bluuebunny/crossref_metadata_2025 huggingface dataset:
Current infectious disease research practices with forcibly displaced people in the top ten low- and middle-income host countries: A Systematic Review
Authors: Gross Neila , Tarnas Maia C. , Sayeeda Rashmina J. , Ching Carly , Flynn David , Zaman Muhammad H
Published: September 2024

Infectious disease research is essential for disease prevention and management within refugee camps and informal settlements. We aim to assess the state of infectious disease research with displaced communities in the top ten refugee-hosting low- and middle-income countries. We searched three journal databases for primary research that explicitly included refugees or was conducted in a refugee camp, informal settlement, or displaced people-serving hospital and focused directly on an infectious disease following PRISMA guidelines. Forty studies (out of 1,179) met the inclusion criteria. Common research challenges included population mobility, limited external validity, and low recruitment. No studies included the community in the initial study conception or investigated the research impact on the community. Community involvement was often through community health workers (45%). Of the 18 studies that studied a resource-based intervention, 20% explicitly noted that the intervention was unsustainable. Such context-specific considerations are vital in research with displaced communities.
Avian interferon regulatory factor (IRF) family reunion: IRF3 and IRF9 found
Authors: Ungrová Lenka , Geryk Josef , Kohn Marina , Kučerová Dana , Krchlíková Veronika , Hron Tomáš , Pečenka Vladimír , Pajer Petr , Gáliková Eliška , Pecnová Ľubomíra , Kaspers Bernd , Hejnar Jiří , Nehyba Jiří , Elleder Daniel
Published: September 2024

Interferon regulatory factors (IRFs) are a family of transcription factors in jawed vertebrates with important functions in immunity and many other key cellular processes. The genomes of most vertebrates encode ten IRF genes (IRF1 to IRF10). IRF3 and IRF9 have key roles in the interferon (IFN) induction and signaling. Most of our knowledge about the IFN pathways originates from the study of the mammalian IFN system, and the description of the corresponding avian components is not as complete. Both IRF3 and IRF9 were considered missing from the chicken genome and also from the genomes of all other avian species. Here we describe multiple avian IRF3 and IRF9 genes, all with difficult GC-rich sequence context which prevented their earlier characterization. IRF3 orthologs are more narrowly distributed and are present in the avian infraclass Palaeognathae residing in a syntenic genomic locus shared with other vertebrates. In contrast, IRF9 orthologs were found in most avian species with the notable exception of the order Galliformes. In about half of the avian orders analyzed, IRF9 was located in noncanonical chromosomal positions indicating past evolutionary translocations. Importantly, phylogenetic analysis confirmed the correct orthology of all newly described avian IRFs. We performed a series of experiments using duck (Anas platyrhynchos) IRF9, confirming its key role in the IFN signaling pathway. Knockout of IRF9 in duck embryonal fibroblasts decreases the induction of IFN-stimulated genes (ISGs). Full induction of ISGs in duck cells requires both intact IRF9 and canonical IFN-stimulated response element (ISRE). Lastly, intact IRF9 is needed for IFN-mediated protection of duck cells against vesicular stomatitis virus (VSV)-induced cytopathic effect. The identification of avian IRFs fills an important gap in our understanding of avian immunology and brings new questions related to the evolution of the IRF family.
Slit3 Fragments Orchestrate Neurovascular Expansion and Thermogenesis in Brown Adipose Tissue
Authors: Duarte Afonso Serdan Tamires , Cervantes Heidi , Frank Benjamin , Tian Qiyu , Choi Chan Hee J. , Hoffmann Anne , Cohen Paul , Blüher Matthias , Schwartz Gary J , Shamsi Farnaz
Published: September 2024

Brown adipose tissue (BAT) represents an evolutionary innovation enabling placental mammals to regulate body temperature through adaptive thermogenesis. Brown adipocytes are surrounded by a dense network of blood vessels and sympathetic nerves that support their development and thermogenic function. Cold exposure stimulates BAT thermogenesis through the coordinated induction of brown adipogenesis, angiogenesis, and sympathetic innervation. However, how these distinct processes are coordinated remains unclear. Here, we identify Slit guidance ligand 3 (Slit3) as a new niche factor that mediates the crosstalk among adipocyte progenitors, endothelial cells, and sympathetic nerves. We show that adipocyte progenitors secrete Slit3 which regulates both angiogenesis and sympathetic innervation in BAT and is essential for BAT thermogenesis in vivo. Proteolytic cleavage of Slit3 generates secreted Slit3-N and Slit3-C fragments, which activate distinct receptors to stimulate angiogenesis and sympathetic innervation, respectively. Moreover, we introduce bone morphogenetic protein-1 (Bmp1) as the first Slit protease identified in vertebrates. In summary, this study underscores the essential role of Slit3-mediated neurovascular network expansion in enabling cold-induced BAT adaptation. The co-regulation of neurovascular expansion by Slit3 fragments provides a bifurcated yet harmonized approach to ensure a synchronized response of BAT to environmental challenges. This study presents the first evidence that adipocyte progenitors regulate tissue innervation, revealing a previously unrecognized dimension of cellular interaction within adipose tissue.
Characterisation of Gas Vesicles as Cavitation Nuclei for Ultrasound Therapy using Passive Acoustic Mapping
Authors: Smith Cameron A. B. , Bar-Zion Avinoam , Wu Qiang , Malounda Dina , Bau Luca , Stride Eleanor , Shapiro Mikhail G. , Coussios Constantin C.
Published: September 2024

