bluuebunny/crossref_metadata_2025 huggingface dataset:
The COP9 Signalosome Suppresses Cardiomyocyte Necroptosis
Authors: Xiao Peng , Wang Changhua , Lewno Megan T. , Wu Penglong , Li Jie , Su Huabo , Sternburg Jack O. , Liu Jinbao , Wang Xuejun
Published: December 2019

Background

Loss of cardiomyocyte (CMs) due to apoptosis and regulated necrosis contributes to heart failure. However, the molecular mechanisms governing regulated CM necrosis remain obscure. The COP9 signalosome (CSN) formed by 8 unique protein subunits (COPS1 through COPS8) functions to deneddylate Cullin-RING ligases (CRLs), thereby regulating the functioning of the CRLs. Mice with CM-restricted knockout ofCops8(Cops8-cko) die prematurely, following reduced myocardial performance of autophagy and the ubiquitin-proteasome system (UPS) as well as massive CM necrosis. This study was aimed to determine the nature and underlying mechanisms of the CM necrosis in Cops8-cko mice.

Methods

We examined myocardial expression and activities of key proteins that reflect the status of the RIPK1-RIPK3 pathway, redox, and caspase 8 in Cops8-cko mice. Moreover, we used in vivo CM uptake of Evan’s blue dye (EBD) as an indicator of necrosis and performed Kaplan-Meier survival analyses to test whether treatment with a RIPK1 kinase inhibitor (necrostatin-1) or an antioxidant (N-acetyl-L-cysteine), global knockout of theRIPK3or thePpifgene, CM-restricted knockout of theNrf2gene, or cardiacHMOX1overexpression could rescue the Cops8-cko phenotype.

Results

Compared with littermate control mice, myocardial protein levels of RIPK1, RIPK3, MLKL, the RIPK1-bound RIPK3, protein carbonyls, full-length caspase 8, Nrf2, Ser40-phosphorylated Nrf2 and BCL2, as well as histochemical staining of superoxide anions were significantly increased but the cleaved caspase 8 and the overall caspase 8 activity were markedly decreased in Cops8-cko mice, indicating that the RIPK1-RIPK3 and the Nrf2 pathways are activated and caspase 8 activation is suppressed by Cops8-cko. Continuous necrostatin-1 infusion initiated at 2 weeks of age nearly completely blocked CM necrosis at 3 weeks and markedly delayed premature death of Cops8-cko mice.RIPK3haploinsufficiency or cardiac-specificNrf2heterozygous knockout discernably attenuated CM necrosis and/or delayed mouse premature death; conversely,Ppifknockout, N-acetyl-L-cysteine treatment, and cardiac overexpression of HMOX1 exacerbated CM necrosis and mouse premature death.

Conclusions

Cardiac Cops8/CSN malfunction causes RIPK1-RIPK3 mediated CM necroptosis in mice; sustained Nrf2 activation and reductive stress pivot cardiomyocytes to necroptosis when autophagy and the UPS are impaired; and the CSN plays an indispensable role in suppressing CM necroptosis.
Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population
Authors: Mitsuhashi Satomi , Frith Martin C , Matsumoto Naomichi
Published: December 2019

Tandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. However, it is difficult to predict which tandem repeats may cause a disease. We performed a genome-wide survey of the millions of human tandem repeats using long read genome sequencing data from 16 humans. We found that known Mendelian disease-causing or disease-associated repeats, especially coding CAG and 5’UTR GGC repeats, are relatively long and polymorphic in the general population. This method, especially if used in GWAS, may indicate possible new candidates of pathogenic or biologically important tandem repeats in human genomes.
Expression of inhibitory checkpoint ligands by Glioblastoma Multiforme cells and the implications of an enhanced stem cell-like phenotype
Authors: Robilliard Laverne D , Joseph Wayne , Finlay Graeme , Angel Catherine E , Graham E Scott
Published: December 2019

Glioblastoma Multiforme is a highly aggressive brain malignancy commonly refractory to classical and novel chemo-, radio- and immuno-therapies, with median survival times of ~15 months following diagnosis. Poor immunological responses exemplified by the down-regulation of T-cell activity, and upregulation of immunosuppressive cells within the tumour micro-environment have limited the effectiveness of immunotherapy in GBM to date. Here we show that GBM cells express a large repertoire of inhibitory checkpoint ligands. Furthermore, GBM cells with an enhanced stem cell-like phenotype exhibit heightened levels of inhibitory checkpoint ligands, compared to non-stem cell-like GBM cells. Understanding how GBM modulates an extensive repertoire of immune checkpoint ligands and the functional consequence on immune evasion are necessary to develop effective immuno-therapeutics.
The Potential of Lipolytic Filamentous Fungi Isolated from Landfill Soil as Poly-β-Hydroxybutirate (PHB) Bioplastic Degrader
Authors: Yanti Nur Arfa , Sriwahyuni Endang , La Omi Nur Rayani , Muhiddin Nurhayani H. , Ahmad Sitti Wirdhana
Published: December 2019

