scholarly journals ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research

2021 ◽  
Author(s):  
J. Michael Harnish ◽  
Lucian Li ◽  
Sanja Rogic ◽  
Guillaume Poirier-Morency ◽  
Seon-Young Kim ◽  
...  
Keyword(s):  
Non Profit ◽  
Functional Studies ◽  
Disease Research ◽  
Undiagnosed Disease ◽  
Disease Gene Discovery ◽  
Human Genes ◽  
Therapeutic Research ◽  
Undiagnosed Diseases ◽  
Shared Gene

AbstractNext-generation sequencing is a prevalent diagnostic tool for undiagnosed diseases, and has played a significant role in rare disease gene discovery. While this technology resolves some cases, others are given a list of possibly damaging genetic variants necessitating functional studies. Productive collaborations between scientists, clinicians, and patients can help resolve such medical mysteries, and provide insights into in vivo function of human genes. Furthermore, facilitating interactions between scientists and research funders, including non-profit organizations or commercial entities, can dramatically reduce the time to translate discoveries from bench to bedside. Several systems designed to connect clinicians and researchers with a shared gene of interest have been successful. However, these platforms exclude some stakeholders based on their role or geography. Here we describe ModelMatcher, a global online matchmaking tool designed to facilitate cross-disciplinary collaborations, especially between scientists and other stakeholders of rare and undiagnosed disease research. ModelMatcher is integrated into the Rare Diseases Models and Mechanisms Network and Matchmaker Exchange, allowing users to identify potential collaborators in other registries. This living database decreases the time from when a scientist or clinician is making discoveries regarding their genes of interest, to when they identify collaborators and sponsors to facilitate translational and therapeutic research.

scholarly journals POLRMT mutations impair mitochondrial transcription causing neurological disease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Monika Oláhová ◽  
Bradley Peter ◽  
Zsolt Szilagyi ◽  
Hector Diaz-Maldonado ◽  
Meenakshi Singh ◽  
...  
Keyword(s):  
Progressive External Ophthalmoplegia ◽  
Global Developmental Delay ◽  
Disease Mechanism ◽  
Mitochondrial Transcription ◽  
Functional Studies ◽  
Mtdna Deletions ◽  
Molecular Nature ◽  
Important Disease

AbstractWhile >300 disease-causing variants have been identified in the mitochondrial DNA (mtDNA) polymerase γ, no mitochondrial phenotypes have been associated with POLRMT, the RNA polymerase responsible for transcription of the mitochondrial genome. Here, we characterise the clinical and molecular nature of POLRMT variants in eight individuals from seven unrelated families. Patients present with global developmental delay, hypotonia, short stature, and speech/intellectual disability in childhood; one subject displayed an indolent progressive external ophthalmoplegia phenotype. Massive parallel sequencing of all subjects identifies recessive and dominant variants in the POLRMT gene. Patient fibroblasts have a defect in mitochondrial mRNA synthesis, but no mtDNA deletions or copy number abnormalities. The in vitro characterisation of the recombinant POLRMT mutants reveals variable, but deleterious effects on mitochondrial transcription. Together, our in vivo and in vitro functional studies of POLRMT variants establish defective mitochondrial transcription as an important disease mechanism.

scholarly journals The ER–Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Liang Ge ◽  
David Melville ◽  
Min Zhang ◽  
Randy Schekman
Keyword(s):  
Autophagosome Formation ◽  
Functional Studies ◽  
A Cell ◽  
Intermediate Compartment ◽  
Membrane Isolation ◽  
Necessary And Sufficient ◽  
Organelle Membrane ◽  
Catabolic Process

Autophagy is a catabolic process for bulk degradation of cytosolic materials mediated by double-membraned autophagosomes. The membrane determinant to initiate the formation of autophagosomes remains elusive. Here, we establish a cell-free assay based on LC3 lipidation to define the organelle membrane supporting early autophagosome formation. In vitro LC3 lipidation requires energy and is subject to regulation by the pathways modulating autophagy in vivo. We developed a systematic membrane isolation scheme to identify the endoplasmic reticulum–Golgi intermediate compartment (ERGIC) as a primary membrane source both necessary and sufficient to trigger LC3 lipidation in vitro. Functional studies demonstrate that the ERGIC is required for autophagosome biogenesis in vivo. Moreover, we find that the ERGIC acts by recruiting the early autophagosome marker ATG14, a critical step for the generation of preautophagosomal membranes.

