bluuebunny/crossref_metadata_2025 huggingface dataset:
Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain
Authors: Fernández-Castañeda Anthony , Lu Peiwen , Geraghty Anna C. , Song Eric , Lee Myoung-Hwa , Wood Jamie , Yalçın Belgin , Taylor Kathryn R. , Dutton Selena , Acosta-Alvarez Lehi , Ni Lijun , Contreras-Esquivel Daniel , Gehlhausen Jeff R. , Klein Jon , Lucas Carolina , Mao Tianyang , Silva Julio , Peña-Hernández Mario A. , Tabachnikova Alexandra , Takahashi Takehiro , Tabacof Laura , Tosto-Mancuso Jenna , Breyman Erica , Kontorovich Amy , McCarthy Dayna , Quezado Martha , Hefti Marco , Perl Daniel , Folkerth Rebecca , Putrino David , Nath Avi , Iwasaki Akiko , Monje Michelle
Published: January 2022

Survivors of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection frequently experience lingering neurological symptoms, including impairment in attention, concentration, speed of information processing and memory. This long-COVID cognitive syndrome shares many features with the syndrome of cancer therapy-related cognitive impairment (CRCI). Neuroinflammation, particularly microglial reactivity and consequent dysregulation of hippocampal neurogenesis and oligodendrocyte lineage cells, is central to CRCI. We hypothesized that similar cellular mechanisms may contribute to the persistent neurological symptoms associated with even mild SARS-CoV-2 respiratory infection. Here, we explored neuroinflammation caused by mild respiratory SARS-CoV-2 infection – without neuroinvasion - and effects on hippocampal neurogenesis and the oligodendroglial lineage. Using a mouse model of mild respiratory SARS-CoV-2 infection induced by intranasal SARS-CoV-2 delivery, we found white matter-selective microglial reactivity, a pattern observed in CRCI. Human brain tissue from 9 individuals with COVID-19 or SARS-CoV-2 infection exhibits the same pattern of prominent white matter-selective microglial reactivity. In mice, pro-inflammatory CSF cytokines/chemokines were elevated for at least 7-weeks post-infection; among the chemokines demonstrating persistent elevation is CCL11, which is associated with impairments in neurogenesis and cognitive function. Humans experiencing long-COVID with cognitive symptoms (48 subjects) similarly demonstrate elevated CCL11 levels compared to those with long-COVID who lack cognitive symptoms (15 subjects). Impaired hippocampal neurogenesis, decreased oligodendrocytes and myelin loss in subcortical white matter were evident at 1 week, and persisted until at least 7 weeks, following mild respiratory SARS-CoV-2 infection in mice. Taken together, the findings presented here illustrate striking similarities between neuropathophysiology after cancer therapy and after SARS-CoV-2 infection, and elucidate cellular deficits that may contribute to lasting neurological symptoms following even mild SARS-CoV-2 infection.
Application of sequential cyclic compression on cancer cells in a flexible microdevice
Authors: Onal Sevgi , Alkaisi Maan M. , Nock Volker
Published: January 2022

Mechanical forces shape physiological structure and function within cell and tissue microenvironments, during which cells strive to restore their shape or develop an adaptive mechanism to maintain cell integrity depending on strength and type of the mechanical loading. While some cells are shown to experience permanent plastic deformation after a repetitive mechanical tensile loading and unloading, the impact of such repetitive compression on plastic deformation of cells is yet to be understood. As such, the ability to apply cyclic compression is crucial for any experimental setup aimed at the study of mechanical compression taking place in cell and tissue microenvironments. Here, we demonstrate such cyclic compression using a microfluidic compression platform on live cell actin in SKOV-3 ovarian cancer cells. Live imaging of the actin cytoskeleton dynamics of the compressed cells was performed for varying pressures applied sequentially in ascending order during cell compression. Additionally, recovery of the compressed cells was investigated by capturing actin cytoskeleton and nuclei profiles of the cells at zero time and 24 h-recovery after compression in end point assays. This was performed for a range of mild pressures within the physiological range. Results showed that the phenotypical response of compressed cells during recovery after compression with 20.8 kPa differed observably from that for 15.6 kPa. This demonstrated the ability of the platform to aid in the capture of minute differences in cell behaviour as a result of being compressed at various pressures in physiologically relevant manner. Differences observed between compressed cells fixed at zero time or after 24 h-recovery suggest that SKOV-3 cells exhibit deformations at the time of the compression, a proposed mechanism cells use to prevent mechanical damage. The extent of recovery of compressed cells, inferred by imaging cell membrane bulges and actin cytoskeleton and measuring the shape descriptors of cell nuclei, can give insights into the plasticity of cancer cells. Thus, biomechanical responses of SKOV-3 ovarian cancer cells to sequential cyclic compression and during recovery after compression could be revealed in a flexible microdevice. As demonstrated in this work, the microfluidic platform could control the strength and duration of cyclic compression, while enabling the observation of morphological, cytoskeletal and nuclear changes and recovery in compressed cells, thus providing a powerful new tool for the study of mechanobiological processes in cancer and cell biology.
Deviation from the Residue-Based Linear Free Energy Relationship Reveals a Non-Native Structure in Protein Folding
Authors: Fujinami Daisuke , Hayashi Seiichiro , Kohda Daisuke
Published: January 2022