The present study was investigated the potential of lipolytic fungi (molds) isolated from landfill soil in degrading Poly-β-hydroxybutyrate (PHB). Screening of PHB-degrading lipolytic molds was done in two stages, such as screening of lipolytic molds which was identified by the formation of orange fluorescent halos around the colony on rhodamine B agar medium and the degradation PHB ability test was identified by the formation of clear zone around colony on PHB emulsion medium. Characterization of isolates was done based on phenotypic characters and the identification was done by numerical-phenetic analysis. Three lipolytic mold isolates that have ability in degrading PHB bioplastic i.e isolate KC1, KE1 and KE6. These molds have asexual spore form conidia, foot cell, septate hyphae, unbranched conidiophore, and spore mass located at the apex of phialid. The identification results showed that isolate KC1 is identic toAspergillus terreus, KE1 is identic toAspergillus nigerand KE6 is identic toAspergillus fumigatus.
Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2
Authors: Bell Ryan A.V. , Al-Khalaf Mohammad H. , Brunette Steve , Chu Alphonse , Dechant Georg , Apostolova Galina , Dilworth Jeffrey , Megeney Lynn A.
Published: December 2019

Induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. Here, we report that removal of special AT-rich binding protein 2 (SATB2), a nuclear protein that binds matrix attachment regions, is a key event in initiating myogenic differentiation. Deletion of SATB2 in muscle cell culture models and in vivo, accelerates differentiation and depletes the muscle progenitor pool, respectively. Genome wide analysis indicates that SATB2 binding is both repressive and inductive, as loss of SATB2 leads to expression of differentiation regulatory factors and inhibition of genes that impair this process. Finally, we noted that the differentiation-specific decline in SATB2 protein is dependent on a caspase 7-mediated cleavage event. Taken together, this study demonstrates that temporal control of SATB2 protein is critical for shaping the chromatin environment and coordinating the myogenic differentiation program.

Graphical Abstract
Open the LID: LXRα regulates ChREBPα transactivity in a target gene-specific manner through an agonist-modulated LBD-LID interaction
Authors: Fan Qiong , Nørgaard Rikke C. , Grytten Ivar , Ness Cecilie M. , Lucas Christin , Vekterud Kristin , Soedling Helen , Matthews Jason , Lemma Roza B. , Gabrielsen Odd S. , Bindesbøll Christian , Ulven Stine M. , Nebb Hilde I. , Grønning-Wang Line M. , Sæther Thomas
Published: December 2019

The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in liver. We have previously shown that LXR regulates ChREBP transcription and activity; however, the underlying mechanisms are unclear. In the current study, we demonstrate that LXRα and ChREBPα interact physically, and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα, and regulates ChREBP-specific target genesin vitroandin vivo. This co-activation is dependent on functional recognition elements for ChREBP, but not for LXR, indicating that ChREBPα recruits LXRα to chromatin intrans. The two factors interact via their key activation domains; ChREBPα’s low glucose inhibitory domain (LID) and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα that was overlooked due to LXR lipogenesis-promoting function.
Partial loss of colonic primary cilia promotes inflammation and carcinogenesis
Authors: Tang Ruizhi , Paul Conception , Lattanzio Rossano , Eguether Thibaut , Tulari Hulya , Bremond Julie , Maurizy Chloé , Poupeau Sophie , Turtoi Andrei , Svrcek Magali , Seksik Philippe , Castronovo Vincent , Delvenne Philippe , Lemmers Bénédicte , Janke Carsten , Pinet Valérie , Hahne Michael
Published: December 2019

Primary cilia (PC) are important signaling hubs in cells and their deregulation has been associated with various diseases including cancer. Here we explored the role of PC in colorectal cancer (CRC) and colitis. In the colon we found PC to be mostly present on different subtypes of fibroblasts. Colons of mice exposed to either chemically induced colitis-associated colon carcinogenesis (CAC) or dextran sodium sulfate (DSS)-induced colitis had decreased numbers of PC. We employed conditional knock-out strains for the PC essential genes,Kif3AandIft88, to generate mice with reduced numbers of PC on colonic fibroblasts. These mice showed an increased susceptibility in the CAC model as well as in DSS-induced colitis. Colons from DSS-treated mice with PC-deficiency on fibroblasts displayed an elevated production of the pro-inflammatory cytokine IL-6 and colonic epithelial cells had diminished levels of HES-1, a key transcription factor of Notch signaling. Notably, an analysis of PC presence on biopsies of patients with ulcerative colitis as well as CRC patients revealed decreased numbers of PC on colonic fibroblasts in pathological versus surrounding normal tissue. Taken together, we provide evidence that a decrease in colonic PC numbers promotes colitis and CRC.