Genetically encodable gas filled particles known as gas vesicles (GVs) have shown promise as a biomolecular contrast agent for ultrasound imaging and have the potential to be used as cavitation nuclei for ultrasound therapy. In this study, we used passive acoustic mapping techniques to characterize GV-seeded cavitation, utilizing 0.5 and 1.6 MHz ultrasound over peak rarefactional pressures ranging from 100 to 2200 kPa. We found that GVs produce cavitation for the duration of the first applied pulse, up to at least 5000 cycles, but that bubble activity diminishes rapidly over subsequent pulses. At 0.5 MHz the frequency content of cavitation emissions was predominantly broadband in nature, whilst at 1.6 MHz narrowband content at harmonics of the main excitation frequency dominated. Simulations and high-speed camera imaging suggest that the received cavitation emissions come not from individual GVs but instead from the coalescence of GV-released gas into larger bubbles during the applied ultrasound pulse. These results will aid the future development of GVs as cavitation nuclei in ultrasound therapy.
Cryo-EM structures of human GPR155 elucidate its regulatory and transport mechanisms
Authors: Sharma Mansi , Jaijyan Dabbu K. , Nanda Sristi , Samso Montserrat , Hu Wenhui , Singh Shikha , Singh Appu K.
Published: September 2024

GPR155 is a polymodal lysosomal membrane “transceptor” comprising both a transporter domain and a GPCR domain, predominantly expressed in brain. GPR155 facilitates cholesterol-dependent mTORC1 signaling and is implicated in neurological disorders like Huntington’s disease. The GPCR domain likely does not bind extracellular ligands canonically, and the functional relationship between GPR155 domains remains unclear. Here, we report the first structures of monomeric human GPR155 and two distinct dimers, revealing an inward-open transporter domain and an inactivated GPCR domain with a unique luminal loop 7 conformation occupying orthosteric pocket. The dimeric assembly is cholesterol-sensitive: at low cholesterol, the transporter domain resembles plant PIN transporters and transports auxin molecules; at high cholesterol, it forms a unique dimer stabilized by cholesterol. Altogether, these findings have implications for uncovering new lysosomal signaling pathways.
Assessing the role ofAtGRP7 arginine 141, a target of dimethylation by PRMT5, in flowering time control
Authors: Steffen Alexander , Dombert Katarzyna , Iglesias María José , Nolte Christine , de Leone María José , Yanovsky Marcelo J. , Mateos Julieta L. , Staiger Dorothee
Published: September 2024

Arginine (R) methylation, catalyzed by PROTEIN ARGININE METHYLTRANSFERASES (PRMTs), is critical for regulation of gene expression at the transcriptional and post-transcriptional level. Among nine PRMT genes in Arabidopsis, PRMT5 catalyzing symmetric R dimethylation of its targets is best characterized. PRMT5 mutants are late flowering and show altered responses to environmental stress. Among PRMT5 targets areArabidopsis thalianaGLYCINE RICH RNA BINDING PROTEIN 7 (AtGRP7) andAtGRP8 that promote the transition to flowering.AtGRP7 R141 has been shown to be modified by PRMT5. Here, we tested whether this symmetric dimethylation of R141 is important forAtGRP7’s physiological role in flowering time control. We constructedAtGRP7 mutant variants with non-methylable R141 (R141A, R141K). Genomic clones containing these variants complemented the late flowering phenotype of thegrp7-1mutant to the same extend as wild-typeAtGRP7. Furthermore, overexpression ofAtGRP7 R141A or R141K promoted flowering similar to overexpression of the wild-type protein. Thus, flowering time does not depend on R141 and its modification. However,AtGRP7 R141 contributes to the activity of GRP7 in response to abscisic. Immunoprecipitation ofAtGRP7-GFP in theprmt5background revealed that antibodies against dimethylated arginine still recognizedAtGRP7, suggesting that additional methyltransferases may be responsible for modification ofAtGRP7.
A Graph-Informed Modeling Framework Empowering Gene Pathway Discovery
Authors: Wang Yihao , Wang Yue , Jin Jin
Published: September 2024

This study introduces a novel graph-informed modeling framework for improving the statistical analysis of gene expression data, particularly in the context of identifying differentially expressed gene pathways and gene expression-assisted disease classification in a high-dimensional data setting. By integrating gene regulatory network information into hypothesis testing for the difference between mean vectors and linear discriminant analysis, we aim to effectively capture and utilize previously validated external gene interaction information. Our method leverages a block-coordinate descent approach which enables us to incorporate mixed graph information into linear structural equation modeling, accommodating directed/undirected edges and potential cycles in gene regulatory networks. Extensive simulations under various data scenarios have demonstrated the effectiveness of our approach with improved power for gene pathway tests and disease classification over existing methods. An application to a lung cancer dataset from the Cancer Genome Atlas Program (TCGA) further exemplifies the potential of our graph-informed approach in empowering the detection of differentially expressed gene pathways and gene expression-based classification of different lung cancer stages. Our findings underscore the potential utility of incorporating gene regulatory network information in gene pathway analysis, setting the stage for future advancements in gene pathway discovery, disease diagnosis, and treatment strategies.
Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213
Authors: Casado Ana Crespillo , Pothukuchi Prathyush , Naydenova Katerina , Yip Matthew C. J. , Young Janet M. , Boulanger Jerome , Dharamdasani Vimisha , Harper Ceara , Hammoudi Pierre-Mehdi , Otten Elsje G. , Boyle Keith , Gogoi Mayuri , Malik Harmit S. , Randow Felix
Published: September 2024

Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition receptors to detect cognate pathogens while ignoring others. How the E3 ubiquitin ligase RNF213 can respond to phylogenetically distant pathogens, including Gram-negativeSalmonella, Gram-positiveListeria,and eukaryoticToxoplasma, remains unknown. Here we report that the evolutionary history of RNF213 is indicative of repeated adaptation to diverse pathogen target structures, especially in and around its newly identified CBM20 carbohydrate-binding domain, which we have resolved by cryo-EM. We find that RNF213 forms coats on phylogenetically distant pathogens. ATP hydrolysis by RNF213’s dynein-like domain is essential for coat formation on all three pathogens studied as is RZ finger-mediated E3 ligase activity for bacteria. Coat formation is not diffusion-limited but instead relies on rate-limiting initiation events and subsequent cooperative incorporation of further RNF213 molecules. We conclude that RNF213 responds to evolutionarily distant pathogens through enzymatically amplified cooperative recruitment.
The wheat VIH2-3B, a functional PPIP5K controls the localization of fasciclin-like arabinogalactan protein
Authors: Shukla Anuj , Tanwar Rahul , Agrwal Kanupriya , Ghosh Riya , Jessen Henning Jacob , Laha Debabrata , Pandey Ajay K
Published: September 2024

Inositol pyrophosphates (PP[InsPs) are important signalling molecules, that participate in multiple physiological processes across a wide range of eukaryotes. Metabolic pathway kinases (VIP1/VIHs) leading to the production of PP-InsPs are now well characterized in yeast and plants. Previously, the wheat inositol pyrophosphate kinase (TaVIH2) was shown to encode a catalytic active kinase domain. Heterologousexpression ofTaVIH2inArabidopsis thalianashowed enhanced drought tolerance by modulating the cell composition. In this study, we attempted to identify the interacting protein targets of wheat VIH2-3B using a yeast two-hybrid (Y2H) cDNA library screen, identifying 52 putative interactors that are primarily involved in cell wall-related functions. Notably, fasciclin-like arabinogalactan protein (FLA7), a glycosylphosphatidylinositol (GPI)-anchored protein emerged as the most frequently interacting partner in the screen. Further analysis using pull-down assays validated the interaction between TaVIH2-3B and TaFLA7in vivo. Using the reporter fusion studies, we observed the localization of TaFLA7 to be a plasma membrane. We also observed that this localization of the FLA7 was perturbed in the yeastvip1Δ strain. The expression of TaVIH2-3B bearing PP-InsP5K enzymatic activity in yeast mutants rescued the localisation of the FLA7 to the membrane. Expression analysis ofTaFLA7showed differential expression response under drought in wheat shoot tissues.TaFLA7was also found to be highly expressed during grain development, particularly in the endosperm and seed coat during grain maturation. Taken together, these findings highlight the potential role of TaVIH2 in cell wall remodelling and stress response pathways, offering new insights into the functional roles of VIH proteins in plants.

Key word:Inositol pyrophosphates, kinases, cell wall maintenance.
Short-term persistence of foliar insecticides and fungicides in pumpkin plants and their pollinators
Authors: Novotny Jessie Lanterman , Hung Keng-Lou James , Lybbert Andrew H , Kaplan Ian , Goodell Karen
Published: September 2024

To minimize the risk to bees and other beneficial insects, plant protection chemicals are typically applied to pollinator-dependent crop plants when flowers are absent or unopened. However, this approach does not entirely remove the risk of pollinator exposure. Much research has focused on negative effects of systemic insecticides (e.g., seed treatments) on pollinators, but less is known about the level of hazard posed by translocation of non-systemic foliar-applied pesticides to pollen and nectar that bees consume. In this study we assess the frequency and persistence of six foliar-applied pesticides in pumpkin (Cucurbita pepo) tissues and in their bee visitors. We analyzed residues of three insecticides (carbaryl, lambda-cyhalothrin, permethrin) and three fungicides (chlorothalonil, quinoxyfen, triflumizole) in pumpkin leaves, pollen, and nectar collected from five farms in the north-central USA, one day before a spray event, and one, three, and seven days after. Bees foraging on pumpkin flowers were collected one day before and one day after spray and screened for the same pesticides. Overall, insecticides were present in 56% of leaf samples. Compared to leaves, fewer pollen (insecticide detected in 16%, fungicide in 16%) and nectar samples (14%, 0%) contained pesticides. We detected one insecticide (carbaryl) in two out of 69 samples of foraging bees, and only in male squash bees (not in bumble or honey bees), which have life history traits that bring them into prolonged close contact with the sprayed crop plants. The persistence of some agrochemicals in leaves, pollen, and nectar up to a week following application merits consideration when managing pollinator-dependent crops. Even pesticides that are traditionally considered contact-based and applied when flowers are unopened can reach pollen and nectar and produce measurable risk to bees.
Cgasdeficiency promotes tumor growth by supporting B cell persistence and angiogenesis
Authors: Chantawichitwong Papasara , Kumpunya Sarinya , Wongtangprasert Tossapon , Visitchanakun Peerapat , Pisitkun Trairak , Pisitkun Prapaporn
Published: September 2024