Multiprobe measurements, such as NMR and hydrogen exchange study, can provide the equilibrium constant K and kinetic rate constant k of the structural changes of a polypeptide on a per-residue basis. We previously found a linear relationship between residue-specific log K values and residuespecific log k values for the two-state topological isomerization of a 27-residue peptide. To test the general applicability of the residue-based linear free energy relationship (rbLEFR), we performed a literature search to collect residue-specific equilibrium and kinetic constants in various exchange processes, including protein folding, coupled folding and binding of intrinsically disordered peptides, and structural fluctuations of folded proteins. The good linearity in a substantial number of log-log plots proved that the rbLFER holds for the structural changes in a wide variety of protein-related phenomena. Protein molecules quickly fold into their native structures and change their conformations smoothly. Theoretical studies and molecular simulations advocate that the physicochemical basis is the consistency principle and the minimal frustration principle: Non-native structures/interactions are absent or minimized along the folding pathway. The linearity of the residue-based free energy relationship demonstrates experimentally the absence of non-native structures in transition states. In this context, the hydrogen exchange study of apomyoglobin folding intermediates is particularly interesting. We found that the residues that deviated from the linear relationship corresponded to the non-native structure, which had been identified by other experiments. The rbLFER provides a unique and practical method to probe the dynamic aspects of the transition states of protein molecules.

Highlights

A collection of equilibrium and kinetic constants of structural changes of proteins

Residue-based linear free energy relationship widely holds between the two constants

rbLFER indicates the absence of non-ground state structures in transition states

rbLFER is an experiment proof of the consistency principle of protein folding

Deviations from the linear relation suggest special structures in transition states

Abstract Figure
Fluorescence visualization of deep-buried hollow organs
Authors: Feng Zhe , Li Yuanyuan , Chen Siyi , Yu Xiaoming , Ying Yanyun , Zheng Junyan , Wu Tianxiang , Li Jin , Fan Xiaoxiao , Zhang Dan , Qian Jun
Published: January 2022

High-definition fluorescence imaging of deep-buried organs is still challenging. Here, we develop bright fluorophores emitting to 1700 nm by enhancing electron donating ability and reducing donor-acceptor distance. In parallel, the heavy water functions as the solvent of the delicately designed fluorophores, effectively reducing the fluorescent signal loss caused by the absorption by water. The near-infrared-II (NIR-II, 900-1880 nm) emission is eventually recovered and extended beyond 1400 nm. Compared with the spectral range beyond 1500 nm, the one beyond 1400 nm gives a more accurate fluorescence visualization of the hollow organs, owing to the absorption-induced scattering suppression. In addition, the intraluminal lesions containing much water are simultaneously negatively stained, leading to a stark contrast for precise diagnosis. Eventually, the intraluminally perfused fluorescent probes are excreted from mice and thus no obvious side effects emerge. This general method can provide new avenues for future biomedical imaging of deep and highly scattering tissues.
Engineering a 3D hydrogel system to study optic nerve head astrocyte morphology and behavior in response to glaucomatous insult
Authors: Strat Ana N. , Kirschner Alexander , Yoo Hannah , Singh Ayushi , Bagué Tyler , Li Haiyan , Herberg Samuel , Ganapathy Preethi S.
Published: January 2022

In glaucoma, astrocytes within the optic nerve head (ONH) rearrange their actin cytoskeleton, while becoming reactive and upregulating intermediate filament glial fibrillary acidic protein (GFAP). Increased transforming growth factor beta 2 (TGFβ2) levels have been implicated in glaucomatous ONH dysfunction. A key limitation of using conventional 2D culture to study ONH astrocyte behavior is the inability to faithfully replicate the in vivo ONH microenvironment. Here, we engineer a 3D ONH astrocyte hydrogel to better mimic in vivo mouse ONH astrocyte (MONHA) morphology, and test induction of MONHA reactivity using TGFβ2. Primary MONHAs were isolated from C57BL/6J mice and cell purity confirmed. To engineer 3D cell-laden hydrogels, MONHAs were mixed with photoactive extracellular matrix components (collagen type I, hyaluronic acid) and crosslinked for 5 minutes using a photoinitiator (0.025% riboflavin) and UV light (405-500 nm, 10.3 mW/cm2). MONHA-encapsulated hydrogels were cultured for 3 weeks, and then treated with TGFβ2 (2.5, 5.0 or 10 ng/ml) for 7 days to assess for reactivity. Following encapsulation, MONHA retained high cell viability in hydrogels and continued to proliferate over 4 weeks as determined by live/dead staining and MTS assays. Sholl analysis demonstrated that MONHAs within hydrogels developed increasing process complexity with longer process length over time. Cell processes connected with neighboring cells, coinciding with Connexin43 expression within astrocytic processes. Treatment with TGFβ2 induced reactivity in MONHA-encapsulated hydrogels as determined by altered F-actin cytoskeletal morphology, increased GFAP expression, and elevated fibronectin and collagen IV deposition. Our data sets the stage for future use of this 3D biomimetic ONHA-encapsulated hydrogel to investigate ONHA behavior in response to glaucomatous insult.
Intravenous gene transfer throughout the brain of infant Old World primates using AAV
Authors: Chuapoco Miguel R. , Flytzanis Nicholas C. , Goeden Nick , Octeau J. Christopher , Roxas Kristina M. , Chan Ken Y. , Scherrer Jon , Winchester Janet , Blackburn Roy J. , Campos Lillian J. , Arokiaraj Cynthia M. , Miles Timothy F. , Jang Min J. , Vendemiatti Julia , Deverman Benjamin E. , Pickel James , Fox Andrew S. , Gradinaru Viviana
Published: January 2022