Graphical Abstract
TIP5 safeguards genome architecture of ground-state pluripotent stem cells
Authors: Dalcher Damian , Tan Jennifer Yihong , Bersaglieri Cristiana , Peña-Hernández Rodrigo , Vollenweider Eva , Zeyen Stefan , Schmid Marc W. , Bianchi Valerio , Butz Stefan , Kuzyakiv Rostyslav , Baubec Tuncay , Marques Ana Claudia , Santoro Raffaella
Published: December 2019

Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. However, how genome compartmentalization is regulated remains elusive. We analyzed two closely and developmentally related pluripotent cell types: ground-state ESCs that have an open and active chromatin and developmentally advanced ESCs that display a more closed and repressed state. We show that these two ESC types differ in their regulation of genome organization due to their differential dependency on TIP5, a component of the chromatin remodeling complex NoRC. We show that TIP5 interacts on ESC chromatin with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. TIP5 associates with sub-domains within the active A compartment that strongly intersect through long-range contacts in ESCs. We found that only ground-state chromatin requires TIP5 to limit the invasion of active domains into repressive compartments. Depletion of TIP5 increased chromatin accessibility particularly at B compartments and decreased their repressive features. Furthermore, TIP5 acts as a barrier for the repressive H3K27me3 spreading, a process that also requires TOP2A activity. Finally, ground-state ESCs require TIP5 for growth, differentiation capacity, and correct expression of developmental genes. Our results revealed the propensity of open and active chromatin domains to invade repressive domains, an action counteracted by chromatin remodeling and the relief of chromatin torsional stress. This effort in controlling open/active chromatin domains is required to establish active and repressed genome partitioning and preserves cell function and identity.
Postnatal Expansion, Maturation and Functionality of MR1T Cells in Humans
Authors: Swarbrick Gwendolyn M. , Gela Anele , Cansler Meghan E. , Null Megan D. , Duncan Rowan B. , Nemes Elisa , Shey Muki , Nsereko Mary , Mayanja-Kizza Harriet , Kiguli Sarah , Koh Jeffrey , Hanekom Willem A. , Hatherill Mark , Lancioni Christina , Lewinsohn David M. , Scriba Thomas J. , Lewinsohn Deborah A.
Published: December 2019

MR1-restricted T (MR1T) cells are defined by their recognition of metabolite antigens presented by the monomorphic MHC class 1-related molecule, MR1, the most highly conserved MHC class I related molecule in mammalian species. Mucosal-associated invariant T (MAIT) cells are the predominant subset of MR1T cells expressing an invariant TCR α-chain, TRAV1-2. These cells comprise a T cell subset that recognizes and mediates host immune responses to a broad array of microbial pathogens, includingMycobacterium tuberculosis. Here, we sought to characterize development of circulating human MR1T cells as defined by MR1-5-OP-RU tetramer labelling and of the TRAV1-2+MAIT cells defined by expression of TRAV1-2 and high expression of CD26 and CD161 (TRAV1-2+CD161++CD26++cells). We analysed postnatal expansion, maturation and functionality of peripheral blood MR1-5-OP-RU tetramer+MR1T cells in cohorts from three different geographic settings with different tuberculosis (TB) vaccination practices, levels of exposure to and infection withM. tuberculosis.Early after birth, frequencies of MR1-5-OP-RU tetramer+MR1T cells increased rapidly by several fold. This coincided with the transition from a predominantly CD4+and TRAV1-2−population in neonates, to a predominantly TRAV1-2+CD161++CD26++CD8+population. We also observed that tetramer+MR1T cells that expressed TNF upon mycobacterial stimulation were very low in neonates, but increased ∼10-fold in the first year of life. These functional MR1T cells in all age groups were MR1-5-OP-RU tetramer+TRAV1-2+and highly expressed CD161 and CD26, markers that appeared to signal phenotypic and functional maturation of this cell subset. This age-associated maturation was also marked by the loss of naïve T cell markers on tetramer+TRAV1-2+MR1T cells more rapidly than tetramer+TRAV1-2−MR1T cells and non-MR1T cells. These data suggest that neonates have infrequent populations of MR1T cells with diverse phenotypic attributes; and that exposure to the environment rapidly and preferentially expands the MR1-5-OP-RU tetramer+TRAV1-2+population of MR1T cells, which becomes the predominant population of functional MR1T cells early during childhood.
Skin microbiota dynamics of dairy cows affected by digital dermatitis
Authors: Ariza Juan Manuel , Döpfer Dörte , Oberle Kenny , Anklam Kelly , Labrut Sophie , Bareille Nathalie , Relun Anne , Guatteo Raphaël
Published: December 2019

Bovine digital dermatitis (DD), is a highly prevalent disease among dairy cattle characterized by ulcerative and painful lesions. While multiple management factors are involved in the disease, its precise etiology remains uncertain and the effectiveness of current control strategies remains highly variable. The major role ofTreponemaspp. in the development of the disease is consistently recognized. Nevertheless, it remains unclear how other bacterial communities are relevant to the onset and progression of the disease, and how the skin microbiota is affected by the environment during the course of the disease. The objective of this study was to describe the dynamics of microbiota recovered from DD affected feet under field conditions. This study described the diversity, structure, and composition of DD lesion microbiota over 45 days according to different clinical and management factors. The results of this investigation confirmed the existence of a specific skin microbiota associated with DD lesions, dominated byTreponemaspp. and very different from the microbiota of healthy skin. Interestingly, the diversity and structure of the microbiota in DD lesions did not vary with the footbath disinfectant or the individual topical antibiotic treatments used. In addition, microbiotas from proliferative lesions evidenced a different structure and diversity in comparison to non-proliferative lesions. Our results confirm the major role ofTreponemaspp. And highlight the potential role ofMycoplasmopsisspp. in the DD lesion onset. Further studies are needed to confirm whether the clinical course of DD lesions is driven by a particular microbiota and how that microbiota may induce disease.

