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  1. Article ; Online: A novel VPS13B mutation in Cohen syndrome

    Sara Momtazmanesh / Elham Rayzan / Sepideh Shahkarami / Meino Rohlfs / Christoph Klein / Nima Rezaei

    BMC Medical Genetics, Vol 21, Iss 1, Pp 1-

    a case report and review of literature

    2020  Volume 6

    Abstract: Abstract Background Cohen syndrome, an autosomal recessive syndrome, is a rare syndrome with diverse clinical manifestations including failure to thrive, hypotonia, hypermobile joints, microcephaly, intellectual disabilities, craniofacial and limb ... ...

    Abstract Abstract Background Cohen syndrome, an autosomal recessive syndrome, is a rare syndrome with diverse clinical manifestations including failure to thrive, hypotonia, hypermobile joints, microcephaly, intellectual disabilities, craniofacial and limb anomalies, neutropenia and a friendly character. It is associated with mutations of the vacuolar protein sorting 13 homolog B (VPS13B) gene, which is involved in the development of the ocular, hematological and central nervous systems. This gene encodes a transmembrane protein playing a crucial role in preserving the integrity of the Golgi complex. To date, more than 150 mutations of VPS13B have been reported in over 200 Cohen syndrome patients. Missense or nonsense mutations are the most common mutations. Case presentation A 4-year-old girl, born to consanguineous parents, was referred to the pediatric clinical immunology outpatient clinic for investigation of recurrent neutropenia with a history of recurrent infections in the past year. On physical examination, she had the characteristic facial features of Cohen syndrome, developmental delay and speech disorder. She had a cheerful disposition, and her mother gave a history of feeding difficulties in her first months of life. She did not present any ophthalmologic or cardiac abnormalities. Her lab results revealed moderate neutropenia. Serum IgG, IgM, IgA and IgE levels were normal. She fulfilled the clinical diagnostic criteria for Cohen syndrome. WES revealed a novel homozygous frameshift variant in VPS13B (LRG_351t1: c.7095del; p.Ser2366AlafsTer49). Currently, she is not experiencing any severe problem, and she undergoes irregular medical treatment once her neutrophil count decreases under the normal limit. Her verbal and motor abilities have improved as a result of speech and occupational therapies. Conclusion We reported a novel homozygous frameshift variant in VPS13B (LRG_351t1: c.7095del; p.Ser2366AlafsTer49) in a 4-year-old girl with Cohen syndrome. Cohen syndrome should be considered in differential diagnosis of any child with intellectual disability and neutropenia.
    Keywords Cohen syndrome ; Neutropenia ; Frameshift mutation ; Vesicular transport proteins ; VPS13B protein ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
    Subject code 610
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: SmartPhase

    Paul Hager / Hans-Werner Mewes / Meino Rohlfs / Christoph Klein / Tim Jeske

    PLoS Computational Biology, Vol 16, Iss 2, p e

    Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases.

    2020  Volume 1007613

    Abstract: There is an increasing need to use genome and transcriptome sequencing to genetically diagnose patients suffering from suspected monogenic rare diseases. The proper detection of compound heterozygous variant combinations as disease-causing candidates is ... ...

