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Search Results for all work with filters:

  • complex
  • protein

Work 1-10 of 86

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Article

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies

by Bo Yuan; Juanita Neira Fresneda; Davut Pehlivan; Teresa Santiago-Sim; Xiaofei Song; Jill Rosenfeld; Jennifer E. Posey; Vipulkumar Patel; Weihong Jin; Margaret P. Adam; Emma L. Baple; John Dean; Chin-To Fong; Scott E. Hickey; Louanne Hudgins; Eyby Leon; Suneeta Madan-Khetarpal; Lettie Rawlins; Cecilie F. Rustad; Asbjorg Stray-Pedersen; Kristian Tveten; Olivia Wenger; Jullianne Diaz; Laura Jenkins; Laura Martin; Marianne McGuire; Marguerite Pietryga; Linda Ramsdell; Leah Slattery; Farida Abid; Alison Bertuch; Dorothy Grange; LaDonna Immken; Christian P Schaaf; Hilde Van Esch; Weimin Bi; Sau Wai Cheung; Amy M. Breman; Janice L. Smith; Chad Shaw; Andrew H. Crosby; Christine Eng; Yaping Yang; James R. Lupski; Rui Xiao; Pengfei Liu

2019

Subjects
  • Biology, Genetics
  • Biology, Molecular
  • File Download
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Abstract:Close

Purpose: Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective. Methods: We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization. Results: Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS. Conclusion: CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.

Article

ARF GTPases and their GEFs and GAPs: concepts and challenges

by Elizabeth Sztul; Pei-Wen Chen; James E. Casanova; Jacqueline Cherfils; Joel B. Decks; David G. Lambright; Fang-Jen S. Lee; Paul A. Randazzo; Lorraine C. Santy; Annette Schuermann; Ilka Wilhelmi; Marielle E. Yohe; Richard A Kahn

2019

Subjects
  • Chemistry, Biochemistry
  • Biology, Cell
  • File Download
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Abstract:Close

German Institute of Human Nutrition Detailed structural, biochemical, cell biological, and genetic studies of any gene/ protein are required to develop models of its actions in cells. Studying a protein family in the aggregate yields additional information, as one can include analyses of their coevolution, acquisition or loss of functionalities, structural pliability, and the emergence of shared or variations in molecular mechanisms. An even richer understanding of cell biology can be achieved through evaluating functionally linked protein families. In this review, we summarize current knowledge of three protein families: the ARF GTPases, the guanine nucleotide exchange factors (ARF GEFs) that activate them, and the GTPase-activating proteins (ARF GAPs) that have the ability to both propagate and terminate signaling. However, despite decades of scrutiny, our understanding of how these essential proteins function in cells remains fragmentary. We believe that the inherent complexity of ARF signaling and its regulation by GEFs and GAPs will require the concerted effort of many laboratories working together, ideally within a consortium to optimally pool information and resources. The collaborative study of these three functionally connected families (≥70 mammalian genes) will yield transformative insights into regulation of cell signaling.

Article

Neuroepigenetic mechanisms in disease

by Michael A. Christopher; Stephanie M. Kyle; David J Katz

2017

Subjects
  • Biology, Cell
  • Biology, Molecular
  • Biology, General
  • File Download
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Abstract:Close

Epigenetics allows for the inheritance of information in cellular lineages during differentiation, independent of changes to the underlying genetic sequence. This raises the question of whether epigenetic mechanisms also function in post-mitotic neurons. During the long life of the neuron, fluctuations in gene expression allow the cell to pass through stages of differentiation, modulate synaptic activity in response to environmental cues, and fortify the cell through age-related neuroprotective pathways. Emerging evidence suggests that epigenetic mechanisms such as DNA methylation and histone modification permit these dynamic changes in gene expression throughout the life of a neuron. Accordingly, recent studies have revealed the vital importance of epigenetic players in the central nervous system and during neurodegeneration. Here, we provide a review of several of these recent findings, highlighting novel functions for epigenetics in the fields of Rett syndrome, Fragile X syndrome, and Alzheimer's disease research. Together, these discoveries underscore the vital importance of epigenetics in human neurological disorders.

