Abstract
ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. ...Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/.
Graphical Abstract
Graphical Abstract
ProteoVision is a webserver designed to visualize phylogenetic, structural, and physicochemical properties of proteins by integration of four mutually synchronized applets that visually represent map data for each amino-acid simultaneously on levels of a (i) multiple sequence alignment; (ii) secondary structure; (iii) 3D structure and (iv) frequency box plot graph.
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•RiboVision2 is aimed to visualize phylogenetic and structural data about ribosomes.•It enables saving of RNA visualizations as publication-quality images.•This tool supports ...visualization of any RNA molecule in the User-upload mode.•RiboVision2 represents a major upgrade of the original RiboVision.
RiboVision2 is a web server designed to visualize phylogenetic, structural, and evolutionary properties of ribosomal RNAs simultaneously at the levels of primary, secondary, and three-dimensional structure and in the context of full ribosomal complexes. RiboVision2 instantly computes and displays a broad variety of data; it has no login requirements, is open-source, free for all users, and available at https://ribovision2.chemistry.gatech.edu.
Frontotemporal dementia and amyotrophic lateral sclerosis are clinically and pathologically overlapping disorders with shared genetic causes. We previously identified a disease locus on chromosome ...16p12.1-q12.2 with genome-wide significant linkage in a large European Australian family with autosomal dominant inheritance of frontotemporal dementia and amyotrophic lateral sclerosis and no mutation in known amyotrophic lateral sclerosis or dementia genes. Here we demonstrate the segregation of a novel missense variant in CYLD (c.2155A>G, p.M719V) within the linkage region as the genetic cause of disease in this family. Immunohistochemical analysis of brain tissue from two CYLD p.M719V mutation carriers showed widespread glial CYLD immunoreactivity. Primary mouse neurons transfected with CYLDM719V exhibited increased cytoplasmic localization of TDP-43 and shortened axons. CYLD encodes a lysine 63 deubiquitinase and CYLD cutaneous syndrome, a skin tumour disorder, is caused by mutations that lead to reduced deubiquitinase activity. In contrast with CYLD cutaneous syndrome-causative mutations, CYLDM719V exhibited significantly increased lysine 63 deubiquitinase activity relative to the wild-type enzyme (paired Wilcoxon signed-rank test P = 0.005). Overexpression of CYLDM719V in HEK293 cells led to more potent inhibition of the cell signalling molecule NF-κB and impairment of autophagosome fusion to lysosomes, a key process in autophagy. Although CYLD mutations appear to be rare, CYLD's interaction with at least three other proteins encoded by frontotemporal dementia and/or amyotrophic lateral sclerosis genes (TBK1, OPTN and SQSTM1) suggests that it may play a central role in the pathogenesis of these disorders. Mutations in several frontotemporal dementia and amyotrophic lateral sclerosis genes, including TBK1, OPTN and SQSTM1, result in a loss of autophagy function. We show here that increased CYLD activity also reduces autophagy function, highlighting the importance of autophagy regulation in the pathogenesis of frontotemporal dementia and amyotrophic lateral sclerosis.
Mutations that perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7833 probands with developmental disorders (DDs) and their unaffected ...parents, as well as more than 60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice sites and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects, and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. By using mutational burden analyses in this large cohort of proband-parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking noncanonical positions (27%), and calculate the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at noncanonical positions in splice sites. We estimate 35%-40% of pathogenic variants in noncanonical splice site positions are missing from public databases.
Heterogeneity in reported outcomes can limit the synthesis of research evidence. A core outcome set informs what outcomes are important and should be measured as a minimum in all future studies. We ...report the development of a core outcome set applicable to observational and interventional studies of pregnant women with multimorbidity.
We developed the core outcome set in four stages: (i) a systematic literature search, (ii) three focus groups with UK stakeholders, (iii) two rounds of Delphi surveys with international stakeholders and (iv) two international virtual consensus meetings. Stakeholders included women with multimorbidity and experience of pregnancy in the last 5 years, or are planning a pregnancy, their partners, health or social care professionals and researchers. Study adverts were shared through stakeholder charities and organisations.