    Abstract There is an increasing need to use genome and transcriptome sequencing to genetically diagnose patients suffering from suspected monogenic rare diseases. The proper detection of compound heterozygous variant combinations as disease-causing candidates is a challenge in diagnostic workflows as haplotype information is lost by currently used next-generation sequencing technologies. Consequently, computational tools are required to phase, or resolve the haplotype of, the high number of heterozygous variants in the exome or genome of each patient. Here we present SmartPhase, a phasing tool designed to efficiently reduce the set of potential compound heterozygous variant pairs in genetic diagnoses pipelines. The phasing algorithm of SmartPhase creates haplotypes using both parental genotype information and reads generated by DNA or RNA sequencing and is thus well suited to resolve the phase of rare variants. To inform the user about the reliability of a phasing prediction, it computes a confidence score which is essential to select error-free predictions. It incorporates existing haplotype information and applies logical rules to determine variants that can be excluded as causing a recessive, monogenic disease. SmartPhase can phase either all possible variant pairs in predefined genetic loci or preselected variant pairs of interest, thus keeping the focus on clinically relevant results. We compared SmartPhase to WhatsHap, one of the leading comparable phasing tools, using simulated data and a real clinical cohort of 921 patients. On both data sets, SmartPhase generated error-free predictions using our derived confidence score threshold. It outperformed WhatsHap with regard to the percentage of resolved pairs when parental genotype information is available. On the cohort data, SmartPhase enabled on average the exclusion of approximately 22% of the input variant pairs in each singleton patient and 44% in each trio patient. SmartPhase is implemented as an open-source Java tool and freely available at ...
    Keywords Biology (General) ; QH301-705.5
    Subject code 616
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Valosin-containing protein-regulated endoplasmic reticulum stress causes NOD2-dependent inflammatory responses

    Maryam Ghalandary / Yue Li / Thomas Fröhlich / Thomas Magg / Yanshan Liu / Meino Rohlfs / Sebastian Hollizeck / Raffaele Conca / Tobias Schwerd / Holm H. Uhlig / Philip Bufler / Sibylle Koletzko / Aleixo M. Muise / Scott B. Snapper / Fabian Hauck / Christoph Klein / Daniel Kotlarz

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 12

    Abstract: Abstract NOD2 polymorphisms may affect sensing of the bacterial muramyl dipeptide (MDP) and trigger perturbed inflammatory responses. Genetic screening of a patient with immunodeficiency and enteropathy revealed a rare homozygous missense mutation in the ...

    Abstract Abstract NOD2 polymorphisms may affect sensing of the bacterial muramyl dipeptide (MDP) and trigger perturbed inflammatory responses. Genetic screening of a patient with immunodeficiency and enteropathy revealed a rare homozygous missense mutation in the first CARD domain of NOD2 (ENST00000300589; c.160G > A, p.E54K). Biochemical assays confirmed impaired NOD2-dependent signaling and proinflammatory cytokine production in patient’s cells and heterologous cellular models with overexpression of the NOD2 mutant. Immunoprecipitation-coupled mass spectrometry unveiled the ATPase valosin-containing protein (VCP) as novel interaction partner of wildtype NOD2, while the binding to the NOD2 variant p.E54K was abrogated. Knockdown of VCP in coloncarcinoma cells led to impaired NF-κB activity and IL8 expression upon MDP stimulation. In contrast, tunicamycin-induced ER stress resulted in increased IL8, CXCL1, and CXCL2 production in cells with knockdown of VCP, while enhanced expression of these proinflammatory molecules was abolished upon knockout of NOD2. Taken together, these data suggest that VCP-mediated inflammatory responses upon ER stress are NOD2-dependent.
    Keywords Medicine ; R ; Science ; Q
    Subject code 571
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Author Correction

    Marcin Łyszkiewicz / Natalia Ziętara / Laura Frey / Ulrich Pannicke / Marcel Stern / Yanshan Liu / Yanxin Fan / Jacek Puchałka / Sebastian Hollizeck / Ido Somekh / Meino Rohlfs / Tuğba Yilmaz / Ekrem Ünal / Musa Karakukcu / Türkan Patiroğlu / Christina Kellerer / Ebru Karasu / Karl-Walter Sykora / Atar Lev /
    Amos Simon / Raz Somech / Joachim Roesler / Manfred Hoenig / Oliver T. Keppler / Klaus Schwarz / Christoph Klein

    Nature Communications, Vol 11, Iss 1, Pp 1-

    Human FCHO1 deficiency reveals role for clathrin-mediated endocytosis in development and function of T cells

    2020  Volume 1

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Keywords Science ; Q
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Author Correction

