Abstract
N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic ...characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing four different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared with parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
Graphical Abstract
Graphical Abstract
Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy, ...and seizures. NGLY1’s activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.
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•NGLY1 neurons develop ProteoStat-positive aggregates that can be partially rescued•Profiling protein aggregates unveils links to other neurodegenerative diseases•NGLY1 phenotypes appear to be predominantly observed in neurons
Manole et al. employ cutting-edge techniques including laser capture microscopy to scrutinize the protein aggregates accumulating in NGLY1-deficient neurons. Their study unveils a significant enrichment of specific proteins associated with neurodegenerative diseases, providing novel insights into the pathological mechanisms underlying NGLY1 deficiency and shedding light on potential therapeutic targets.
We describe a Database of Simulated Molecular Motions (DSMM). This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM ...is accessible via a webserver at: http://projects.villa-bosch.de/mcm/database/dsmm.
From the mid-nineteen sixties and into the mid-seventies, a significant number of women film and videomakers in the United States crafted experimental works that were simultaneously in dialogue with ...the concerns of the American avant-garde cinema and the (emergent) Second Wave feminist movement. Committed to both artistic innovation and political struggle, these women mediamakers often turned their cameras towards their own bodies in an attempt to perform both the female body and the experimental cinema as sites/sights of radical becoming. Their films and videos operate as convergences of these sites/sights: they invite interpretation, just as they resist easy categorization. Our Bodies, Our Cameras takes up their invitation, and through the investigation of thirty of these film and video texts created by over twenty different women, it re-thinks the history of American experimental cinema. Explicitly representing the female body with (formal and thematic) complexity, women experimental mediamakers of the sixties and seventies established this period as a time marked by and through the body. My project's historical parameters are constituted by this type of textual production—from Schneemann's Fuses in 1964 to Lisa Steele's Birthday Suit—with scars and defects in 1976. Importantly, these years take us through the rise of women's experimental filmmaking from a small sub-group within the sixties avant-garde to a larger, independent feminist film culture by the mid-seventies. Though my project sometimes draws from the personal histories of many of these women mediamakers, it is not an auteur study. Instead, it locates and interprets the strategies, pre-occupations, and themes that emerge across and among these women's texts. The individual chapters in Our Bodies, Our Cameras (1) flesh out the patterns of what I call "subjunctivity" in women's experimental "body" films and videos, (2) survey feminist mediamakers' on-screen negotiations of domesticity, (3) mine the intertextual relationships between women's avant-garde media projects and popular culture of the period, and (4) tune into and study the reverberations between Second and Third Wave feminist cinema.
Objective Inflammatory diseases of the aorta, other than those of known infective etiology, are poorly understood. We analyzed a large series of affected patients who had histologic diagnoses with a ...view to improving the classification of the extent of aortitis to enable a more targeted approach of treatment. Methods Between 1996 and 2012, we operated on 7551 patients with ascending or aortic arch disease, of whom 279 had clinically diagnosed inflammatory disease. Of these, 156 (2%) were found to have aortitis on histologic examination. Results Patients were divided into 4 histologically based groups: giant cell aortitis, 31% (49/156); Takayasu arteritis, 5.1% (8/156); isolated aortitis, 59% (92/156); and other, 4.5% (7/156). Patterns of anatomic extent were also analyzed, and in particular it was noted that giant cell aortitis and isolated aortitis had more extensive disease. In addition, specimen analysis suggested early indications of unrecognized preexistent infections. Death after surgery occurred in 3.2% (5/156), and stroke in 1.9% (3/156). Kaplan-Meier survival at 8 years was 55%. We present a classification for disease extent and management. Conclusions Aortitis continues to be a conundrum; however, good results are achievable with surgery. Intervention should be based on a clearer understanding of the histologic pattern and extent of disease, which helps in subsequent targeted disease management.
Objective
Noninfectious aortitis may occur in the context of a recognized systemic disease or as a topographically limited lesion without systemic features, which is called clinically isolated ...aortitis (CIA). This study was undertaken to better define and stress the limitations of this diagnostic category in a large population of patients in a single center dedicated to aortic diseases and to suggest recommendations for care.
Methods
Records of patients undergoing thoracic aortic surgery (1996–2012) at the Cleveland Clinic were reviewed to identify 196 patients with histopathologically proven aortitis. Clinical diagnoses (giant cell arteritis GCA, Takayasu arteritis TAK, CIA, or Other) were determined at the time of surgery. Clinical features, laboratory findings, and imaging results were recorded throughout the follow‐up period. At least 6 months of follow‐up data were available for 73 CIA patients.
Results
The mean age of the patients at time of surgery was 65.6 years (range 15–88 years); 67% of patients were female, and 90.3% were white. At the time of surgery, 129 patients (65.8%) met criteria for CIA, 42 (21.4%) for GCA, 14 (7.1%) for TAK, and 11 (5.6%) met criteria for other systemic inflammatory diseases. During a mean follow‐up period of 56.2 months, 19% of CIA patients developed new symptoms, 45% developed new radiographic vascular lesions, 40% underwent additional vascular surgery, and 12% died (n = 9). Eleven of 73 patients (15%) initially classified as having CIA developed features of a systemic disease, most often GCA.
Conclusion
The majority of patients (66%) with histopathologically proven aortitis have CIA at the time of surgery. CIA patients infrequently report new symptoms over time, but new vascular lesions requiring surgery commonly occur. Serial follow‐up including large vessel imaging is strongly advised for all aortitis patients.
Objective
Anti–topoisomerase I (anti–topo I) autoantibodies in systemic sclerosis (SSc) are associated with diffuse skin involvement and interstitial lung fibrosis. Thus far, however, the ...relationship between anti–topo I antibody response and disease course has not yet been fully evaluated. This study was undertaken to gain insight into the association between characteristics of the anti–topo I antibody response and clinical disease course in SSc patients positive for anti–topo I antibodies.
Methods
Levels of anti–topo I IgG, anti–topo I IgM, and anti–topo I IgA were assessed in consecutive serum samples obtained from patients at baseline who were positive for anti–topo I IgG in the Leiden Combined Care In Systemic Sclerosis (CCISS) cohort. One‐year disease progression was defined by a relevant increase in modified Rodnan skin thickness score (MRSS), decline in pulmonary function, development of digital ulcers, renal crisis, and pulmonary hypertension, and/or mortality. Validation was performed in SSc patients who were positive for anti–topo I from the Oslo University Hospital and University Hospital Zurich.
Results
Of the 103 patients with anti–topo I IgG in the CCISS cohort, clinical data were available to assess 1‐year disease progression in 81 patients. Of these 81 patients, 23 (28%) had disease progression. At baseline, patients with disease progression were significantly more often anti–topo I IgM–positive than those who did not experience disease progression (21 91% of 23 versus 33 57% of 58; P < 0.01). This finding was confirmed in the independent validation samples.
Conclusion
In SSc patients who were anti–topo I IgG–positive, presence of anti–topo I IgM, which might be considered as a surrogate for an ongoing autoreactive B cell immune response, is associated with disease progression.
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