Adeno-associated viruses (AAVs) can enable robust and safe gene delivery to the mammalian central nervous system (CNS). While the scientific community has developed numerous neurotropic AAV variants for systemic gene-transfer to the rodent brain, there are few AAVs that efficiently access the CNS of higher order primates. We describe here AAV.CAP-Mac, an engineered AAV variant that enables systemic, brain-wide gene delivery in infants of two Old World primate species—the rhesus macaque (Macaca mulatta) and the green monkey (Chlorocebus sabaeus). We identified CAP-Mac using a multi-species selection strategy, initially screening our library in the adult common marmoset (Callithrix jacchus) and narrowing our pool of test-variants for another round of selection in infant macaques. In individual characterization, CAP-Mac robustly transduces human neurons in vitro and Old World primate neurons in vivo, where it targets all lobes of cortex, the cerebellum, and multiple subcortical regions of disease relevance. We use CAP-Mac for Brainbow-like multicolor labeling of macaque neurons throughout the brain, enabling morphological reconstruction of both medium spiny neurons and cortical pyramidal cells. Because of its broad distribution throughout the brain and high neuronal efficiency in infant Old World primates compared to AAV9, CAP-Mac shows promise for researchers and clinicians alike to unlock novel, noninvasive access to the brain for efficient gene transfer.
Polymer-directed inhibition of reversible to irreversible attachment prevents Pseudomonas aeruginosa biofilm formation
Authors: Carabelli Alessandro M. , Dubern Jean-Frédéric , Papangeli Maria , Farthing Nicola E. , Sanni Olutoba , Heeb Stephan , Hook Andrew L. , Alexander Morgan R. , Williams Paul
Published: January 2022

Non-toxic, biocompatible materials that inhibit bacterial biofilm formation on implanted medical devices and so prevent infection are urgently required. Weakly amphiphilic acrylate polymers with rigid hydrocarbon pendant groups resist bacterial biofilm formation in vitro and in vivo but the biological mechanism involved is not known. By comparing biofilm formation on polymers with the same acrylate backbone but with different pendant groups, we show that poly(ethylene glycol dicyclopentenyl ether acrylate; pEGdPEA) but not neopentyl glycol propoxylate diacrylate (pNGPDA) inhibited the transition from reversible to irreversible attachment. By using single-cell tracking algorithms and controlled flow microscopy we observed that fewer Pseudomonas aeruginosa PAO1 cells accumulated on pEGdPEA compared with pNGPDA. Bacteria reaching the pEGdPEA surface exhibited shorter residence times and greater asymmetric division with more cells departing from the surface post-cell division, characteristic of reversible attachment. Migrating cells on pEGdPEA deposited fewer exopolysaccharide trails and were unable top adhere strongly. Discrimination between the polymers required type IV pili and flagella. On pEGdPEA, the lack of accumulation of cyclic diguanylate or expression of sadB were consistent with the failure to transit from reversible to irreversible attachment. Constitutive expression of sadB increased surface adhesion sufficient to enable P. aeruginosa to form biofilms in a Mot flagellar stator dependent manner. These findings were extendable to other biofilm resistant acrylates highlighting their unique ability to inhibit reversible to irreversible attachment as a mechanism for preventing biofilm-associated infections.

Significance

Bacteria readily attach to surfaces forming biofilms. These are commonly associated with medical device-associated infections and highly refractory to antibiotics. Biocompatible, weakly amphiphilic acrylate polymers with large hydrophobic pendant groups that inhibit biofilm formation and can prevent such infections have been described. However, the biological mechanism involved is not understood. By comparing a biofilm-inhibiting with a biofilm-supporting acrylate, we showed that Pseudomonas aeruginosa PAO1 cells responded differentially to the two polymers and were unable to accumulate and adhere strongly, activate cyclic diguanylate signalling or transit from reversible to irreversible attachment on the inhibitory polymer. Constitutive expression of sadB increased surface adhesion sufficient to enable P. aeruginosa to form biofilms in a flagellar stator dependent manner overcoming the biofilm inhibitory properties of the polymer.
Toxoflavin secreted byPseudomonas alcaliphilainhibits growth ofLegionella pneumophilaand its hostVermamoeba vermiformis
Authors: Faucher Sebastien P. , Matthews Sara , Nickzad Arvin , Vounba Passoret , Shetty Deeksha , Bédard Émilie , Prévost Michele , Déziel Eric , Paranjape Kiran
Published: January 2022