A vector system for fast-forward studies of the HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome in the model plant Nicotiana benthamiana

2021 ◽  
Author(s):  
Adeline Harant ◽  
Hsuan Pai ◽  
Toshiyuki Sakai ◽  
Sophien Kamoun ◽  
Hiroaki Adachi
Keyword(s):  
Nicotiana Benthamiana ◽  
Cell Biology ◽  
Plant Immunity ◽  
Transient Gene Expression ◽  
Coiled Coil ◽  
Experimental System ◽  
Vector System ◽  
In Planta ◽  
Functional Studies

Abstract Nicotiana benthamiana has emerged as a complementary experimental system to Arabidopsis thaliana. It enables fast-forward in vivo analyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of nucleotide-binding leucine-rich repeat (NLR) plant immune receptors has greatly advanced following the discovery of the Arabidopsis HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome. Here, we describe a vector system of 72 plasmids that enables functional studies of the ZAR1 resistosome in N. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs (CC-NLRs) for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as the N. benthamiana ortholog of Arabidopsis ZAR1. Effector-activated and autoactive NbZAR1 trigger the cell death response in N. benthamiana and this activity is dependent on a functional N-terminal α1 helix. C-terminally tagged NbZAR1 remains functional in N. benthamiana, thus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source pZA plasmid collection forms an additional experimental system to Arabidopsis for in planta resistosome studies.

Gastric cancer is the world's second-largest death cause. Peptides can be used to deliver radiation or other fatal chemicals to tumors

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Gastric Cancer ◽  
High Efficiency ◽  
Specific Activity ◽  
High Specific Activity ◽  
Systemic Circulation ◽  
Efficient Delivery ◽  
Liver And Kidney ◽  
Targeting Ability ◽  
Therapeutic Research

Gastric cancer is the world's second-largest death cause. Developing suitable medical therapies can help individuals live longer. So far, GC treatment has depended on several pharmaceutical techniques. Chemotherapy and surgery are GC patients' most frequent treatment choices. The most major hurdles to effective GC therapy are chemotherapeutic resistance and non-selective targeting. Recent GC-targeted therapeutic research has focused on building more selective and effective anti-GC pharmacological approaches. Because molecular focused therapy can greatly exacerbate the current inefficacy of normal GC therapy procedures, peptide base synthesis can be used as a carrier to deliver radiation or other fatal chemicals to tumor locations with precise protein overexpression. Different types of peptides with special binding affinity to GC overexpressed receptors have been identified for targeted therapy and imaging. Although some of these peptides have excellent GC targeting ability, they also need great GC penetration capacity and no systemic in vivo toxicity before they can be employed in clinical studies. One of these peptides' most notable limitations is their short plasma half-life, limiting their efficient delivery to tumor locations. Sluggish binding pharmacokinetics, along with in vivo instability, can produce targeted treatment failure. Using an appropriate modification strategy to boost blood circulation time may be advantageous.The key to producing successful, innovative anti-cancer targeting drugs with specific targeting capabilities is to mark the peptide with distinct diagnostic and therapeutic radioisotopes. Although a peptide's radiolabeling or enzymatic degradation may not affect its targeting capabilities, the radiation dose delivery impact on it is obvious. Selecting an appropriate type of radionuclide to achieve high-specific activity, using a simple and high-efficiency radiolabeling process, and selecting an adequate spacer and chelator to manage peptide biodistribution are all important considerations when designing a peptide-based radiopharmaceutical. High internalization and significant systemic circulation washout are other essential tumor targeting needs. Many of the peptides described in this work lack these critical features. The radiolabeled peptide should also remain intact and have a short blood washout period, allowing targeted imaging and therapy. SPECT and PET are the most extensively used technologies in nuclear medicine. Although PET has a greater resolution, SPECT technology gives a comparable sensitivity at a lesser cost. Combining fast binding pharmacokinetics with suitable stability in vivo can result in efficient tumor contrast. Non-target liver and kidney accumulation is required when employing radiolabeled peptides to target GC. When a radiolabeled peptide accumulates more in the liver and intestine than in the GC tumor, the image quality degrades. However, using the proper chelator and spacer can assist decrease non-target accumulation in the kidneys. Finally, considering all these conditions and being positive, it is conceivable to produce a unique peptide with avid binding to GC cells.