Article

In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer

by Caitlin L. Grzeskowiak; Samrat T. Kundu; Xiulei Mo; Andrey Andreyevich Ivanov; Oksana Zagorodna; Hengyu Lu; Richard H. Chapple; Yiu Huen Tsang; Daniela Moreno; Maribel Mosqueda; Karina Eterovic; Jared J. Fradette; Sumreen Ahmad; Femgju Chen; Zechen Chong; Ken Chen; Chad J. Creighton; Haian Fu; Gordan B. Mills; Don L. Gibbons; Kenneth L. Scott

2018

Subjects
  • Health Sciences, Oncology
  • Biology, Molecular
  • File Download
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Abstract:Close

Genetic aberrations driving pro-oncogenic and pro-metastatic activity remain an elusive target in the quest of precision oncology. To identify such drivers, we use an animal model of KRAS-mutant lung adenocarcinoma to perform an in vivo functional screen of 217 genetic aberrations selected from lung cancer genomics datasets. We identify 28 genes whose expression promoted tumor metastasis to the lung in mice. We employ two tools for examining the KRAS-dependence of genes identified from our screen: 1) a human lung cell model containing a regulatable mutant KRAS allele and 2) a lentiviral system permitting co-expression of DNA-barcoded cDNAs with Cre recombinase to activate a mutant KRAS allele in the lungs of mice. Mechanistic evaluation of one gene, GATAD2B, illuminates its role as a dual activity gene, promoting both pro-tumorigenic and pro-metastatic activities in KRAS-mutant lung cancer through interaction with c-MYC and hyperactivation of the c-MYC pathway.

Article

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket

by Pierrick Craveur; Anna T. Gres; Karen Kirby; Dandan Liu; John A. Hammond; Yisong Deng; Stefano Forli; David S. Goodsell; James R. Williamson; Stefan Sarafianos; Arthur J. Olson

2019

Subjects
  • Health Sciences, Public Health
  • Biology, Microbiology
  • Biology, Molecular
  • File Download
  • View Abstract

Abstract:Close

HIV-1 capsid protein (CA) plays critical roles in both early and late stages of the viral replication cycle. Mutagenesis and structural experiments have revealed that capsid core stability significantly affects uncoating and initiation of reverse transcription in host cells. This has led to efforts in developing antivirals targeting CA and its assembly, although none of the currently identified compounds are used in the clinic for treatment of HIV infection. A specific interaction that is primarily present in pentameric interfaces in the HIV-1 capsid core was identified and is reported to be important for CA assembly. This is shown by multidisciplinary characterization of CA site-directed mutants using biochemical analysis of virus-like particle formation, transmission electron microscopy of in vitro assembly, crystallographic studies, and molecular dynamic simulations. The data are consistent with a model where a hydrogen bond between CA residues E28 and K30= from neighboring N-terminal domains (CA NTD s) is important for CA pentamer interactions during core assembly. This pentamer-preferred interaction forms part of an N-terminal domain interface (NDI) pocket that is amenable to antiviral targeting.

Article

Gab2 and Gab3 Redundantly Suppress Colitis by Modulating Macrophage and CD8(+) T-Cell Activation

by Zhengqi Wang; Tamisha Y. Vaughan; Wandi Zhu; Yuhong Chen; Guoping Fu; Magdalena Medrzycki; Hikaru Nishio; Silvia Bunting; Pamela A. Hankey-Giblin; Asma Nusrat; Charles A. Parkos; Renren Wen; Kevin Bunting

2019

Subjects
  • Health Sciences, Pathology
  • Health Sciences, Immunology
  • File Download
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Abstract:Close

Inflammatory Bowel Disease (IBD) is a multi-factorial chronic inflammation of the gastrointestinal tract prognostically linked to CD8+ T-cells, but little is known about their mechanism of activation during initiation of colitis. Here, Grb2-associated binding 2/3 adaptor protein double knockout mice (Gab2/3-/-) were generated. Gab2/3-/- mice, but not single knockout mice, developed spontaneous colitis. To analyze the cellular mechanism, reciprocal bone marrow (BM) transplantation demonstrated a Gab2/3-/- hematopoietic disease-initiating process. Adoptive transfer showed individual roles for macrophages and T-cells in promoting colitis development in vivo. In spontaneous disease, intestinal intraepithelial CD8+ but much fewer CD4+, T-cells from Gab2/3-/- mice with rectal prolapse were more proliferative. To analyze the molecular mechanism, reduced PI3-kinase/Akt/mTORC1 was observed in macrophages and T-cells, with interleukin (IL)-2 stimulated T-cells showing increased pSTAT5. These results illustrate the importance of Gab2/3 collectively in signaling responses required to control macrophage and CD8+ T-cell activation and suppress chronic colitis.

Article

Spatial targeting of type II protein kinase A to filopodia mediates the regulation of growth cone guidance by cAMP

by Jianzhong Han; Liang Han; Priyanka Tiwari; Zhexing Wen; James Zheng

2007

Subjects
  • Biology, Cell
  • Biology, Neuroscience
  • File Download
  • View Abstract

Abstract:Close

The second messenger cyclic adenosine monophosphate (cAMP) plays a pivotal role in axonal growth and guidance, but its downstream mechanisms remain elusive. In this study, we report that type II protein kinase A (PKA) is highly enriched in growth cone filopodia, and this spatial localization enables the coupling of cAMP signaling to its specific effectors to regulate guidance responses. Disrupting the localization of PKA to filopodia impairs cAMP-mediated growth cone attraction and prevents the switching of repulsive responses to attraction by elevated cAMP. Our data further show that PKA targets protein phosphatase-1 (PP1) through the phosphorylation of a regulatory protein inhibitor-1 (I-1) to promote growth cone attraction. Finally, we find that I-1 and PP1 mediate growth cone repulsion induced by myelin-associated glycoprotein. These findings demonstrate that the spatial localization of type II PKA to growth cone filopodia plays an important role in the regulation of growth cone motility and guidance by cAMP.