Legionella pneumophilais a natural inhabitant of water systems. From there, it can be transmitted to humans by aerosolization resulting in severe pneumonia. Most large outbreaks are caused by cooling towers contaminated withL. pneumophila. The resident microbiota of the cooling tower is a key determinant for the colonization and growth ofL. pneumophila. The genusPseudomonascorrelates negatively with the presence ofL. pneumophila, but it is not clear which species is responsible. Therefore, we identified thePseudomonasspecies inhabiting 14 cooling towers using aPseudomonas-specific 16S rRNA amplicon sequencing strategy. Cooling towers free ofL. pneumophilacontained a high relative abundance of members from thePseudomonas alcaliphila/oleovoransphylogenetic cluster.In vitro,P. alcaliphilaJCM 10630 inhibited the growth ofL. pneumophilaon agar plates. Analysis of theP. alcaliphilagenome revealed the presence of a genes cluster predicted to produce toxoflavin.L. pneumophilagrowth was inhibited by pure toxoflavin and by extract fromP. alcaliphilaculture found to contain toxoflavin by LC-ESI-MS. In addition, toxoflavin inhibits growth ofVermameoba vermiformis, a host cell ofL. pneumophila. Our study indicates thatP. alcaliphilamay be important to restrict growth ofL. pneumophilain water systems through the production of toxoflavin. A sufficiently high concentration is likely not achieved in the bulk water but might have a local inhibitory effect such as in biofilm.
NOX4 inhibition promotes the remodeling of dystrophic muscle
Authors: Hammers David W.
Published: January 2022

The muscular dystrophies (MDs) are genetic muscle diseases that result in progressive muscle degeneration followed by the fibrotic replacement of affected muscles as regenerative processes fail. Therapeutics that specifically address the fibrosis and failed regeneration associated with MDs represent a major unmet clinical need for MD patients, particularly those with advanced stage disease progression. The current study investigates targeting NAD(P)H oxidase (NOX) 4 as a potential strategy to reduce fibrosis and promote regeneration in disease-burdened muscle that models Duchenne muscular dystrophy (DMD). NOX4 is elevated in the muscles of dystrophic mice and DMD patients, localizing primarily to interstitial cells located between muscle fibers. Genetic and pharmacological targeting of NOX4 significantly reduces fibrosis in dystrophic respiratory and limb muscles. Mechanistically, NOX4 targeting decreases the number of fibrosis-depositing cells (myofibroblasts) and restores the number of muscle-specific stem cells (satellite cells) to their physiological niche, thereby, rejuvenating muscle regeneration. Furthermore, acute inhibition of NOX4 is sufficient to induce apoptotic clearing of myofibroblasts within dystrophic muscle. These data indicate that targeting NOX4 is an effective strategy to promote the beneficial remodeling of disease-burdened muscle representative of DMD and, potentially, other MDs and muscle pathologies.

SIGNIFICANCE STATEMENT

Muscular dystrophies are progressive muscle diseases. Therapeutics capable of combating the severe fibrosis that replaces functional muscle in these devastating diseases is a major unmet clinical need, particularly for the treatment of older patients. The current work reveals that targeting NOX4 in dystrophic muscle promotes the beneficial remodeling of disease-burdened musculature. This is achieved by the removal of disease-causing cells, known as myofibroblasts, which results in reduced muscle fibrosis and rejuvenation of muscle regeneration. NOX4-targeting strategies, therefore, represent remodeling therapeutics capable of improving muscle disease caused by muscular dystrophy, and, likely, other muscle pathologies.
Transcriptome-based phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha) reveals patterns of lineage expansion in a series of new adaptive zones
Authors: Armisén David , Viala Séverine , da Rocha Silva Cordeiro Isabelle , Crumière Antonin Jean Johan , Hendaoui Elisa , Le Bouquin Augustin , Duchemin Wandrille , Santos Emilia , Toubiana William , Vargas-Lowman Aidamalia , Floriano Carla Fernanda Burguez , Polhemus Dan A. , Wang Yan-hui , Rowe Locke , Moreira Felipe Ferraz Figueiredo , Khila Abderrahman
Published: January 2022