The cGAS sensor activates STING/IFN signaling, which is crucial for immune defense against pathogens and triggers inflammation in autoimmune diseases and antitumor responses. This study investigated the cGAS-mediated immune response in tumorigenesis using the MC-38 tumor model.Cgas-/-mice exhibited significantly larger tumors and lower survival rates than wild-type (WT) mice. Tumors inCgas-/-mice showed increased fibrosis and neovascularity. WT mice mounted a more robust T-cell-mediated antitumor response, with higher levels of NK and effector T cells, whileCgas-/-mice showed an expansion of B cells, including regulatory B cells producing IL-10. B cells from tumor-bearingCgas-/-mice survived better in the tumor- conditioned medium than those from WT mice. B cell depletion significantly reduced tumor size in WT mice but had minimal effect inCgas-/-mice, where fibrosis and tumor vasculature persisted. Despite B cell depletion, B cells remained in the tumors ofCgas-/-mice, in contrast to WT mice, where their reduction correlated with an increase in CD8+infiltrating cells. Expression ofTlr7andTlr9remained elevated and unaffected by B cell depletion inCgas-/-tumors, whileBaffexpression was higher and further increased after B cell depletion.Cgas-/-B cells promoted angiogenesis, as indicated by enhanced endothelial tube formation. In summary, cGAS deficiency fosters a tumor microenvironment that supports B cell survival, promotes a pro-tumor immune environment, and enhances angiogenesis, contributing to tumor progression.
AUK3 is required for faithful nuclear segregation in the bloodstream form ofTrypanosoma brucei
Authors: Black J.A. , Poulton B.C. , Gonzaga B.S. , Iskantar A. , Tosi L.R.O. , McCulloch R
Published: September 2024

Eukaryotic chromosomes segregate faithfully prior to nuclear division to ensure genome stability. If segregation becomes defective, the chromosome copy number of the cell may alter leading to aneuploidy and/or polyploidy, both common hallmarks of cancers. In eukaryotes, aurora kinases regulate chromosome segregation during mitosis and meiosis, but their functions in the divergent, single-celled eukaryotic pathogenTrypanosoma bruceiare less understood. Here, we focused on one of three aurora kinases in these parasites, TbAUK3, a homologue of the human aurora kinase AURKC, whose functions are primarily restricted to meiosis. We show that RNAi targeted depletion of TbAUK3 correlates with nuclear segregation defects, reduced proliferation, and decreased DNA synthesis, suggestive of a role for TbAUK3 during mitotic, not meiotic, chromosome segregation. Moreover, we uncover a putative role for TbAUK3 during the parasite’s response to DNA damage since we show that depletion of TbAUK3 enhances DNA instability and sensitivity to genotoxic agents.

HIGHLIGHTS

The C-terminus of TbAUK3 is disordered

TbAUK3 depletion coincides with nuclear segregation defects

Depletion of TbAUK3 enhances DNA instability
Turning the tables: Loss of adaptive immunity reverses sex differences in tuberculosis
Authors: Hertz David , Eggers Lars , von Borstel Linda , Goldmann Torsten , Lotter Hannelore , Schneider Bianca E.
Published: September 2024

Sex-based differences in innate immunity may play a crucial role in susceptibility to and progression of tuberculosis (TB), a disease that disproportionately affects men. This study aimed to examine whether early host-pathogen interactions contribute to the heightened vulnerability of males toMycobacterium tuberculosis(Mtb) infection. Using recombination activating gene knockout (RAG KO) mice, which lack adaptive immunity, we were able to isolate and analyze innate immune responses toMtbwithout the influence of T and B cells. Surprisingly, and in stark contrast to wild-type mice that reflect the male bias as observed in humans, female RAG KO mice were more susceptible toMtbthan their male counterparts. Increased lung CFU in females was accompanied by a significant rise in inflammation, indicated by elevated levels of inflammatory cytokines and chemokines, as well as a massive influx of neutrophils into the lungs. In contrast, male mice exhibited higher levels of IFN-γ and CCL5, along with a greater presence of NK cells in their lungs, suggesting that, in the absence of adaptive immunity, males benefit from a more robust NK cell response, potentially offering greater protection by better controlling inflammation and slowing disease progression.
Engineering Human ARMMs as Therapeutic Non-Viral Vehicles forin vivoDelivery of Genome Editing Payloads
Authors: Wang Qiyu , Liu Shu-Lin , Zhao Wen-Ning , von Kleeck Ryan , Thomas Michael , Luther Kristin , Vahramian Zahra , Sun Yumei , Vyas Komal , Moharil Pearl , Chatzinakos Chris , Semple Carson O. , Badji Jennifer A. , Gens Leah , Bryant Alysia , Greenway Steve , Chang Chou-Wei , Francoeur Adam , Valkov Nedyalka , O’Brien Killian , Nabhan Joseph F.
Published: September 2024

The ability to edit the human genome to treat previously incurable diseases or to modify previously undruggable targets has the potential to transform the lives of patients. However, delivery of genome editing machineriesin vivo, and in a transient manner, continues to be a major challenge. We engineered human cell-derived ARRDC1-mediated microvesicles (ARMMs) as non-viral vehicles that mediate intracellular delivery of proteins, including DNA-modifying enzymes such as Cre recombinase and Cas9/guide RNA ribonucleoproteins (RNPs). ARMMs packaged multiple payloads per vesicle in our production system, yielding dose-dependent functional delivery of Cre or Cas9/gRNA RNP to a variety of cell types, including primary mouse and human cells. Oropharyngeal aspiration of ARMMs loaded with Cre led to biodistribution to alveolar macrophages (AMs), whereas intravenous administration predominantly to Kupffer cells (KCs), liver sinusoidal endothelial cells (LSECs), and splenocytes. Suprisingly, one administration of ARMMs loaded with Cas9 RNPs by oropharyngeal aspiration or intravenously resulted in efficient knockout of multiple genes in AMs or KCs, suggesting potential therapeutic utility. Through intravenous administration of ARMMs loaded with Cas9/NLRP3 gRNA we showed amelioration of drug-induced liver injury in a mouse model, supporting the use of ARMMs as human cell-derived therapeutic vehicles for genome editor deliveryin vivo.
Characterization of non-coding variants associated with transcription factor binding through ATAC-seq-defined footprint QTLs in liver
Authors: Dudek Max F. , Wenz Brandon M. , Brown Christopher D. , Voight Benjamin F. , Almasy Laura , Grant Struan F.A.
Published: September 2024