Twenty-six studies were included in the systematic literature search (2017 to 2021) reporting 185 outcomes. Thematic analysis of the focus groups added a further 28 outcomes. Two hundred and nine stakeholders completed the first Delphi survey. One hundred and sixteen stakeholders completed the second Delphi survey where 45 outcomes reached Consensus In (≥70% of all participants rating an outcome as Critically Important). Thirteen stakeholders reviewed 15 Borderline outcomes in the first consensus meeting and included seven additional outcomes. Seventeen stakeholders reviewed these 52 outcomes in a second consensus meeting, the threshold was ≥80% of all participants voting for inclusion. The final core outcome set included 11 outcomes. The five maternal outcomes were as follows: maternal death, severe maternal morbidity, change in existing long-term conditions (physical and mental), quality and experience of care and development of new mental health conditions. The six child outcomes were as follows: survival of baby, gestational age at birth, neurodevelopmental conditions/impairment, quality of life, birth weight and separation of baby from mother for health care needs.
Multimorbidity in pregnancy is a new and complex clinical research area. Following a rigorous process, this complexity was meaningfully reduced to a core outcome set that balances the views of a diverse stakeholder group.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
BackgroundT cell therapies offer a promising, targeted approach for patients with relapsed/refractory (r/r) solid tumors. Patient-derived multi tumor-associated antigen-specific T cell (TAA-T) ...products targeting WT1, PRAME, and survivin have been safely administered to patients with r/r disease with disease stabilization but no objective clinical responses. Lymphodepleting chemotherapy (LD) prior to therapy with chimeric antigen receptor (CAR) T cell and tumor-infiltrating lymphocyte (TIL) products has been necessary for efficacy. We hypothesized that TAA-T treatment is enhanced using LD pre TAA-T by promoting homeostatic lymphoproliferation, altering the tumor microenvironment, and increasing TAA-T persistence in vivo.MethodsTAA-T products were administered after LD (cyclophosphamide and fludarabine) at recommended dose level (4 x 107/m2/dose) with repeat doses without LD in the absence of disease progression. Clinical and immunobiological studies were performed using TCR sequencing, flow cytometry and IFNy ELISpot assays to assess immunologic and anti-tumor responses.ResultsTAA-T products were generated from 9 patients (age range 5–38 years) with r/r solid tumors with a median of 2 (range 1–8) infusions per patient without therapy-related severe adverse events. 7 of 9 patients achieved disease stabilization for a median of 3+ months (range 1.4–23.4+) with no objective clinical responses (figure 1). Compared to patients who received TAA-T without LD, there was greater expansion of TAA-T product-derived TCR clonotypes in vivo (figure 2). Conversely, patients who received TAA-T products following LD demonstrated less antigen spreading with a reduced IFNy response (mean pre-infusion 6 IFNy SFC/1e5 cells, range 0–61, and mean post-infusion 42 IFNy SFC/1e5 cells, range 3–132) compared to patients who received TAA-T products alone (mean pre-infusion 21 IFNy SFC/1e5 cells, range 0–82, and mean post-infusion 66 IFNy SFC/1e5 cells, range 0–270) (figure 3). Investigation of circulating cytokines in patients post LD and TAA-T product infusion showed elevated levels of IL-8 in patients with disease progression.ConclusionsLD with TAA-T was well-tolerated with enhanced TAA-T expansion in vivo. However, the blunted antigen spreading response as well as product-related factors could explain the lack of objective clinical responses. As seen in previous patients, elevated IL-8 was correlated with disease progression representing a potential biomarker for future study. Other future directions will seek to investigate strategies to enhance product potency including using third-party, healthy donor derived, partially HLA-matched TAA-T as an off-the-shelf therapy (NCT05238792) and gene modification to sink IL-8 from the tumor microenvironment.AcknowledgementsWe acknowledge the support of the Department of Defense Peer Reviewed Cancer Research Program Career Development Award.Ethics ApprovalInformed consent was obtained from patients meeting standard eligibility requirements including performance status and organ function parameters prior to cell procurement and TAA-T infusion. This study was approved by the US Food and Drug Administration (IND 16135) and Children’s National Hospital Institutional Review Board (NCT02789228).Abstract 612 Figure 1(A) Patients received multiple TAA-T infusions safely on dose escalation phase (B) Patients with WT on expansion cohort received TAA-T infusions safely with LD on dose level 3. Patients received median 2 (range1–8) infusions per patient. OS: osteosarcoma; WT: Wilms tumor; NB: neuroblastoma; STS; soft tissue sarcoma; ES: Ewing sarcoma; RMS: rhabdomyososarcoma; Data censored at January 1, 2023Abstract 612 Figure 2Greater expansion of product-derived clonotypes in a patient following LD prior to TAA-T administration (right) compared to a patient who received TAA-T product without LD (left), supporting T-cell persistence, expansionAbstract 612 Figure 3Antigen spreading in patients without LD (A) and preserved with LD but blunted (B)
The aim of this study was to define the frequency and associated clinical phenotype of anti-MDA5 autoantibodies in a large UK based, predominantly Caucasian, cohort of patients with juvenile ...dermatomyositis (JDM).