Key innovations enable access to new adaptive zones and are often linked to increased species diversification. As such, they have attracted much attention, yet their concrete consequences on the subsequent evolutionary trajectory and diversification of the bearing lineages remain unclear. The monophyletic group of water striders and relatives (Hemiptera: Heteroptera: Gerromorpha) represent a group of insects that transited to live on the water-air interface and diversified to occupy ponds, puddles, streams, mangroves and even oceans. This lineage offers an excellent model to study the patterns and processes underlying species diversification following the conquest of new adaptive zones. However, such studies require a reliable and comprehensive phylogeny of the infraorder. Based on whole transcriptomic datasets of 97 species and fossil records, we reconstructed a new phylogeny of the Gerromorpha that resolved inconsistencies and uncovered strong support for previously unknown relationships between some important taxa. We then used this phylogeny to reconstruct the ancestral state of a set of adaptations associated with water surface invasion (fluid locomotion, dispersal and transition to saline waters) and sexual dimorphism. Our results uncovered important patterns and dynamics of phenotypic evolution revealing how the initial event of water surface invasion enabled multiple subsequent transitions to new adaptive zones, representing distinct niches of water surfaces, and further diversification of the group. This phylogeny and the associated transcriptomic datasets constitute highly valuable resources, making Gerromorpha an attractive model lineage to study phenotypic evolution.
The Cryo-EM Structures of two Amphibian Antimicrobial Cross-β Amyloid Fibrils
Authors: Bücker Robert , Seuring Carolin , Cazey Cornelia , Veith Katharina , García-Alai Maria , Grünewald Kay , Landau Meytal
Published: January 2022

The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs) across kingdoms of life. Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 displayed substantial polymorphism with a protofilament of two mated β-sheets. The determined structure was a polymorph showing a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by a crystal structure, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked segments) found in human functional amyloids. The amyloidal properties of antimicrobial peptides shed light on a mechanism of regulation of animicrobial activity involving self-assembly and fibril morphological variations. Moreover, the known endurance of amyloid structures can provide a template for the design of sturdy antimicrobials.
OptiDiff: structural variation detection from single optical mapping reads
Authors: Akdel Mehmet , de Ridder Dick
Published: January 2022

Detecting structural variation (SV) in eukaryotic genomes is of broad interest due to its often dramatic phenotypic effects, but remains a major, costly challenge based on DNA sequencing data. A cost-effective alternative in detecting large-scale SV has become available with advances in optical mapping technology. However, the algorithmic approaches to identifying SVs from optical mapping data are limited. Here, we propose a novel, open-source SV detection tool, OptiDiff, which employs a single molecule based approach to detect and classify homozygous and heterozygous SVs at coverages as low as 20x, showing better performance than the state of the art.
Visual threats reduce blood-feeding and trigger escape responses in Aedes aegypti mosquitoes
Authors: Wynne Nicole E. , Chandrasegaran Karthikeyan , Fryzlewicz Lauren , Vinauger Clément
Published: January 2022

The diurnal mosquitoes Aedes aegypti are vectors of several arboviruses, including dengue, yellow fever, and Zika viruses. To find a host to feed on, they rely on the sophisticated integration of olfactory, visual, thermal, and gustatory cues reluctantly emitted by the hosts. If detected by their target, this latter may display defensive behaviors that mosquitoes need to be able to detect and escape. In humans, a typical response is a swat of the hand, which generates both mechanical and visual perturbations aimed at a mosquito. While the neuro-sensory mechanisms underlying the approach to the host have been the focus of numerous studies, the cues used by mosquitoes to detect and identify a potential threat remain largely understudied. In particular, the role of vision in mediating mosquitoes’ ability to escape defensive hosts has yet to be analyzed. Here, we used programmable visual displays to generate expanding objects sharing characteristics with the visual component of an approaching hand and quantified the behavioral response of female mosquitoes. Results show that Ae. aegypti is capable of using visual information to decide whether to feed on an artificial host mimic. Stimulations delivered in a LED flight arena further reveal that landed females Ae. aegypti display a stereotypical escape strategy by taking off at an angle that is a function of the distance and direction of stimulus introduction. Altogether, this study demonstrates mosquitoes can use isolated visual cues to detect and avoid a potential threat.

Summary Statement

In isolation, visual stimuli programmed to mimic a human swat prevent mosquitoes from blood-feeding by triggering take-offs and escape responses.
Proteome-wide Mendelian randomization in global biobank meta-analysis reveals multi-ancestry drug targets for common diseases
Authors: Zhao Huiling , Rasheed Humaria , Nøst Therese Haugdahl , Cho Yoonsu , Liu Yi , Bhatta Laxmi , Bhattacharya Arjun ,   Global Biobank Meta-analysis Initiative, Hemani Gibran , Smith George Davey , Brumpton Ben Michael , Zhou Wei , Neale Benjamin M. , Gaunt Tom R. , Zheng Jie
Published: January 2022

Proteome-wide Mendelian randomization (MR) shows value in prioritizing drug targets in Europeans, but limited data has made identification of causal proteins in other ancestries challenging. Here we present a multi-ancestry proteome-wide MR analysis pipeline based on cross-population data from the Global Biobank Meta-analysis Initiative (GBMI). We estimated the causal effects of 1,545 proteins on eight complex diseases in up to 32,658 individuals of African ancestries and 1.22 million individuals of European ancestries. We identified 45 and seven protein-disease pairs with MR and genetic colocalization evidence in the two ancestries respectively. 15 protein-disease pairs showed evidence of differential effects between males and females. A multi-ancestry MR comparison identified two protein-disease pairs with MR evidence of an effect in both ancestries, seven pairs with European-specific effects and seven with African-specific effects. Integrating these MR signals with observational and clinical trial evidence, we were able to evaluate the efficacy of one existing drug, identify seven drug repurposing opportunities and predict seven novel effects of proteins on diseases. Our results highlight the value of proteome-wide MR in informing the generalisability of drug targets across ancestries and illustrate the value of multi-cohort and biobank meta-analysis of genetic data for drug development.