Non-coding variants discovered by genome-wide association studies (GWAS) are enriched in regulatory elements harboring transcription factor (TF) binding motifs, strongly suggesting a connection between disease association and the disruption of cis-regulatory sequences. Occupancy of a TF inside a region of open chromatin can be detected in ATAC-seq where bound TFs block the transposase Tn5, leaving a pattern of relatively depleted Tn5 insertions known as a “footprint”. Here, we sought to identify variants associated with TF-binding, or “footprint quantitative trait loci” (fpQTLs) in ATAC-seq data generated from 170 human liver samples. We used computational tools to scan the ATAC-seq reads to quantify TF binding likelihood as “footprint scores” at variants derived from whole genome sequencing generated in the same samples. We tested for association between genotype and footprint score and observed 693 fpQTLs associated with footprint-inferred TF binding (FDR < 5%). Given that Tn5 insertion sites are measured with base-pair resolution, we show that fpQTLs can aid GWAS and QTL fine-mapping by precisely pinpointing TF activity within broad trait-associated loci where the underlying causal variant is unknown. Liver fpQTLs were strongly enriched across ChIP-seq peaks, liver expression QTLs (eQTLs), and liver-related GWAS loci, and their inferred effect on TF binding was concordant with their effect on underlying sequence motifs in 80% of cases. We conclude that fpQTLs can reveal causal GWAS variants, define the role of TF binding site disruption in disease and provide functional insights into non-coding variants, ultimately informing novel treatments for common diseases.

Graphical Abstract

We leverage footprinting methods to infer transcription factor binding likelihood genome-wide across 170 liver ATAC-seq samples and implicate 693 SNPs with a genetic influence on binding. Unlike other comparable approaches, this analytical method is not limited in resolution by the constraints of linkage disequilibrium, and can prioritize likely causal variants at GWAS loci for subsequent experimental validation.
Location-biased β-arrestin conformations direct GPCR signaling
Authors: Pham Uyen , Chundi Anand , Stępniewski Tomasz Maciej , Darbha Srikrishna , Eiger Dylan Scott , Gazula Sonia , Gardner Julia , Hicks Chloe , Selent Jana , Rajagopal Sudarshan
Published: September 2024

β-arrestins are multifunctional intracellular proteins that regulate the desensitization, internalization and signaling of over 800 different G protein-coupled receptors (GPCRs) and interact with a diverse array of cellular partners1,2. Beyond the plasma membrane, GPCRs can initiate unique signaling cascades from various subcellular locations, a phenomenon known as “location bias”3,4. Here, we investigate how β-arrestins direct location-biased signaling of the angiotensin II type I receptor (AT1R). Using novel bioluminescence resonance energy transfer (BRET) conformational biosensors and extracellular signal-regulated kinase (ERK) activity reporters, we reveal that in response to the endogenous agonist Angiotensin II and the β-arrestin-biased agonist TRV023, β-arrestin 1 and β-arrestin 2 adopt distinct conformations across different subcellular locations, which are intricately linked to differential ERK activation profiles. We also uncover a population of receptor-free catalytically activated β-arrestins in the plasma membrane that exhibits insensitivity to different agonists and promotes ERK activation on the plasma membrane independent of G proteins. These findings deepen our understanding of GPCR signaling complexity and also highlight the nuanced roles of β-arrestins beyond traditional G protein pathways.
ADENYLATE CYCLASE 3 MEDIATES CAROTID BODY ACTIVATION AND AUTONOMIC DYSFUNCTION IN A SLEEP APNEA MODEL
Authors: Peng Ying-Jie , Nanduri Jayasri , Wang Ning , Su Xiaoyu , Hildreth Matthew , Prabhakar Nanduri R.
Published: September 2024

Patients with obstructive sleep apnea (OSA) experience chronic intermittent hypoxia (CIH). OSA patients and CIH-treated rodents exhibit autonomic dysfunction, characterized by overactive sympathetic nervous system and hypertension, mediated through hyperactive carotid body (CB) chemoreflex. Activation of olfactory receptor 78 (Olfr78) by hydrogen sulfide (H2S) is implicated in CB activation and autonomic responses to CIH, but the downstream signaling pathways remain unknown. Given that odorant receptor signaling is coupled to adenylyl cyclase 3 (Adcy3), we hypothesized that Adcy3-dependent cAMP contributes to CB and autonomic responses to CIH. Our findings show that CIH increases cAMP levels in the CB, a response absent inAdcy3,Cth, andOlfr78null mice. CBs fromCthandOlfr78mutant mice lacked persulfidation response to CIH, indicating that Adcy3 activation by CIH requires Olfr78 activation by H2S. CIH also enhanced glomus cell Ca2+influx, an effect absent inCnga2andAdcy3mutants, suggesting that CIH-induced cAMP mediates enhanced Ca2+responses through cyclic nucleotide-gated channels. Furthermore,Adcy3null mice did not exhibit neither CB activation nor autonomic dysfunction by CIH. These results demonstrate that Adcy3-dependent cAMP is a downstream signaling pathway to H2S/Olfr78, mediating CIH-induced CB activation and autonomic dysfunction.
Differential roles of cyclin-CDK1 complexes in cell migration and invasion
Authors: Hetmanski Joseph H R , Jones Michael J , Caswell Patrick T , Jones Matthew C
Published: September 2024