Serum samples and clinical data were obtained from 285 patients with JDM recruited to the UK Juvenile Dermatomyositis Cohort and Biomarker Study. The presence of anti-MDA5 antibodies was determined by immunoprecipitation and confirmed by ELISA using recombinant MDA5 protein. Results were compared with matched clinical data, muscle biopsies (scored by an experienced paediatric neuropathologist) and chest imaging (reviewed by an experienced paediatric radiologist).
Anti-MDA5 antibodies were identified in 7.4% of JDM patients and were associated with a distinct clinical phenotype including skin ulceration (P = 0.03) oral ulceration (P = 0.01), arthritis (P <0.01) and milder muscle disease both clinically (as determined by Childhood Myositis Assessment Score (P = 0.03)) and histologically (as determined by a lower JDM muscle biopsy score (P <0.01)) than patients who did not have anti-MDA5 antibodies. A greater proportion of children with anti-MDA5 autoantibodies achieved disease inactivity at two years post-diagnosis according to PRINTO criteria (P = 0.02). A total of 4 out of 21 children with anti-MDA5 had interstitial lung disease; none had rapidly progressive interstitial lung disease.
Anti-MDA5 antibodies can be identified in a small but significant proportion of patients with JDM and identify a distinctive clinical sub-group. Screening for anti-MDA5 autoantibodies at diagnosis would be useful to guide further investigation for lung disease, inform on prognosis and potentially confirm the diagnosis, as subtle biopsy changes could otherwise be missed.
Viral infections remain a major risk in immunocompromised pediatric patients, and virus-specific T cell (VST) therapy has been successful for treatment of refractory viral infections in prior ...studies. We performed a phase II multicenter study (NCT03475212) for the treatment of pediatric patients with inborn errors of immunity and/or post allogeneic hematopoietic stem cell transplant with refractory viral infections using partially-HLA matched VSTs targeting cytomegalovirus, Epstein-Barr virus, or adenovirus. Primary endpoints were feasibility, safety, and clinical responses (>1 log reduction in viremia at 28 days). Secondary endpoints were reconstitution of antiviral immunity and persistence of the infused VSTs. Suitable VST products were identified for 75 of 77 clinical queries. Clinical responses were achieved in 29 of 47 (62%) of patients post-HSCT including 73% of patients evaluable at 1-month post-infusion, meeting the primary efficacy endpoint (>52%). Secondary graft rejection occurred in one child following VST infusion as described in a companion article. Corticosteroids, graft-versus-host disease, transplant-associated thrombotic microangiopathy, and eculizumab treatment correlated with poor response, while uptrending absolute lymphocyte and CD8 T cell counts correlated with good response. This study highlights key clinical factors that impact response to VSTs and demonstrates the feasibility and efficacy of this therapy in pediatric HSCT.
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has demonstrated the need to share data and biospecimens broadly to ...optimize clinical outcomes for US military Veterans.
In response, the Veterans Health Administration established VA SHIELD (Science and Health Initiative to Combat Infectious and Emerging Life-threatening Diseases), a comprehensive biorepository of specimens and clinical data from affected Veterans to advance research and public health surveillance and to improve diagnostic and therapeutic capabilities.
VA SHIELD now comprises 12 sites collecting de-identified biospecimens from US Veterans affected by SARS-CoV-2. In addition, 2 biorepository sites, a data processing center, and a coordinating center have been established under the direction of the Veterans Affairs Office of Research and Development. Phase 1 of VA SHIELD comprises 34 157 samples. Of these, 83.8% had positive tests for SARS-CoV-2, with the remainder serving as contemporaneous controls. The samples include nasopharyngeal swabs (57.9%), plasma (27.9%), and sera (12.5%). The associated clinical and demographic information available permits the evaluation of biological data in the context of patient demographics, clinical experience and management, vaccinations, and comorbidities.
VA SHIELD is representative of US national diversity with a significant potential to impact national healthcare. VA SHIELD will support future projects designed to better understand SARS-CoV-2 and other emergent healthcare crises. To the extent possible, VA SHIELD will facilitate the discovery of diagnostics and therapeutics intended to diminish COVID-19 morbidity and mortality and to reduce the impact of new emerging threats to the health of US Veterans and populations worldwide.
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