Graphical abstract

Notation: genome-wide association study (GWAS); Mendelian randomization (MR); primary open-angle glaucoma (POAG); idiopathic pulmonary fibrosis (IPF); chronic obstructive pulmonary disease (COPD); heart failure (HF), venous thromboembolism (VTE). European ancestry (EUR); African ancestry (AFR)*For the seven protein-disease associations, one association passed FDR threshold of 0.05 in proteome-wide MR, six additional associations passed FDR of 0.05 in the multi-ancestry comparison analysis.

Highlights

A multi-ancestry proteome-wide Mendelian randomization (MR) analysis of 1,545 proteins on eight diseases in more than 1.26 million individuals from a disease GWAS meta-analysis of 19 biobanks.

We find evidence for putative causal effects in 45 protein-disease pairs in European ancestry and seven protein-disease pairs in African ancestry, with 15 pairs showing sex specific effects.

We identify evidence of causality for two protein-disease pairs that are common to both African and European ancestries, seven pairs with European-specific effects and seven pairs with African-specific effects.

Triangulating with clinical trial and observational evidence prioritizes seven new targets, seven drug repurposing opportunities and one existing drug target that generalise to African ancestry.
BML-257, a small molecule that protects against drug induced liver injury in zebrafish
Authors: Jagtap Urmila , Basu Sandeep , Lokhande Lavanya , Bharti Nikhil , Sachidanandan Chetana
Published: January 2022

The use of many essential drugs is restricted due to their deleterious effects on the liver. Molecules that can prevent or protect the liver from drug induced liver injury (DILI) would be valuable in such situations. We used hepatocyte-specific expression of bacterial nitroreductase in zebrafish to cause temporally controlled liver damage. This transgenic line was used to run a whole organism based chemical screen in zebrafish larvae. In this screen we identified BML-257, a potent small molecule AKT inhibitor, that protected the liver against metronidazole-induced liver injury. BML-257 also showed potent prophylactic and pro-regenerative activity in this liver damage model. BML-257 also showed remarkable protective action in two independent toxicological models of liver injury caused by acetaminophen and Isoniazid. This suggests that BML-257 may have the potential to protect against multiple kinds of drug induced liver injury.
Estradiol mediates stress-susceptibility in the male brain
Authors: Georgiou Polymnia , Mou Ta-Chung M. , Potter Liam E. , An Xiaoxian , Zanos Panos , Patton Michael S. , Pultorak Katherine J. , Clark Sarah M. , Ngyuyen Vien , Powels Chris F. , Prokai-Tatrai Katalin , Merchenthaler Istvan , Prokai Laszlo , McCarthy Margaret M. , Mathur Brian N. , Gould Todd D.
Published: January 2022

In susceptible populations, stress is a major risk factor for the development of mental disorders, including depression. Estradiol, often considered a female hormone, is distributed in the male brain via aromatization of testosterone. The role of estrogen receptors (ERs) in male stress susceptibility and depression is not well understood. We found that absence of ERβ is associated with susceptibility to stress in male mice and that activity of ERβ-projecting neurons from the basolateral amygdala to nucleus accumbens is reduced in hypogonadal mice subjected to stress, while activation of this circuit reverses stress-induced maladaptive behaviors. We identified that absence of estradiol, but not testosterone per se, underlies stress susceptibility and that brain-selective delivery of estradiol prevents the development of depression-related behaviors. Our findings provide evidence for an estrogen-based mechanism underlying stress susceptibility and offer an unexpected therapeutic strategy for treating depression in males.
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Authors: Faure Léon , Mollet Bastien , Liebermeister Wolfram , Faulon Jean-Loup
Published: January 2022

Constraint-based metabolic models have been used for decades to predict the phenotype of microorganisms in different environments. However, quantitative predictions are limited unless labor-intensive measurements of media uptake fluxes are performed. We show how hybrid neural-mechanistic models can serve as an architecture for machine learning providing a way to improve phenotype predictions. We illustrate our hybrid models with growth rate predictions ofEscherichia coliandPseudomonas putidagrown in different media and with phenotype predictions of gene knocked-outEscherichia colimutants. Our neural-mechanistic models systematically outperform constraint-based models and require training set sizes orders of magnitude smaller than classical machine learning methods. Our hybrid approach opens a doorway to enhancing constraint-based modeling: instead of constraining mechanistic models with additional experimental measurements, our hybrid models grasp the power of machine learning while fulfilling mechanistic constrains, thus saving time and resources in typical systems biology or biological engineering projects.
Pericentriolar matrix integrity relies on cenexin and Polo-Like Kinase (PLK)1
Authors: Aljiboury Abrar , Mujcic Amra , Curtis Erin , Cammerino Thomas , Magny Denise , Lan Yiling , Bates Michael , Freshour Judy , Ahmed-Braimeh Yasir H. , Hehnly Heidi
Published: January 2022