Highlights

Multiple bacteria have been identified in DD lesions. However, many of these microorganisms are inhabitants of the foot skin and the farm environment. For the first time, the microbiota of DD lesions was monitored for 45 days under field conditions to describe its evolution over time. The results of this investigation highlighted a particular microbiota dominated byTreponemaspp. present on the skin of DD affected animals and highly different from those microbiotas of healthy skin. The microbiota of DD lesions evolved over the study period and differential bacteria were identified. Further studies are warranted to determine the role of the bacteria composing these microbiotas on lesion onset and outcome.
Support for the Adaptive Decoupling Hypothesis from Whole-Transcriptome Profiles of a Hypermetamorphic and Sexually Dimorphic Insect,Neodiprion lecontei
Authors: Herrig Danielle K. , Vertacnik Kim L. , Kohrs Anna R. , Linnen Catherine R.
Published: December 2019

Though seemingly bizarre, the dramatic post-embryonic transformation that occurs during metamorphosis is one of the most widespread and successful developmental strategies on the planet. The adaptive decoupling hypothesis (ADH) proposes that metamorphosis is an adaptation for optimizing expression of traits across life stages that experience opposing selection pressures. Similarly, sex-biased expression of traits is thought to evolve in response to sexually antagonistic selection. Both hypotheses predict that traits will be genetically decoupled among developmental stages and sexes, but direct comparisons between stage-specific and sex-specific decoupling are rare. Additionally, tests of the ADH have been hampered by a lack of suitable traits for among-stage comparisons and by uncertainties regarding how much decoupling is to be expected. To fill these voids, we characterize transcriptome-wide patterns of gene-expression decoupling in the hypermetamorphic and sexually dimorphic insect,Neodiprion lecontei. This species has three ecologically and morphologically distinct larval stages separated by molts, as well as a complete metamorphic transition that produces dimorphic adult males and females. Consistent with the ADH, we observe that: (1) the decoupling of gene expression becomes more pronounced as the ecological demands of developmental stages become more dissimilar and (2) gene-expression traits that mediate changing ecological interactions show stronger and more variable decoupling than expression traits that are likely to experience more uniform selection. We also find that gene-expression decoupling is more pronounced among major life stages than between the sexes. Overall, our results demonstrate that patterns of gene-expression decoupling can be predicted based on gene function and organismal ecology.
Frontopolar cortex is a mediator of network modularity in the primate brain
Authors: Wu Zhemeng , Ainsworth Matthew , Browncross Helen , Bell Andrew H. , Buckley Mark J.
Published: December 2019

Primate frontopolar cortex (FPC), occupied by area 10, sits atop a functional hierarchy of prefrontal cortical regions yet little is known about its causal role influencing cognition and brain networks. We studied resting-state-functional-connectivity (rsfc) networks in rhesus monkeys with or without FPC; 86 cortical regions showed significant differences in inter-area rsfc measures in lesioned animals versus controls. K-means clustering showed these regions were organized into two distinct networks in lesioned animals, whereas the same areas clustered into four networks in control animals. These networks extended within and beyond prefrontal cortex. These results suggest that FPC is involved in mediating cortical networks in the primate brain, both within and beyond prefrontal cortex. Even after 40 months only partial recovery of lesion-induced reduced modularity had occurred. We therefore suggest that FPC might help implement long-standing diverse neural network dynamics.
Image Reconstruction Reveals the Impact of Aging on Face Perception
Authors: Chang Chi-Hsun , Nemrodov Dan , Drobotenko Natalia , Nestor Adrian , Lee Andy C. H.
Published: December 2019

Extensive work has demonstrated a decline in face recognition abilities associated with healthy aging. To date, however, there has been limited insight into the nature and the extent of aging-related alterations in internal face representations. Here, we sought to address these issues by using an image reconstruction approach that capitalizes on the structure of behavioral data to reveal the pictorial content of visual representations. To this end, healthy young and older adults provided similarity judgments with pairs of face images. Facial shape and surface features were subsequently derived from the structure of the data for each participant and combined into image reconstructions of facial appearance. Our findings revealed that image reconstruction was successful for every participant, irrespective of age. However, reconstruction accuracies of shape and surface information were lower for older individuals than young individuals. Specifically, facial features diagnostic for face perception, such as eye shape and skin tone, were reconstructed poorly in older adults relative to young adults. At the same time, we found that age-related effects only accounted for a relatively small proportion of individual variability in face representations. Thus, our results provide novel insight into age-related changes in visual perception, they account for the decline in facial recognition occurring with age and they demonstrate the utility of image reconstruction to uncovering internal representations across a variety of populations.
Susceptible host availability modulates climate effects on dengue dynamics
Authors: Nova Nicole , Deyle Ethan R. , Shocket Marta S. , MacDonald Andrew J. , Childs Marissa L. , Rypdal Martin , Sugihara George , Mordecai Erin A.
Published: December 2019

