTR function improves innate mucosal immunity and reduces immune cell inflammatory responses in the upper airways of children with CF at the single cell level, highlighting the potential to restore epithelial homeostasis and host defense in CF airways by early initiation of ETI therapy. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).
    Language English
    Publishing date 2024-01-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202310-1836OC
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uh II Zs.80: Show issues Location:
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  9. Article ; Online: Single-cell RNA sequencing of adult mouse testes.

    Lukassen, Soeren / Bosch, Elisabeth / Ekici, Arif B / Winterpacht, Andreas

    Scientific data

    2018  Volume 5, Page(s) 180192

    Abstract: Spermatogenesis is an efficient and complex system of continuous cell differentiation. Previous studies investigating the transcriptomes of different cell populations in the testis relied either on sorting cells, cell depletion, or juvenile animals where ...

    Abstract Spermatogenesis is an efficient and complex system of continuous cell differentiation. Previous studies investigating the transcriptomes of different cell populations in the testis relied either on sorting cells, cell depletion, or juvenile animals where not all stages of spermatogenesis have been completed. We present single-cell RNA sequencing (scRNA-Seq) data of 2,500 cells from the testes of two 8-week-old C57Bl/6J mice. Our dataset includes all spermatogenic stages from preleptotene to condensing spermatids as well as individual spermatogonia, Sertoli and Leydig cells. The data capture the full continuity of the meiotic and postmeiotic stages of spermatogenesis, and is thus ideally suited for marker discovery, network inference and similar analyses for which temporal ordering of differentiation processes can be exploited. Furthermore, it can serve as a reference for future studies involving single-cell RNA-Seq in mice where spermatogenesis is perturbed.
    MeSH term(s) Animals ; Leydig Cells ; Male ; Mice ; Mice, Inbred C57BL ; RNA/biosynthesis ; Sequence Analysis, RNA ; Single-Cell Analysis ; Spermatids ; Spermatogenesis/genetics ; Spermatogonia ; Testis/cytology ; Testis/metabolism
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2018-09-11
    Publishing country England
    Document type Dataset ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2775191-0
    ISSN 2052-4463 ; 2052-4463
    ISSN (online) 2052-4463
    ISSN 2052-4463
    DOI 10.1038/sdata.2018.192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Lymphocyte Immune Response and T Cell Differentiation in Fontan Patients with protein-losing enteropathy.

    Moosmann, Julia / Toka, Okan / Lukassen, Sören / Ekici, Arif B / Mackensen, Andreas / Völkl, Simon / Dittrich, Sven

    The Thoracic and cardiovascular surgeon

    2021  Volume 69, Issue S 03, Page(s) e10–e20

    Abstract: Background: Protein-losing enteropathy (PLE) is a severe complication of the Fontan circulation. There is increasing discussion about whether lymphatic dysregulation is involved as pathomechanism of PLE. This investigation focuses on the interplay ... ...

    Abstract Background: Protein-losing enteropathy (PLE) is a severe complication of the Fontan circulation. There is increasing discussion about whether lymphatic dysregulation is involved as pathomechanism of PLE. This investigation focuses on the interplay between alteration of lymphatic cells and immunologic pathway alterations.
    Methods: Micro-ribonucleic acid (miRNA) expression profiling was performed in 49 patients (
    Results: miRNAs pathway analysis of Fontan patients with PLE revealed 20 significantly changed networks of which four of the ten largest were associated with immunologic processes. This finding is supported by significant T cell deficiency with decreased CD4+ count (
    Conclusion: PLE in Fontan patients is associated with severe lymphopenia, T cell deficiency, significant alterations of T cell differentiation, and increased Treg frequency reflecting an immune status of chronic inflammation and shortened protection against pathogens and autoimmunity. These cellular alterations seemed to be dysregulated by several miRNA controlled immunological pathways.
    MeSH term(s) Adolescent ; Animals ; Autoimmunity ; Case-Control Studies ; Cell Differentiation ; Child ; Child, Preschool ; Databases, Factual ; Female ; Fontan Procedure/adverse effects ; Gene Expression Profiling ; Gene Regulatory Networks ; Heart Defects, Congenital/surgery ; Humans ; Immunophenotyping ; Infant ; Lymphopenia/diagnosis ; Lymphopenia/genetics ; Lymphopenia/immunology ; Lymphopenia/microbiology ; Male ; Mice ; MicroRNAs/genetics ; Phenotype ; Protein-Losing Enteropathies/diagnosis ; Protein-Losing Enteropathies/genetics ; Protein-Losing Enteropathies/immunology ; T-Lymphocyte Subsets/immunology ; Transcriptome ; Treatment Outcome ; Young Adult
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2021-02-19
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 800050-5
    ISSN 1439-1902 ; 0171-6425 ; 0946-4778 ; 0172-6137
    ISSN (online) 1439-1902
    ISSN 0171-6425 ; 0946-4778 ; 0172-6137
    DOI 10.1055/s-0041-1723781
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Uk I Zs.186: Show issues Location:
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