Polo-Like-Kinase (PLK) 1 activity is associated with maintaining the functional and physical properties of the centrosome’s pericentriolar matrix (PCM). In this study, we use a multimodal approach of human cells (HeLa) and zebrafish embryos in parallel to phylogenic analysis to test the role of a PLK1 binding protein, cenexin, in regulating the PCM. Our studies identify that cenexin is required for tempering microtubule nucleation and that a conserved C-terminal PLK1 binding site between humans and zebrafish is needed for PCM maintenance through mediating PLK1-dependent substrate phosphorylation events. PCM architecture in cenexin-depleted zebrafish embryos was rescued with wild-type human cenexin, but not with a C-terminal cenexin mutant (S796A) deficient in PLK1 binding. We propose a model where cenexin’s C-terminus acts in a conserved manner in eukaryotes, excluding nematodes and arthropods, to anchor PLK1 moderating its potential to phosphorylate PCM substrates required for PCM maintenance and function.
LinkExplorer: Predicting, explaining and exploring links in large biomedical knowledge graphs
Authors: Ott Simon , Barbosa-Silva Adriano , Samwald Matthias
Published: January 2022

Machine learning algorithms for link prediction can be valuable tools for hypothesis generation. However, many current algorithms are black boxes or lack good user interfaces that could facilitate insight into why predictions are made. We present LinkExplorer, a software suite for predicting, explaining and exploring links in large biomedical knowledge graphs. LinkExplorer integrates our novel, rule-based link prediction engine SAFRAN, which was recently shown to outcompete other explainable algorithms and established black box algorithms. Here, we demonstrate highly competitive evaluation results of our algorithm on multiple large biomedical knowledge graphs, and release a web interface that allows for interactive and intuitive exploration of predicted links and their explanations.

Availability and Implementation

A publicly hosted instance, source code and further documentation can be found athttps://github.com/OpenBioLink/Explorer.

Contact

matthias.samwald@meduniwien.ac.at

Supplementary information

Supplementary data are available atBioinformaticsonline.
Functional dissection of neural connectivity in generalized anxiety disorder
Authors: Steinhäuser Jonas L. , Teed Adam R. , Al-Zoubi Obada , Hurlemann René , Chen Gang , Khalsa Sahib S.
Published: January 2022

Differences in the correlated activity of networked brain regions have been reported in individuals with generalized anxiety disorder (GAD) but an overreliance on the null-hypothesis significance testing (NHST) framework limits the identification and characterization of disorder-relevant relationships. In this preregistered study, we applied a Bayesian statistical framework as well as NHST to the analysis of resting-state fMRI scans from females with GAD and demographically matched healthy comparison females. Eleven a-priori hypotheses about functional correlativity (FC) were evaluated using Bayesian (multilevel model) and frequentist (t-test) inference. Reduced FC between the ventromedial prefrontal cortex (vmPFC) and the posterior-mid insula (PMI) was confirmed by both statistical approaches. FC between the vmPFC-anterior insula, the amygdala-PMI, and the amygdala-dorsolateral prefrontal cortex (dlPFC) region pairs did not survive multiple comparison correction using the frequentist approach. However, the Bayesian model provided evidence for these region pairs having decreased FC in the GAD group. Leveraging Bayesian modeling, we demonstrate decreased FC of the vmPFC, insula, amygdala, and dlPFC in females with GAD. Exploiting the Bayesian framework revealed FC abnormalities between region pairs excluded by the frequentist analysis, as well as other previously undescribed regions, demonstrating the benefits of applying this statistical approach to resting state FC data.
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease
Authors: Gupta Chirag , Xu Jielin , Jin Ting , Khullar Saniya , Liu Xiaoyu , Alatkar Sayali , Cheng Feixiong , Wang Daifeng
Published: January 2022

Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern target gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, it is still challenging to understand how cell type networks work abnormally under AD. To address this, we integrated single-cell multi-omics data and predicted the gene regulatory networks in AD and control for four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes. Importantly, we applied network biology approaches to analyze the changes of network characteristics across these cell types, and between AD and control. For instance, many hub TFs target different genes between AD and control (rewiring). Also, these networks show strong hierarchical structures in which top TFs (master regulators) are largely common across cell types, whereas different TFs operate at the middle levels in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell-type-specific TF-TF cooperativities in gene regulation. The cell type networks are highly modular. Several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes and putative targets of approved and pending AD drugs, suggesting possible cell-type genomic medicine in AD. Finally, using the cell type gene regulatory networks, we developed machine learning models to classify and prioritize additional AD genes. We found that top prioritized genes predict clinical phenotypes (e.g., cognitive impairment). Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals mechanisms on cell-type gene dyregulation in AD.
Differential recognition and cytokine induction by the peptidorhamnomannan from Sporothrix brasiliensis and S. schenckii
Authors: Kischkel Brenda , Lopes-Bezerra Leila , Taborda Carlos P. , Joosten Leo A. B. , dos Santos Jéssica Cristina , Netea Mihai G.
Published: January 2022