Two key hallmarks of cancer are dysregulated proliferation and metastasis, which are co- ordinated at the single cell level by regulation of cell-cycle progression and invasive cell migration respectively. We have previously described a central role for CDK1 at the nexus of adhesion signalling and cell cycle progression, demonstrating that CDK1 has a non-canonical role in regulating integrin adhesion complexes and in the migration of cancer cells in 3D interstitial matrix. Here we show that the CDK1 binding partners cyclinB1 and cyclinA2 also have roles in cell migration and invasion in both cancer and non-transformed cells. CyclinB1 plays a key role in RhoA activation to promote rear retraction in a membrane tension dependent manner, while cyclinA2 has a general role in promoting motility. Knockdown of either cyclin significantly perturbs migration with contrasting phenotypes, while knockdown of both together has an additive effect which arrests both migration and division. We find that the cell migration specific role of CDK1 is independent of cell-cycle phase, with inhibition or knockdown of CDK1 perturbing migration in G0/G1 arrested cells, while CDK1-cyclin expression correlates strongly with invasive potential of bladder cancer cell lines. Our findings therefore describe how cyclin-CDK1 complexes orchestrate migration as well as division of cells and that cyclinA2-CDK1 and cyclinB1-CDK1 complexes play distinct roles in motility. Furthermore, these findings suggest that targeting CDK1 signalling in aggressive and invasive tumours may have an unexpected dual potential to combat metastasis in addition to proliferation.
RanBALL: An Ensemble Random Projection Model for Identifying Subtypes of B-Cell Acute Lymphoblastic Leukemia
Authors: Li Lusheng , Xiao Hanyu , Wu Xinchao , Tang Zhenya , Khoury Joseph D. , Wang Jieqiong , Wan Shibiao
Published: September 2024

As the most common pediatric malignancy, B-cell acute lymphoblastic leukemia (B-ALL) has multiple distinct subtypes characterized by recurrent and sporadic somatic and germline genetic alterations. Identifying B-ALL subtypes can facilitate risk stratification and enable tailored therapeutic design. Existing methods for B-ALL subtyping primarily depend on immunophenotyping, cytogenetic tests and genomic profiling, which would be costly, complicated, and laborious. To overcome these challenges, we presentRanBALL(an ensembleRandom projection-based model for identifyingB-ALLsubtypes), an accurate and cost-effective model for B-ALL subtype identification. By leveraging random projection (RP) and ensemble learning, RanBALL can preserve patient-to-patient distances after dimension reduction and yield robustly accurate classification performance for B-ALL subtyping. Benchmarking results based on >1700 B-ALL patients demonstrated that RanBALL achieved remarkable performance (accuracy: 0.93, F1-score: 0.93, and Matthews correlation coefficient: 0.93), significantly outperforming state-of-the-art methods like ALLSorts in terms of all performance metrics. In addition, RanBALL performs better than tSNE in terms of visualizing B-ALL subtype information. We believe RanBALL will facilitate the discovery of B-ALL subtype-specific marker genes and therapeutic targets to have consequential positive impacts on downstream risk stratification and tailored treatment design. To extend its applicability and impacts, a Python-based RanBALL package is available athttps://github.com/wan-mlab/RanBALL.
LOCAS: Multi-label mRNALocalization with Supervised Contrastive Learning
Authors: Abir Abrar Rahman , Tahmid Md Toki , Rahman M. Saifur
Published: September 2024

Traditional methods for mRNA subcellular localization often fail to account for multiple compartmentalization. Recent multi-label models have improved performance, but still face challenges in capturing complex localization patterns. We introduce LOCAS (Localization with Supervised Contrastive Learning), which integrates an RNA language model to generate initial embeddings, employs supervised contrastive learning (SCL) to identify distinct RNA clusters, and uses a multi-label classification head (ML-Decoder) with cross-attention for accurate predictions. Through extensive ablation studies and multi-label overlapping threshold tuning, LOCAS achieves state-of-the-art performance across all metrics, providing a robust solution for RNA localization tasks.
Auto-antibodies against interferons are common in people living with chronic hepatitis B virus infection and associate with PegIFN non-response
Authors: Fink DL , Etoori D , Hill R , Idilli O , Kartikapallil N , Payne O , Griffith S , Bradford HF , Mauri C , Kennedy PTF , McCoy LE , Maini MK , Gill US
Published: September 2024

Background and aims

Type one (T1) and three interferons (T3IFNs) are implicated in Chronic Hepatitis B (CHB) immunopathogenesis. IFN remains the only licenced immune modulating therapy for CHB. We measured the prevalence of auto-antibodies (auto-Abs) against T1 and T3IFNs to examine the hypothesis that they impact Hepatitis B Virus (HBV) control and treatment response, as highlighted by COVID-19.

Methods

Our multi-centre retrospective longitudinal study accessed two CHB cohorts, auto-Ab levels and neutralisation status were measured against T1IFN and T3IFN. Associations were tested against HBV clinical parameters.

Results

Overall, 11.9% (33/276) of CHB patients had any detectable anti-IFN auto-Abs and 9.8% (27/276) anti-T3IFN auto-Abs, with high incidence of PegIFNα-inducedde novoauto-Ab (25.7%, 9/35). However, only a minority of auto-Ab-positive sera demonstrated neutralisationin vitro(3/33, 9.1%). Auto-Ab-positivity correlated with higher median HBsAg levels (p=0.0024). All individuals with detectable auto-Ab were PegIFNαnon-responders including those without auto-Ab against IFNαspecifically.

Conclusions

Non-neutralising anti-IFN auto-Abs are common in CHB and associate with higher median HBsAg levels. Further prospective study of anti-cytokine auto-Ab in CHB are required to characterise association with long-term outcomes.