Experiments and models suggest that climate affects mosquito-borne disease transmission. However, disease transmission involves complex nonlinear interactions between climate and population dynamics, which makes detecting climate drivers at the population level challenging. By analyzing incidence data, estimated susceptible population size, and climate data with methods based on nonlinear time series analysis (collectively referred to as empirical dynamic modeling), we identified drivers and their interactive effects on dengue dynamics in San Juan, Puerto Rico. Climatic forcing arose only when susceptible availability was high: temperature and rainfall had net positive and negative effects, respectively. By capturing mechanistic, nonlinear, and context-dependent effects of population susceptibility, temperature, and rainfall on dengue transmission empirically, our model improves forecast skill over recent, state-of-the-art models for dengue incidence. Together, these results provide empirical evidence that the interdependence of host population susceptibility and climate drive dengue dynamics in a nonlinear and complex, yet predictable way.
mtorHaploinsufficiency Ameliorates Renal Cyst Formation in Adult Zebrafishtmem67Mutants
Authors: Zhu Ping , Qiu Qi , Harris Peter C. , Xu Xiaolei , Lin Xueying
Published: December 2019

Although zebrafish embryos have been utilized to study ciliogenesis and to model polycystic kidney disease (PKD), adult zebrafish remain unexplored. Here, we report the generation and characterization of a zebrafish mutant oftmem67, a homologue of the mammalian causative gene for Meckel syndrome type 3 (MKS3). Although a small population of homozygous embryos exhibited pronephric cysts, all mutants were able to survive to adulthood and developed progressive mesonephric cysts with full penetrance. The cysts in the adult zebrafish kidneys manifested features of mammalian PKD, including switching of cyst origin from the proximal tubules to the collecting ducts, increased proliferation of cyst-lining epithelial cells, and hyperactive mTOR signaling. Consistent ciliary abnormalities were observed in both the embryonic and adult zebrafish mutants compared with the wild-type fish, including shorter and fewer single cilia in the distal pronephros and all segments of the mesonephros and greater numbers of multiciliated cells (MCCs). Lack of single cilium preceded cystogenesis, suggestive of a primary defect. Expansion of MCCs occurred after pronephric cyst formation and was inversely correlated with the severity of cystogenesis in young adult zebrafish, suggesting an adaptive action. Interestingly, mTOR inhibition ameliorated renal cysts in both the embryonic and adult zebrafish models; however, it only rescued ciliary abnormalities in the adult mutants. In summary, we have established atmem67mutant as the first adult zebrafish PKD model, revealed a novel aspect of cilium regulation, and identified sustained mTOR inhibition as a candidate therapeutic strategy fortmem67-based PKD.

Significance Statement

While zebrafish embryos are well recognized for their value in studying ciliogenesis and polycystic kidney disease (PKD), adult zebrafish have not commonly been used. Here, we report the establishment of the first adult zebrafish model for PKD, which exhibits characteristics of mammalian PKD and shows kidney ciliary abnormalities consistent with those observed in an embryonic model. We also provide evidence for mTOR inhibition as a therapeutic strategy for this particular type of cystogenesis. Compared to the embryonic model, the adult fish model exhibits a spectrum of progressive pathogeneses and enables ciliary abnormalities to be discerned as either primary or secondary to cystogenesis. We believe that this novel adult fish model will facilitate mechanistic studies and therapeutic development for PKD.
Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease
Authors: Winkler Thomas W , Grassmann Felix , Brandl Caroline , Kiel Christina , Günther Felix , Strunz Tobias , Weidner Lorraine , Zimmermann Martina E , Korb Christina A. , Poplawski Alicia , Schuster Alexander K , Müller-Nurasyid Martina , Peters Annette , Rauscher Franziska G , Elze Tobias , Horn Katrin , Scholz Markus , Cañadas-Garre Marisa , McKnight Amy Jayne , Quinn Nicola , Hogg Ruth E , Küchenhoff Helmut , Heid Iris M , Stark Klaus J , Weber Bernhard HF
Published: December 2019

Background

Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of the preceding early stages of the diseases.

Methods

To identify genetic factors for early AMD, we conducted a genome-wide association meta-analysis with 14,034 early AMD cases and 91,214 controls from 11 sources of data including data from the International AMD Genomics Consortium (IAMDGC) and the UK Biobank (UKBB). We ascertained early AMD via color fundus photographs by manual grading for 10 sources and by using an automated machine learning approach for >170,000 images from UKBB. We searched for significant genetic loci in a genome-wide association screen (P<5×10-8) based on the meta-analysis of the 11 sources and via a candidate approach based on 13 suggestive early AMD variants from Holliday et al 2013 (P<0.05/13, additional 3,432 early AMD cases and 11,235 controls). For the novel AMD regions, we conducted in-silico follow-up analysis to prioritize causal genes and pathway analyses.

Results

We identified 11 loci for early AMD, 9 novel and 2 known for early AMD. Most of these 11 loci overlapped with known advanced AMD loci (nearARMS2/HTRA1, CFH, APOE, C2, C3, CETP, PVRL2, TNFRSF10A, VEGFA), except two that were completely novel to any AMD. Among the 17 genes within the two novel loci, in-silico functional annotation suggestedCD46andTYRas the most likely responsible genes. We found the presence or absence of an early AMD effect to distinguish known pathways of advanced AMD genetics (complement/lipid pathways or extracellular matrix metabolism, respectively).