Article

The Morphology and Assembly of Respiratory Syncytial Virus Revealed by Cryo-Electron Tomography

by Zunlong Ke; Rebecca S. Dillard; Tatiana Chirkova; Fredrick Leon; Christopher C. Stobart; Cheri M. Hampton; Joshua D. Strauss; Devi Rajan; Christina Rostad; Jeannette V. Taylor; Hong Yi; Raven Shah; Mengtian Jin; Tina V. Hartert; R. Stokes Peebles; Barney S. Graham; Martin L Moore; Larry J Anderson; Elizabeth R. Wright

2018

Subjects
  • Health Sciences, Pathology
  • Biology, Virology
  • File Download
  • View Abstract

Abstract:Close

Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract disease in young children. With repeat infections throughout life, it can also cause substantial disease in the elderly and in adults with compromised cardiac, pulmonary and immune systems. RSV is a pleomorphic enveloped RNA virus in the Pneumoviridae family. Recently, the three-dimensional (3D) structure of purified RSV particles has been elucidated, revealing three distinct morphological categories: spherical, asymmetric, and filamentous. However, the native 3D structure of RSV particles associated with or released from infected cells has yet to be investigated. In this study, we have established an optimized system for studying RSV structure by imaging RSV-infected cells on transmission electron microscopy (TEM) grids by cryo-electron tomography (cryo-ET). Our results demonstrate that RSV is filamentous across several virus strains and cell lines by cryo-ET, cryo-immuno EM, and thin section TEM techniques. The viral filament length varies from 0.5 to 12 μm and the average filament diameter is approximately 130 nm. Taking advantage of the whole cell tomography technique, we have resolved various stages of RSV assembly. Collectively, our results can facilitate the understanding of viral morphogenesis in RSV and other pleomorphic enveloped viruses.

Article

Epigenetic Regulations in Neuropsychiatric Disorders

by Janise N. Kuehner; Emily C. Bruggeman; Zhexing Wen; Bing Yao

2019

Subjects
  • Health Sciences, Mental Health
  • Biology, Genetics
  • Biology, Neuroscience
  • File Download
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Abstract:Close

Precise genetic and epigenetic spatiotemporal regulation of gene expression is critical for proper brain development, function and circuitry formation in the mammalian central nervous system. Neuronal differentiation processes are tightly regulated by epigenetic mechanisms including DNA methylation, histone modifications, chromatin remodelers and non-coding RNAs. Dysregulation of any of these pathways is detrimental to normal neuronal development and functions, which can result in devastating neuropsychiatric disorders, such as depression, schizophrenia and autism spectrum disorders. In this review, we focus on the current understanding of epigenetic regulations in brain development and functions, as well as their implications in neuropsychiatric disorders.

Article

Defective mitochondrial peroxiredoxin-3 results in sensitivity to oxidative stress in Fanconi anemia

by Sudit S. Mukhopadhyay; Kathryn Leung; M. John Hicks; Philip J. Hastings; Hagop Youssoufian; Sharon E. Plon

2006

Subjects
  • Biology, Cell
  • Biology, Genetics
  • File Download
  • View Abstract

Abstract:Close

Cells from patients with Fanconi anemia (FA), an inherited disorder that includes bone marrow failure and cancer predisposition, have increased sensitivity to oxidative stress through an unknown mechanism. We demonstrate that the FA group G (FANCG) protein is found in mitochondria. Wild-type but not G546R mutant FANCG physically interacts with the mitochondrial peroxidase peroxiredoxin-3 (PRDX3). PRDX3 is deregulated in FA cells, including cleavage by a calpainlike cysteine protease and mislocalization. FA-G cells demonstrate distorted mitochondrial structures, and mitochondrial extracts have a sevenfold decrease in thioredoxin-dependent peroxidase activity. Transient overexpression of PRDX3 suppresses the sensitivity of FA-G cells to H2O2, and decreased PRDX3 expression increases sensitivity to mitomycin C. Cells from the FA-A and -C subtypes also have PRDX3 cleavage and decreased peroxidase activity. This study demonstrates a role for the FA proteins in mitochondria witsh sensitivity to oxidative stress resulting from diminished peroxidase activity. These defects may lead to apoptosis and the accumulation of oxidative DNA damage in bone marrow precursors.
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