scholarly journals The Relapsing Fever Spirochete Borrelia hermsiiContains Multiple, Antigen-Encoding Circular Plasmids That Are Homologous to the cp32 Plasmids of Lyme Disease Spirochetes

2000 ◽  
Vol 68 (7) ◽  
pp. 3900-3908 ◽  
Author(s):  
Brian Stevenson ◽  
Stephen F. Porcella ◽  
Katrina L. Oie ◽  
Cecily A. Fitzpatrick ◽  
Sandra J. Raffel ◽  
...  
Keyword(s):  
Lyme Disease ◽  
Direct Detection ◽  
Human Infection ◽  
Relapsing Fever ◽  
Borrelia Hermsii ◽  
Functional Studies ◽  
Dna Library ◽  
Multiple Antigen ◽  
Antigenic Proteins

ABSTRACT Borrelia hermsii, an agent of tick-borne relapsing fever, was found to contain multiple circular plasmids approximately 30 kb in size. Sequencing of a DNA library constructed from circular plasmid fragments enabled assembly of a composite DNA sequence that is homologous to the cp32 plasmid family of the Lyme disease spirochete,B. burgdorferi. Analysis of another relapsing fever bacterium, B. parkeri, indicated that it contains linear homologs of the B. hermsii and B. burgdorfericp32 plasmids. The B. hermsii cp32 plasmids encode homologs of the B. burgdorferi Mlp and Bdr antigenic proteins and BlyA/BlyB putative hemolysins, but homologs of B. burgdorferi erp genes were absent. Immunoblot analyses demonstrated that relapsing fever patients produced antibodies to Mlp proteins, indicating that those proteins are synthesized by the spirochetes during human infection. Conservation of cp32-encoded genes in differentBorrelia species suggests that their protein products serve functions essential to both relapsing fever and Lyme disease spirochetes. Relapsing fever borreliae replicate to high levels in the blood of infected animals, permitting direct detection and possible functional studies of Mlp, Bdr, BlyA/BlyB, and other cp32-encoded proteins in vivo.

scholarly journals Human Enhancer of Invasion-Cluster, a Coiled-Coil Protein Required for Passage through Mitosis

2004 ◽  
Vol 24 (9) ◽  
pp. 3957-3971 ◽  
Author(s):  
Margret B. Einarson ◽  
Edna Cukierman ◽  
Duane A. Compton ◽  
Erica A. Golemis
Keyword(s):  
Cell Cycle ◽  
Coiled Coil ◽  
Cell Cycle Checkpoints ◽  
Mitotic Spindles ◽  
Human Genes ◽  
Hydroxyurea Treatment ◽  
Evolutionarily Conserved ◽  
Defects Analysis ◽  
Spindle Function

ABSTRACT In a cross-species overexpression approach, we used the pseudohyphal transition of Saccharomyces cerevisiae as a model screening system to identify human genes that regulate cell morphology and the cell cycle. Human enhancer of invasion-cluster (HEI-C), encoding a novel evolutionarily conserved coiled-coil protein, was isolated in a screen for human genes that induce agar invasion in S. cerevisiae. In human cells, HEI-C is primarily localized to the spindle during mitosis. Depletion of HEI-C in vivo with short interfering RNAs results in severe mitotic defects. Analysis by immunofluorescence, flow cytometry analysis, and videomicroscopy indicates that HEI-C-depleted cells form metaphase plates with normal timing after G2/M transition, although in many cases cells have disorganized mitotic spindles. Subsequently, severe defects occur at the metaphase-anaphase transition, characterized by a significant delay at this stage or, more commonly, cellular disintegration accompanied by the display of classic biochemical markers of apoptosis. These mitotic defects occur in spite of the fact that HEI-C-depleted cells retain functional cell cycle checkpoints, as these cells arrest normally following nocodazole or hydroxyurea treatment. These results place HEI-C as a novel regulator of spindle function and integrity during the metaphase-anaphase transition.

scholarly journals Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

2021 ◽  
Author(s):  
Shasha Chong ◽  
Thomas G. W. Graham ◽  
Claire Dugast-Darzacq ◽  
Gina M. Dailey ◽  
Xavier Darzacq ◽  
...  
Keyword(s):  
Single Molecule ◽  
Target Genes ◽  
Gene Activation ◽  
Low Complexity ◽  
Intrinsically Disordered ◽  
Human Genes ◽  
Domain Interactions ◽  
Bona Fide ◽  
Liquid Liquid Phase Separation