Conclusions

Our data on early AMD genetics provides a resource comparable to the existing data on advanced AMD genetics, which enables a joint view. Our large GWAS on early AMD identified novel loci, highlighted shared and distinct genetics between early and advanced AMD and provides insights into AMD etiology. The ability of early AMD effects to differentiate the major pathways for advanced AMD underscores the biological relevance of a joint view on early and advanced AMD genetics.
Signature activities of 20S proteasome include degradation of the ubiquitin-tag with the protein under hypoxia
Authors: Sahu Indrajit , Mali Sachitanand M. , Sulkshane Prasad , Rozenberg Andrey , Xu Cong , Morag Roni , Sahoo Manisha Priyadarsini , Singh Sumeet K. , Ding Zhanyu , Wang Yifan , Day Sharleen , Cong Yao , Kleifeld Oded , Brik Ashraf , Glickman Michael H.
Published: December 2019

Careful removal of unwanted proteins is necessary for cell survival. The primary constitutive intracellular protease is the 26S proteasome complex, often found in equilibrium with its free catalytic subcomplex– the 20S core particle. Protein degradation by 26S is tightly regulated by prior ubiquitination of substrates, whereas 20S is amenable to substrates with an unstructured segment. Differentiating their contributions to intracellular proteolysis is challenging due to their common catalytic sites. Here, by chemically synthesizing a synoptic set of homogenous ubiquitinated proteins, we ascribe signature features to 20S function and demonstrate a unique property: degrading the ubiquitin-tag along with the target protein. Cryo-EM confirms that a ubiquitinated substrate can induce asymmetric conformational changes to 20S. Mass-spectrometry of intracellular peptidome under hypoxia and in human failing heart identifies the signature properties of 20S in cells. Moreover, the ability of 20S proteasome to clear toxic proteins rapidly, contributes to better survival under these conditions.
Glutamatergic modulation of auditory cortex connectivity with attentional brain networks in unpredictable perceptual environment
Authors: Kompus K. , Volehaugen V. , Craven A. , Specht K.
Published: December 2019

In a stable environment the brain can minimize processing required for sensory input by forming a predictive model of the surrounding world and suppressing neural response to predicted stimuli. Unpredicted stimuli lead to a prediction error signal propagation through the perceptual network, and resulting adjustment to the predictive model. The inter-regional plasticity which enables the model-building and model-adjustment is hypothesized to be mediated via glutamatergic receptors. While pharmacological challenge studies with glutamate receptor ligands have demonstrated impact on prediction-error indices, it is not clear how inter-individual differences in the glutamate system affect the prediction-error processing in non-medicated state. In the present study we examined 20 healthy young subjects with resting-state proton MRS spectroscopy to characterize glutamate+glutamine (rs-Glx) levels in their Heschl’s gyrus (HG), and related this to HG functional connectivity during a roving auditory oddball protocol. No rs-Glx effects were found within the frontotemporal prediction-error network. Larger rs-Glx signal was related to stronger connectivity between HG and bilateral inferior parietal lobule during unpredictable auditory stimulation. We also found effects of rs-Glx on the coherence of default mode network (DMN) and frontoparietal network (FPN) during unpredictable auditory stimulation. Our results demonstrate the importance of Glx in modulating long-range connections and wider networks in the brain during perceptual inference.
Modelling the emergence of whisker barrels
Authors: James Sebastian S. , Krubitzer Leah A. , Wilson Stuart P.
Published: December 2019

Brain development relies on an interplay between genetic specification and self-organization. Striking examples of this relationship can be found in the somatosensory brainstem, thalamus, and cortex of rats and mice, where the arrangement of the facial whiskers is preserved in the arrangement of cell aggregates to form precise somatotopic maps. We show in simulation how realistic whisker maps can self-organize, by assuming that information is exchanged between adjacent cells only, under the guidance of gene expression gradients. The resulting model provides a simple account of how patterns of gene expression can constrain spontaneous pattern formation to faithfully reproduce functional maps in subsequent brain structures.
Core-2O-glycans are required for galectin-3 interaction with the osteoarthritis related protein lubricin
Authors: Flowers Sarah A. , Thomsson Kristina A. , Ali Liaqat , Huang Shan , Mthembu Yolanda , Regmi Suresh C. , Holgersson Jan , Schmidt Tannin A. , Rolfson Ola , Björkman Lena I , Sundqvist Martina , Karlsson Anna , Jay Gregory D. , Eisler Thomas , Krawetz Roman , Karlsson Niclas G.
Published: December 2019

Synovial fluid lubricin (proteoglycan 4) is a mucin-typeO-linked glycosylated (60% of the mass) biological lubricant involved in osteoarthritis (OA) development. Lubricin has been reported to be cross-linked by synovial galectin-3 on the lubricating articular surface. Here, we confirm that binding to galectin-3 depended on core-2O-linked glycans, where surface plasmon resonance of a recombinant lubricin (rhPRG4) devoid of core-2 structures lacked binding capacity to recombinant galectin-3. Both galectin-3 levels and interactions with synovial lubricin were found to be decreased in late-stage OA patients coinciding with an increase of truncated and less sialylated core 1 O-glycans. These data suggest a defect cross-linking of surface active molecules in OA and provides novel insights into OA molecular pathology.
Genetic background and diet affect brown adipose gene co-expression – metabolic associations
Authors: Carson Caryn , Lawson Heather A
Published: December 2019

