bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide analysis of binge-eating disorder identifies the first three risk loci and implicates iron metabolism
Authors: Burstein David , Griffen Trevor , Therrien Karen , Bendl Jaroslav , Venkatesh Sanan , Dong Pengfei , Modabbernia Amirhossein , Zeng Biao , Mathur Deepika , Hoffman Gabriel , Sysko Robyn , Hildebrandt Tom , Voloudakis Georgios , Roussos Panos
Published: May 2022

Binge-eating disorder (BED) is the most common eating disorder yet its genetic architecture remains largely unknown. Studying BED is challenging because it is often comorbid with obesity, a common and highly polygenic trait, and it is underdiagnosed in biobank datasets. To address this limitation, we apply a supervised machine learning approach to estimate the probability of each individual having BED based on electronic medical records from the Million Veteran Program. We perform a genome-wide association study on individuals of African (n = 77,574) and European (n = 285,138) ancestry while controlling for body mass index to identify three independent loci near the HFE, MCHR2 and LRP11 genes, which are reproducible across three independent cohorts. We identify genetic association between BED and several neuropsychiatric traits and implicate iron metabolism in the pathophysiology of BED. Overall, our findings provide insights into the genetics underlying BED and suggest directions for future translational research.
Transcriptomic meta-analysis of non-Hodgkin’s B-cell lymphomas reveals reliance on pathways associated with the extracellular matrix
Authors: Rapier-Sharman Naomi , Clancy Jeffrey , Pickett Brett E.
Published: May 2022

Approximately 450,000 cases of Non-Hodgkin’s lymphoma are diagnosed annually worldwide, resulting in ∼240,000 deaths. An augmented understanding of the common mechanisms of pathology among relatively large numbers of B-cell Non-Hodgkin’s Lymphoma (BCNHL) patients is sorely needed. We consequently performed a large transcriptomic meta-analysis of available BCNHL RNA-sequencing data from GEO, consisting of 322 relevant samples across ten distinct public studies, to find common underlying mechanisms across BCNHL subtypes. The study was limited to GEO’s publicly available human B-cell RNA-sequencing datasets that met our criteria, and limitations may include lack of diversity in ethnicities and age groups. We found ∼10,400 significant differentially expressed genes (FDR-adjusted p-value < 0.05) and 33 significantly modulated pathways (Bonferroni-adjusted p-value < 0.05) when comparing lymphoma samples to non-diseased samples. Our findings include a significant class of proteoglycans not previously associated with lymphomas as well as significant modulation of extracellular matrix-associated proteins. Our drug prediction results yielded new candidates including ocriplasmin and collagenase. We also used a machine learning approach to identify the BCNHL biomarkers YES1, FERMT2, and FAM98B, novel biomarkers of high predictive fidelity. This meta-analysis validates existing knowledge while providing novel insights into the inner workings and mechanisms of B-cell lymphomas that could give rise to improved diagnostics and/or therapeutics. No external funding was used for this study.
Human Lung-resident Mucosal-Associated Invariant T cells are Abundant, Express Antimicrobial Proteins, and are Cytokine Responsive
Authors: Meermeier Erin W. , Zheng Christina L. , Tran Jessica G , Soma Shogo , Worley Aneta H. , Weiss David I. , Modlin Robert L. , Swarbrick Gwendolyn , Karamooz Elham , Khuzwayo Sharon , Wong Emily B. , Gold Marielle C. , Lewinsohn David M.
Published: May 2022

Mucosal-associated Invariant T (MAIT) cells are an innate-like T cell subset that recognize a broad array of microbial pathogens, including respiratory pathogens. Here we investigate the transcriptional profile of MAIT cells localized to the human lung, and postulate that MAIT cells may play a role in maintaining homeostasis at this mucosal barrier. Using the MR1/5-OP-RU tetramer, we identified MAIT cells and non-MAIT CD8+ T cells in lung tissue not suitable for transplant from human donors. We used RNA-sequencing of MAIT cells compared to non-MAIT CD8+ T cells to define the transcriptome of MAIT cells in the human lung. We show that, as a population, lung MAIT cells are polycytotoxic, secrete the directly antimicrobial molecule IL-26, express genes associated with persistence, and selectively express cytokine and chemokine-related molecules distinct from other lung-resident CD8+ T cells, such as interferon-γ− and IL-12-receptors. These data highlight MAIT cells’ predisposition to rapid pro-inflammatory cytokine responsiveness and antimicrobial mechanisms in human lung tissue, concordant with findings of blood-derived counterparts, and support a function for MAIT cells as early sensors in the defense of respiratory barrier function.
A bacteriophage-based, highly efficacious, needle and adjuvant-free, mucosal COVID-19 vaccine
Authors: Zhu Jingen , Jain Swati , Sha Jian , Batra Himanshu , Ananthaswamy Neeti , Kilgore Paul B. , Hendrix Emily K. , Hosakote Yashoda M. , Wu Xiaorong , Olano Juan P. , Kayode Adeyemi , Galindo Cristi L. , Banga Simran , Drelich Aleksandra , Tat Vivian , Tseng Chien-Te K. , Chopra Ashok K. , Rao Venigalla B.
Published: May 2022