Sporotrichosis is a deep mycosis caused by dimorphic species of the genus Sporothrix, with differences in pathogenicity between S. schenckii and S. brasiliensis species. Recently, it was discovered that the cell wall peptidorhamnomannan (PRM) of Sporothrix spp. is a pathogen associated molecular pattern (PAMP). Interestingly, S. brasiliensis PRM has additional unknown rhamnose residues. We hypothesize that the structural differences of Sporothrix spp PRMs impact the host’s immune response and may explain the severity of sporotrichosis caused by S. brasiliensis. Here we demonstrate that S. brasiliensis yeasts and its PRM (S.b PRM) induced a strong inflammatory response in human PBMCs, with high production of TNF-α, IL-6 and IL-1β and induction of T-helper cytokines IFN-γ, IL-17 and IL-22. In contrast, S. schenckii yeasts and its PRM induced higher concentrations of interleukin-1 receptor antagonist (IL-1Ra), which resulted in low production of T-helper cytokines such as IL-17 and IL-22. CR3 and dectin-1 were required for cytokine induction by both PRMs, while TLR2 and TLR4 were required for the response of S.s PRM and S.b PRM, respectively. IL-1β and IL-1α production induced by S. brasiliensis yeasts and S.b PRM were dependent on inflammasome and caspase-1 activation. S. schenckii and S.s PRM were able to induce IL-1β independent of ROS. In conclusion, these findings improve our understanding of the pathogenesis of Sporothrix spp. by reporting differences of immunological responses induced by S. schenckii and S. brasiliensis. The study also opens the gateway for novel treatment strategies targeting local inflammation and tissue destruction induced by S. brasiliensis infection through IL-1 inhibition.
Targeting Host PIM Protein Kinases Reduces Mayaro Virus Replication
Authors: Sugasti-Salazar Madelaine , Campos Dalkiria , Valdés-Torres Patricia , Galán-Jurado Paola Elaine , González-Santamaría José
Published: January 2022

Mayaro virus (MAYV) manipulates cell machinery to successfully replicate. Thus, identifying host proteins implicated in MAYV replication, represents an opportunity to discover potential antiviral targets. PIM kinases are enzymes that regulate essential cell functions and also appear to be critical factors in the replication of certain viruses. In this study we explored the consequences of PIM kinase inhibition in the replication of MAYV and other arboviruses. Cytopathic effects or viral titers in samples from MAYV-, Chikungunya-, Una-or Zika-infected cells treated with PIM kinase inhibitors were evaluated using an inverted microscope or plaque-forming assays. The expression of viral proteins E1 and nsP1 in MAYV-infected cells was assessed using an immunofluorescence confocal microscope or Western blot. Our results revealed that PIM kinase inhibition partially prevented MAYV-induced cell damage and also promoted a decrease in viral titers for MAYV, UNAV and ZIKV. The inhibitory effect of PIM kinase blocking was observed for each of the MAYV strains tested and also occurred as late as 8 hpi. Finally, PIM kinase inhibition suppressed the expression of MAYV E1 and nsP1 proteins. Taken together, these findings suggest that PIM kinases could represent an antiviral target for MAYV and other arboviruses.
Xtrapol8: automatic elucidation of low-occupancy intermediate-states in crystallographic studies
Authors: De Zitter Elke , Coquelle Nicolas , Barends Thomas R.M. , Colletier Jacques-Philippe
Published: January 2022

Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, hindering structure determination by conventional methods. To automatically extract such structures, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of hitherto unavailable methods; (iii) calculates various types of extrapolated structure factors while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures.
Synthesis of cell-laden alginate microgels with tunable compositions based on microfluidic pico-injection technique
Authors: Zhang Yizhe , Mao Angelo , Mooney David J. , Weitz David A.
Published: January 2022

We report a microfluidic pico-injection-based approach for reliably generating monodisperse cell-laden alginate microgels whose composition can be tunedin situthrough modulation of the cross-linker concentration. Separating the gelation from emulsification allows for a better control over the microgel size with a microfluidic drop-maker, and an instant adjustment of the microgel composition with a pico-injector.
Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing
Authors: Wiarda Jayne E. , Trachsel Julian M. , Sivasankaran Sathesh K. , Tuggle Christopher K. , Loving Crystal L.
Published: January 2022

Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine intestine, includingSELLhiγδT cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular CD4αβT cells, and cycling T/ILCs were enriched in ileum with Peyer’s patches, while non-cyclingγδT, CD8αβT, and group 1 ILCs were enriched in ileum without Peyer’s patches. scRNA-seq findings were leveraged to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry andin situstaining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral porcine ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.