Adipose is a dynamic endocrine organ that is critical for regulating metabolism and is highly responsive to nutritional environment. Brown adipose tissue is an exciting potential therapeutic target, however there are no systematic studies of gene-by-environment interactions affecting function of this organ. We leveraged a weighted gene co-expression network analysis to identify transcriptional networks in brown adipose tissue from LG/J and SM/J inbred mice fed high or low fat diets, and correlate these networks with metabolic phenotypes. We identified 8 primary gene network modules associated with variation in obesity and diabetes-related traits. Four modules were enriched for metabolically relevant processes such as immune and cytokine response, cell division, peroxisome functions, and organic molecule metabolic processes. The relative expression of genes in these modules is highly dependent on both genetic background and dietary environment. Genes in the immune/cytkine response and cell division modules are particularly highly expressed in high fat-fed SM/J mice, which show unique brown adipose-dependent remission of diabetes. The interconnectivity of genes in these modules is also heavily dependent on diet and strain, with most genes showing both higher expression and co-expression under the same context. We highlight 4 candidate genes,Col28a1, Cyp26b1, Bmp8b, andKcnj14, that have distinct expression patterns among strain-by-diet contexts and fall under metabolic QTL previously mapped in an F16generation of an advanced intercross between these two strains. Each of these genes have some connection to obesity and diabetes-related traits, but have not been studied in brown adipose tissue. In summary, our results provide important insights into the relationship between brown adipose and systemic metabolism by being the first gene-by-environment study of brown adipose transcriptional networks and introducing novel candidate genes for follow-up studies of biological mechanisms of action.

Author Summary

Research on brown adipose tissue is a promising new avenue for understanding and potentially treating metabolic dysfunction. However, we do not know how genetic background interacts with dietary environment to affect the brown adipose transcriptional response, and how this might affect systemic metabolism. Here we report the first investigation of gene-by-environment interactions on brown adipose gene expression networks associating with multiple obesity and diabetes-related traits. We identified 8 primary networks correlated with variation in these traits in mice, including networks enriched for immune and cytokine response, cell division, organic molecule metabolism, and peroxisome genes. Characterizing these networks and their distinct diet-by-strain expression and co-expression patterns is an important step towards understanding how brown adipose tissue responds to an obesogenic diet, how this response affects metabolism, and how this can be modified by genetic variation.
Functional NHE1 expression is critical to blood brain barrier integrity and sumatriptan blood to brain uptake
Authors: Liktor-Busa Erika , Blawn Kiera T. , Kellohen Kathryn L. , Wiese Beth M. , Verkhovsky Vani , Wahl Jared , Vivek Anjali , Davis Thomas P. , Vanderah Todd W. , Largent-Milnes Tally M.
Published: December 2019

Disruption of blood-brain barrier integrity and dramatic failure of brain ion homeostasis including fluctuations of pH occurs during cortical spreading depression (CSD) events associated with several neurological disorders, including migraine with aura, traumatic brain injury and stroke. NHE1 is the primary regulator of pH in the central nervous system. The goal of the current study was to investigate the role of sodium-hydrogen exchanger type 1 (NHE1) in blood brain barrier (BBB) integrity during CSD events and the contributions of this antiporter on xenobiotic uptake. Using immortalized cell lines, pharmacologic inhibition and genetic knockdown of NHE1 mitigated the paracellular uptake of radiolabeled sucrose implicating functional NHE1 in BBB maintenance. In contrast, loss of functional NHE1 in endothelial cells facilitated uptake of the anti-migraine therapeutic, sumatriptan. In female rats, cortical KCl but not aCSF selectively reduced total expression of NHE1 in cortex and PAG with limited impact on trigeminal ganglia or trigeminal nucleus caudalis suggesting in vitro observations may have a significancein vivo. Pharmacological inhibition of NHE1 prior to cortical manipulations enhanced the efficacy of sumatriptan at early time-points but induced facial sensitivity alone. Overall, our results suggest that dysregulation of NHE1 contributes to breaches in BBB integrity, drug penetrance, and the behavioral sensitivity to the antimigraine agent, sumatriptan.
Horizontal gene transfer of thepirABgenes responsible for Acute Hepatopancreatic Necrosis Disease (AHPND) turns a non-Vibriostrain into an AHPND-positive pathogen
Authors: Muthukrishnan Sarmila , Defoirdt Tom , Shariff Mohamed , M. Y Ina-Salwany , Yusoff Fatimah Md , Natrah I.
Published: December 2019

In the past decade, shrimp farms, particularly those established in Asia, Mexico and South America suffered from the outbreak of an emergent penaeid shrimp disease known as Acute Hepatopancreatic Necrosis Disease (AHNPD). The PirA and PirB toxins produced by plasmid pVA1 inVibrio parahaemolyticuswere reported to cause the AHPND pathology. More recent research demonstrated thatV. parahaemolyticusis not the only species that can cause AHPND, as otherVibriospecies were also found to contain PirAB-containing plasmid. The present study assessed the Horizontal Gene Transfer (HGT) of AHPND that transforms genes (pirAandpirB) from AHPND positiveV. parahaemolyticusto non-AHPND and non-vibrio species identified asAlgoriphagussp. strain NBP. The HGT ofpirAandpirBgenes from the AHPND positiveV. parahaemolyticustoAlgoriphagussp. strain NBP was found to occur at different temperatures. The conjugation efficiency rate (n°) ofpirABfromV. parahaemolyticustoAlgoriphagussp. strain NBP at 30°C and 40°C showed 80-91% efficiency. Shrimp challenged with thepirAandpirBpositiveAlgoriphagussp. strain NBP also demonstrated typical pathognomonic AHPND lesions during the histopathologic examination.