Impact and implications

HBV and PegIFNαindividually may induce broad auto-reactivity associated with dysregulated anti-viral immune responses. Auto-Ab screening pre-PegIFNαand other immunotherapies may have a critical role in stratifying patient selection.
Charged Molecular Glue Discovery Enabled by Targeted Degron Display
Authors: Zhuang Zhe , Byun Woong Sub , Chrustowicz Jakub , Kozicka Zuzanna , Li Veronica Lynn , Abeja Dinah M , Donovan Katherine A , Sepic Sara , You Inchul , Slabicki Mikolaj , Fischer Eric S , Hinshaw Stephen M , Ebert Benjamin L , Schulman Brenda A , Gray Nathanael S
Published: September 2024

Small molecules that induce protein interactions hold tremendous potential as new medicines, as probes for molecular pathways, and as tools for agriculture. Explosive growth of targeted protein degradation (TPD) drug development has spurred renewed interest in proximity-inducing molecules and especially Molecular Glue Degraders (MGDs). These compounds catalyze destruction of disease-causing proteins by reshaping protein surfaces and promoting cooperative binding between ubiquitylating enzymes and target proteins. MGD discovery for pre-defined targets is a major challenge in contemporary drug discovery. The field is limited by a lack of approaches that can exploit charged ligand-binding pockets, thus excluding a major fraction of ubiquitin ligases (E3s) that evolved to recognize exceedingly common acidic and basic degrons. Here we solve these important chemical challenges through chemocentric MGD discovery of ZZ1, a BET-family protein degrader and a prodrug of a negatively charged glue (c-Glue). ZZ1 activation unmasks a sulfinic acid moiety that binds the modular GID/CTLH ubiquitin ligase complex via a basic pocket in its YPEL5 subunit. YPEL5 is a CRBN structural homolog and an essential non-Cullin ubiquitin ligase cofactor expressed in cancers of the bone marrow. These findings demonstrate a previously unrecognized capacity of YPEL5 to recruit GID/CTLH substrates, and they provide a powerful strategy to discover c-Glues that induce proximity to ubiquitin ligases with similarly desirable properties.
Specific Within-Domain Cognitive Impairments Predict Depression Severity Six-Months After Stroke
Authors: Kelleher Kyle , Demeyere Nele , Kusec Andrea
Published: September 2024

Background

Following stroke, chronic cognitive impairments across multiple domains have been associated with depression. Currently, it is unknown if specific subtypes of cognitive impairments differentially relate to post-stroke depression severity. This study aimed to explore the differential associations between within-domain cognitive impairment to depression severity six-months after stroke.

Method

Participants (n= 385, AgeM= 73.86 years [SD= 12.51], National Institutes of Health Stroke SeverityM= 6.83 [SD= 6.01]) were recruited from an acute stroke ward. Participants completed a self-report mood measure (Hospital Anxiety and Depression Scale; HADS) and a stroke-specific cognitive assessment (Oxford Cognitive Screen; OCS). Separate multiple regressions predicting depression were conducted across 1) OCS domain-specific cognitive impairments of language, memory, attention, praxis, numeracy and executive function, and 2) the novel subtask-specific impairments within each OCS domain. Anxiety severity and years of education attained were included as covariates.

Results

Within-domain impairments that were uniquely associated with depression severity were calculation (b(.57)= 1.44, 95%CI[0.31, 2.56],p= .012), episodic memory (b(.52)= 1.36, 95%CI[0.34, 2.37],p= .009), picture naming (b(.45)= 1.18, 95%CI[0.31, 2.06],p= .008), number writing (b(.46)= 2.54, 95%CI[0.26, 2.07],p= .012), and visuospatial attention (b(.35)= 1.24, 95%CI[0.54, 1.93],p= .001). Analysis in pooled multiply imputed data (N= 430) corroborated complete case analysis findings.

Conclusions

Specific within-domain cognitive impairments have differential relationships with post-stroke depressive symptomology. Accommodating for these impairments in post-stroke depression interventions may potentially enhance therapeutic outcomes.
Development and evaluation of patient-centred polygenic risk score reports for glaucoma screening
Authors: Hollitt Georgina L , Hassall Mark M , Siggs Owen M , Craig Jamie E , Souzeau Emmanuelle
Published: September 2024

Background

Polygenic risk scores (PRS), which provide an individual probabilistic estimate of genetic susceptibility to develop a disease, have shown effective risk stratification for glaucoma onset. However, there is limited best practice evidence for reporting PRS and patient-friendly reports for communicating effectively PRS are lacking. Here we developed patient-centred PRS reports for glaucoma screening based on the literature and evaluated them with participants using a qualitative research approach.

Methods

We first reviewed existing PRS reports and literature on probabilistic risk communication. This informed the development of a draft glaucoma screening PRS report for a hypothetical high risk individual from the general population. We designed three versions of the report to illustrate risk using a pictograph, a pie chart and a bell curve. We then conducted semi-structured interviews to assess preference of visual risk communication aids, understanding of risk, content, format and structure of the reports. Participants were invited from an existing study, which aims to evaluate the clinical validity of glaucoma among individuals >50 years from the general population. Numeracy and literacy levels were assessed.

Results

We interviewed 12 individuals (50% female, 42% university education). Numeracy (mean 2.1±0.9, range 0-3), graph literacy (mean 2.8±0.8, range 0-4) and genetic literacy (mean 24.2±6.2, range -20-+46) showed a range of levels. We analysed the reports under three main themes: visual preferences, understanding risk and reports formatting. The visual component was deemed important to understanding risk, with the pictograph being the preferred visual risk representation, followed by the pie chart and the bell curve. Participants expressed preference for absolute risk in understanding risk, along with the written content explaining the results. The importance of follow-up recommendations and time to glaucoma onset were highlighted. Participants expressed varied opinions in the level of information and the colours used, which informed revisions of the report.