    Marcin Łyszkiewicz / Natalia Ziętara / Laura Frey / Ulrich Pannicke / Marcel Stern / Yanshan Liu / Yanxin Fan / Jacek Puchałka / Sebastian Hollizeck / Ido Somekh / Meino Rohlfs / Tuğba Yilmaz / Ekrem Ünal / Musa Karakukcu / Türkan Patiroğlu / Christina Kellerer / Ebru Karasu / Karl-Walter Sykora / Atar Lev /
    Amos Simon / Raz Somech / Joachim Roesler / Manfred Hoenig / Oliver T. Keppler / Klaus Schwarz / Christoph Klein

    Nature Communications, Vol 11, Iss 1, Pp 1-

    Human FCHO1 deficiency reveals role for clathrin-mediated endocytosis in development and function of T cells

    2020  Volume 1

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Keywords Science ; Q
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Human FCHO1 deficiency reveals role for clathrin-mediated endocytosis in development and function of T cells

    Marcin Łyszkiewicz / Natalia Ziętara / Laura Frey / Ulrich Pannicke / Marcel Stern / Yanshan Liu / Yanxin Fan / Jacek Puchałka / Sebastian Hollizeck / Ido Somekh / Meino Rohlfs / Tuğba Yilmaz / Ekrem Ünal / Musa Karakukcu / Türkan Patiroğlu / Christina Kellerer / Ebru Karasu / Karl-Walter Sykora / Atar Lev /
    Amos Simon / Raz Somech / Joachim Roesler / Manfred Hoenig / Oliver T. Keppler / Klaus Schwarz / Christoph Klein

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 15

    Abstract: FCH domain only 1 (FCHO1) is a key molecule involved in clathrin-mediated endocytosis (CME). Here, the authors report homozygous FCHO1 mutations in individuals with variable T and B cell lymphopenia, which are associated with loss-of-function of FCHO1 ... ...

    Abstract FCH domain only 1 (FCHO1) is a key molecule involved in clathrin-mediated endocytosis (CME). Here, the authors report homozygous FCHO1 mutations in individuals with variable T and B cell lymphopenia, which are associated with loss-of-function of FCHO1 and impaired formation of clathrin-coated pits in T cells.
    Keywords Science ; Q
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms.

    Jayabalan M Joseph / Petra Fey / Nagendran Ramalingam / Xiao I Liu / Meino Rohlfs / Angelika A Noegel / Annette Müller-Taubenberger / Gernot Glöckner / Michael Schleicher

    PLoS ONE, Vol 3, Iss 7, p e

    2008  Volume 2654

    Abstract: Actin belongs to the most abundant proteins in eukaryotic cells which harbor usually many conventional actin isoforms as well as actin-related proteins (Arps). To get an overview over the sometimes confusing multitude of actins and Arps, we analyzed the ... ...

    Abstract Actin belongs to the most abundant proteins in eukaryotic cells which harbor usually many conventional actin isoforms as well as actin-related proteins (Arps). To get an overview over the sometimes confusing multitude of actins and Arps, we analyzed the Dictyostelium discoideum actinome in detail and compared it with the genomes from other model organisms. The D. discoideum actinome comprises 41 actins and actin-related proteins. The genome contains 17 actin genes which most likely arose from consecutive gene duplications, are all active, in some cases developmentally regulated and coding for identical proteins (Act8-group). According to published data, the actin fraction in a D. discoideum cell consists of more than 95% of these Act8-type proteins. The other 16 actin isoforms contain a conventional actin motif profile as well but differ in their protein sequences. Seven actin genes are potential pseudogenes. A homology search of the human genome using the most typical D. discoideum actin (Act8) as query sequence finds the major actin isoforms such as cytoplasmic beta-actin as best hit. This suggests that the Act8-group represents a nearly perfect actin throughout evolution. Interestingly, limited data from D. fasciculatum, a more ancient member among the social amoebae, show different relationships between conventional actins. The Act8-type isoform is most conserved throughout evolution. Modeling of the putative structures suggests that the majority of the actin-related proteins is functionally unrelated to canonical actin. The data suggest that the other actin variants are not necessary for the cytoskeleton itself but rather regulators of its dynamical features or subunits in larger protein complexes.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2008-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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