Author summary

AHPND is a significant threat to the shrimp industry leading to high losses. The results demonstrated that the conjugative transfer of thepirAandpirBpositiveV. parahaemolyticus(donor strain) to a non-Vibrioand non-pathogenic bacterium (recipient strain), successfully transformed the non-pathogenic bacterium into a disease-causing strain with a disease-causing capability similar to the donor strain. Initially,V. parahaemolyticusthat express the PirA and PirB toxins which encoded by a conjugative plasmid cause sloughing and degeneration of shrimp hepatopancreatic.
Wt1 positive neurons in the hindbrain are essential for respiration
Authors: Schnerwitzki Danny , Hayn Christian , Perner Birgit , Englert Christoph
Published: December 2019

Neuronal networks commonly referred to as central pattern generator (CPG) networks coordinate the generation of rhythmic activity like locomotion and respiration. These networks are proposed to exhibit a high degree of homology in their development. Their establishment is influenced by a variety of transcription factors. One of them is the Wilms tumor protein Wt1 that is present in dI6 neurons of the ventral spinal cord, which are involved in the coordination of locomotion. Here we report about the so far undescribed presence of Wt1 in neurons of the caudoventral medulla oblongata and their impact on respiration. By performing marker analyses, we were able to characterize these Wt1 positive (+) cells as dB4 neurons. The temporal pattern of Wt1 occurrence suggests a role for Wt1 in the differentiation of dB4 neurons during embryonic and postnatal development. Conditional knockout ofWt1in these cells caused an altered population size of V0 neurons already in the developing hindbrain leading to a decline in the respiration rate in the adults. Thereby, we confirmed and extended the so far proposed homology between neurons of the dB4 domain in the hindbrain and dI6 neurons of the spinal cord in terms of development and function. Ablation of Wt1+ dB4 neurons resulted in the death of neonates due to the inability to initiate respiration suggesting a vital role for Wt1+ dB4 neurons in breathing. These results extend the role of Wt1 in the CNS and show that in addition to its function in differentiation of dI6 neurons it also contributes to the development of dB4 neurons in the hindbrain that are critically involved in the regulation of respiration.
Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
Authors: Viñes Joaquim , Cuscó Anna , Napp Sebastian , Gonzalez Judith , de Rozas Ana Perez , Francino Olga , Migura-Garcia Lourdes
Published: December 2019

One-Health studies applying massive-parallel and single-molecule sequencing are a suitable approximation to try to understand how antibiotic resistances flow between the human-animal-environment scenario. Colistin has been withdrawn in human medicine due to its toxicity, limiting its usage as a last-resort treatment option for multidrug-resistant Gram-negative bacteria. However, it is still used orally to treatEnterobacteriaceaeinfections in veterinary medicine. Since 2015, colistin resistance appeared to be located in mobile genetic elements, raising the concern of the likelihood of transmission by horizontal gene transfer between animals and humans. In this study, 202 faecal samples were collected in a mixed farm from pigs, calves, and the farmer. PCR forthe mcr-1 gene was positive for 18 of the isolates, and Nanopore sequencing allowed us to determine the location of the gene, either on the chromosome or in plasmids. Three types of replicons were found within the positive isolates harbouring themcr-1: IncX4, IncI2, and IncHI2. Four different genetic contexts probably indicate different stages of gene stabilization, either in the chromosome or plasmid, withISApl1as the main insertion element flanking the gene. Moreover, 43 other resistance genes were found in our samples, related to more than six different antibiotic families (e.g. aminoglycosides, lincosamides, beta-lactams, macrolides, trimethoprim, phenicols, and sulphonamides). We found resistance genes against colistin and that six antibiotic families together in at least one of the isolates from human, swine, and bovine. Isolate 15B-22 harboured one plasmid with seven resistance genes related to four families of antibiotics other than polymyxins, meaning that there are more chances to maintain colistin resistance even with the withdrawn of colistin. Nanopore long reads allowed us to assemble the DNA elements within the isolates easily and determine the genetic context of themcr-1gene. Furthermore, they allowed us to describe and locate more antimicrobial resistance genes to other antibiotic families and antiseptic compounds.
A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Authors: Dhorne-Pollet Sophie , Barrey Eric , Pollet Nicolas
Published: December 2019

Background

We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step.

Results

We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. Finally, we identified SNPs with a precision of 98.1%; recall of 85.2% and a F1-score of 0.912.

Conclusions

Our analyses show that our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.