Conclusions

Our study revealed preferences for reporting PRS information in the context of glaucoma screening, to support the development of clinical PRS reporting. Further research is needed to assess PRS communication in other contexts and with other target audiences (e.g. referring clinicians), and its potential psychosocial impact in the wider community.
Gastrointestinal Dysmotility, Autonomic Function and Small Intestinal Bacterial Overgrowth Among People with Well-Controlled HIV
Authors: Robinson-Papp Jessica , Mehta Mitali , Mueller Bridget R. , Neupane Niyati , Zhao Zhan , Cedillo Gabriela , Coyle Kaitlyn , Campbell Maya , George Mary Catherine , Benn Emma KT , Lee Gina , Semler Jack
Published: September 2024

Introduction

Gastrointestinal dysfunction, including microbiome changes and increased translocation across a compromised gastrointestinal barrier plays a role in the chronic inflammation experienced by people with HIV (PWH). It is unknown whether autonomic neuropathy (AN) may contribute to these mechanisms by altering gastrointestinal motility.

Methods

This is a cross-sectional study of 100 PWH and 89 controls. All participants underwent assessment of gastrointestinal transit times using a wireless motility capsule (WMC). All PWH and a subset of controls also underwent: a standardized battery of autonomic function tests summarized as the Modified Composite Autonomic Severity Score (MCASS) and its adrenergic, cardiovagal and sudomotor sub-scores, breath testing for small intestinal bacterial overgrowth (SIBO), and the Patient Assessment of Upper Gastrointestinal Disorders Symptoms (PAGI-SYM) and Composite Autonomic Symptom Score 31 (COMPASS-31) questionnaires.

Results

PWH displayed shorter gastric emptying times (GET) and longer small bowel and colonic transit times (SBTT, CTT) compared to controls. Among PWH, GET was associated with PAGI-SYM score. The MCASS and its sudomotor sub-score (reflecting peripheral sympathetic function) were associated with SBTT but not GET or CTT. PWH with prolonged SBTT (>6h) were more likely to have SIBO.

Conclusion

Gastrointestinal motility is altered in PWH. This study provides preliminary evidence that changes in autonomic function may influence SBTT in PWH and that prolonged SBTT may contribute to the development of SIBO. Future studies are needed to more fully elucidate the pathophysiologic links between HIV-associated AN, altered gastrointestinal motility, the gastrointestinal microbiome, chronic inflammation, and resulting morbidity and mortality among PWH.
Patient-centered Transcriptomic and Multimodal Neuroimaging Determinants of Clinical Progression, Physical Activity and Treatment Needs in Parkinson’s Disease
Authors: Adewale Quadri , Khan Ahmed Faraz , Lin Sue-Jin , Baumeister Tobias R. , Zeighami Yashar , Carbonell Felix , Ferreira Daniel , Iturria-Medina Yasser
Published: September 2024

Parkinson’s disease is a complex and multifactorial disorder, but how its biological and clinical complexity emerge from molecular to macroscopic brain interactions remains poorly understood. Here, we use a personalized multiscale generative brain model to characterize direct spatiotemporal links between genes and multimodal neuroimaging-derived biological factors in PD. We identified a set of genes modulating PD-associated longitudinal changes in dopamine transporter level, neuronal activity, dendrite density and tissue atrophy. Inter-individual heterogeneity in the gene-mediated biological mechanisms is associated with five distinct configurations of PD motor and non-motor symptoms. Although characterized by distinctive biological pathways, all the symptom configurations are associated with cell cycle processes. Notably, the protein-protein interaction networks underlying these configurations revealed distinct hub genes includingMYC, CCNA2, CCDK1, SRC, STAT3andPSMD4. We also uncovered the biological mechanisms associated with physical activities performance in PD, and observed that leisure and work activities are principally related to neurotypical cholesterol homeostasis and inflammatory response processes, respectively. Finally, patient-tailoredin silicogene perturbations revealed a set of putative disease-modifying drugs with potential to effectively treat PD, most of which are associated with dopamine reuptake and anti-inflammation. Our study constitutes the first self-contained multiscale approach providing comprehensive insights into the complex multifactorial pathogenesis of PD, unravelling key biological modulators of physical and clinical deterioration, and serving as a blueprint for optimum drug selection at personalized level.
Why are telomeres the length that they are? Insight from a phylogenetic comparative analysis
Authors: Benson Derek M. , Padilla Perez Dylan J. , DeNardo Dale F.
Published: September 2024

Telomeres are short repeating nucleotide sequences at the ends of chromosomes that shorten with every cellular replication. Despite the importance of keeping telomere length within a critical homeostatic range, adult telomere length can differ by two orders of magnitude across vertebrate species. Why telomere length varies so widely remains unknown, though popular hypotheses suggest that body size, lifespan, and endothermy are key variables that have coevolved with telomere length. To test the relationship among telomere length, telomerase activity (which extends telomeres), and these variables, we modeled the evolution of telomere length across 122 vertebrate species. We failed to find an influence of body mass, lifespan, or baseline metabolism on telomere length. However, we found a significant interactive effect between baseline metabolism and body mass. The presence of telomerase activity was positively correlated with telomere length across the 58 species where data for both existed. Taken together, our findings suggest that body mass may have differentially influenced the evolution of telomere length in endotherms and ectotherms and indicate that telomerase activity and telomere length may have coevolved.