Gene activation by mammalian transcription factors (TFs) requires dynamic, multivalent, and selective interactions of their intrinsically disordered low-complexity domains (LCDs), but how such interactions mediate transcription remains unclear. It has been proposed that extensive LCD-LCD interactions culminating in liquid-liquid phase separation (LLPS) of TFs is the dominant mechanism underlying transactivation. Here, we investigated how tuning the amount and localization of LCD-LCD interactions in vivo affects transcription of endogenous human genes. Quantitative single-cell and single-molecule imaging reveals that the oncogenic TF EWS/FLI1 requires a finely tuned range of LCD-LCD interactions to efficiently activate target genes. Modest or more dramatic increases in LCD-LCD interactions toward putative LLPS repress EWS/FLI1-driven transcription in patient cells. Likewise, ectopically creating LCD-LCD interactions to sequester EWS/FLI1 into a bona fide LLPS compartment, the nucleolus, inhibits EWS/FLI1-driven transcription and oncogenic transformation. Our findings reveal fundamental principles underlying LCD-mediated transcription and suggest mislocalizing specific LCD-LCD interactions as a novel therapeutic strategy for targeting disease-causing TFs.

scholarly journals Functional human genes typically exhibit epigenetic conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0253250
Author(s):  
Daniel Rud ◽  
Paul Marjoram ◽  
Kimberly Siegmund ◽  
Darryl Shibata
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Single Gene ◽  
Functional Genes ◽  
Human Tissues ◽  
Gene Conservation ◽  
Individual Culture ◽  
Human Genes

Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.

Abstract 181: BET Bromodomain Inhibition Suppresses Endothelial Inflammation and Atherosclerosis

2013 ◽  
Vol 33 (suppl_1) ◽  
Author(s):  
Jonathan Brown ◽  
Qiong Duan ◽  
Gabriel Griffin ◽  
Ronald Paranal ◽  
Steven Bair ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Rna Polymerase Ii ◽  
Umbilical Vein ◽  
Ldl Receptor ◽  
Flow Chamber ◽  
Cancer Therapies ◽  
Functional Studies ◽  
Endothelial Inflammation ◽  
Umbilical Vein Endothelial Cells

Introduction The BET bromodomain-containing family of proteins (BRD2, BRD3, BRD4) are epigenetic readers that coactivate transcription. Recent evidence indicates that BETs promote carcinogenesis and inflammation in sepsis, while BET bromodomain inhibitors are promising anti-cancer therapies. However, the role of chromatin remodeling in atherosclerosis in general and through BETs in particular remains unknown. Hypothesis We hypothesized that BET bromodomain-containing proteins coactivate proinflammatory responses in the vasculature with functional effects that promote atherogenesis. Methods and Results BET bromodomain inhibition, achieved with the highly selective, small-molecule inhibitor JQ1 significantly reduced early atherosclerosis (12 weeks) in cholesterol-fed, LDL receptor-null mice. In pursuing mechanisms for this effect, we identified BET protein expression in mouse and human endothelial cells (ECs) as well as endothelium from human atherosclerotic plaque. Treating human umbilical vein endothelial cells (HUVECs) with either JQ1 or siRNA to BRD2 or BRD4 potently suppresses TNFα-induced expression of adhesion molecules (SELE, VCAM1) and chemokines (CCL2, CXCL8). In chromatin immunoprecipation studies, TNFα stimulation of ECs recruited BETs to adhesion molecule and chemokine promoters coincident with RNA polymerase II and cyclin T1 localization, without altering NF-κB recruitment. In functional studies, JQ1 suppressed 1) monocyte adhesion to TNFα-activated HUVECs, 2) leukocyte rolling on cremaster post-capillary venules (intravital microscopy); 3) leukocyte transmigration (parallel-plate flow chamber); and 4) monocyte recruitment in thioglycolate-induced peritonitis in vivo . Conclusions BET bromodomain-containing proteins are novel determinants of pro-inflammatory transcription in the endothelium. Targeting chromatin by BET bromodomain inhibition may be a therapeutic strategy to limit atherosclerosis and other disorders involving endothelial inflammation.

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