The authorized mRNA- and adenovirus-based SARS-CoV-2 vaccines are intramuscularly injected and effective in preventing COVID-19, but do not induce efficient mucosal immunity, or prevent viral transmission. We developed a bacteriophage T4-based, multicomponent, needle and adjuvant-free, mucosal vaccine by engineering spike trimers on capsid exterior and nucleocapsid protein in the interior. Intranasal administration of T4-COVID vaccine induced higher virus neutralization antibody titers against multiple variants, balanced Th1/Th2 antibody and cytokine responses, stronger CD4+and CD8+T cell immunity, and higher secretory IgA titers in sera and bronchoalveolar lavage with no effect on the gut microbiota, compared to vaccination of mice intramuscularly. The vaccine is stable at ambient temperature, induces apparent sterilizing immunity, and provides complete protection against original SARS-CoV-2 strain and its Delta variant with minimal lung histopathology. This mucosal vaccine is an excellent candidate for boosting immunity of immunized and/or as a second-generation vaccine for the unimmunized population.
Genetic epidemiology of human neutrophil antigen variants suggest significant global variability
Authors: Rophina Mercy , Scaria Vinod
Published: May 2022

Human neutrophil antigens possess significant clinical implications especially in the fields of transfusion and transplantation medicine. Efforts to estimate the prevalence of genetic variations underpinning the antigenic expression are emerging. However, there lacks a precise capture of the global frequency profiles. Our article emphasizes the potential utility of maintaining an organized online repository of evidence on neutrophil antigen associated genetic variants from published literature and reports. This in our opinion, is an emerging area and would significantly benefit from the awareness and understanding of population-level diversities.
Thyroid hormone and ALK5 inhibitor improve maturation of human pluripotent stem cell derived hepatocytes
Authors: Withey Sarah , Gerrard David , Leeson Hannah , Atkinson-Dell Rebecca , Harrison Sean , Baxter Melissa , Wolvetang Ernst , Hanley Neil
Published: May 2022

Hepatocytes derived from human pluripotent stem cells (PSCs) hold great promise for modeling human liver disease, in vitro hepatotoxicity testing, and future cellular therapy. However, current protocols generate hepatocyte-like cells (HLCs) that resemble fetal hepatocytes, and thus do not accurately recapitulate the molecular identity and functions of the adult liver. To address this, we compared the transcriptomes of human fetal and adult liver to PSC-derived HLCs during progressive stages of in vitro differentiation. This revealed that during the final stages of in vitro differentiation the hepatic transcription factors HNF4A and CEBPA were sub-optimally expressed. Computational analyses predicted that ALK5i II (TGF-β receptor inhibitor) and thyroid hormone (T3) would be able to rectify this and improve HLC maturation. We next show that application of these molecules during hepatocyte differentiation indeed increases CEBPA and HNF4A mRNA and protein expression, and that these HLCs show enhanced albumin secretion, a 25-fold increase in CYP3A4 activity, and 10 to 100-fold increased expression of mature hepatic markers. We demonstrate that this improved maturation is effective across different cell lines and HLC differentiation protocols, and exemplifies that our approach provides a tractable template for identifying and targeting additional factors that that will fully mature human liver cells from human pluripotent stem cells.
Touch receptor end-organ innervation and function requires sensory neuron expression of the transcription factor Meis2
Authors: Desiderio Simon , Schwaller Fred , Tartour Kevin , Padmanabhan Kiran , Lewin Gary R. , Carroll Patrick , Marmigère Frédéric
Published: May 2022

Touch sensation is primarily encoded by mechanoreceptors, called Low-Threshold Mechanoreceptors (LTMRs), with their cell bodies in the Dorsal Root Ganglia (DRG). Because of their great diversity in terms of molecular signature, terminal endings morphology and electrophysiological properties, mirroring the complexity of tactile experience, LTMRs are a model of choice to study the molecular cues differentially controlling neuronal diversification. While the transcriptional codes that define different LTMR subtypes have been extensively studied, the molecular players that participate in their late maturation and in particular in the striking diversity of their end-organ morphological specialization are largely unknown. Here we identified the TALE homeodomain transcription factor Meis2 as a key regulator of LTMRs target-field innervation.Meis2is specifically expressed in cutaneous LTMRs and its expression depends on target-derived signals. While LTMRs lackingMeis2survived and are normally specified, their end-organ innervations, electrophysiological properties and transcriptome are differentially and markedly affected, resulting in impaired sensory-evoked behavioral responses. These data establishMeis2as a major transcriptional regulator controlling the orderly formation of sensory neurons innervating peripheral end-organs required for light touch.
Tracing the substrate translocation mechanism in P-glycoprotein
Authors: Gewering Theresa , Waghray Deepali , Parey Kristian , Jung Hendrik , Tran Nghi N.B. , Zapata Joel , Zhao Pengyi , Chen Hao , Januliene Dovile , Hummer Gerhard , Urbatsch Ina L. , Moeller Arne , Zhang Qinghai
Published: May 2022

P-glycoprotein (Pgp) is a prototypical ABC transporter of great biological and clinical significance that confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs1–3. Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds4–9, but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.
Chemical ecology of Himalayan eggplant variety’s antixenosis: Identification of geraniol as an oviposition deterrent against the eggplant shoot and fruit borer
Authors: Ghosh Rituparna , Metze Dennis , Shaikh Maroof , Deshpande Ashish , Firake Dnyaneshwar M. , Pandit Sagar
Published: May 2022

Eggplant (Solanum melongena) suffers severe losses due to a multi-insecticide resistant lepidopteran pest, shoot and fruit borer (SFB,Leucinodes orbonalis). Heavy and combinatorial application of pesticides for SFB control renders eggplant risky for human consumption.

We observed that 1) ovipositing SFB females can find even solitary plants of susceptible varieties and 2) they do not oviposit on Himalayan eggplant variety RC-RL-22 (RL22). We hypothesized that the olfactory cues influence ovipositing female’s host choice.

To find these cues, leaf volatile blends of seven eggplant varieties were profiled using GCMS. Seven compounds were present in >2.5-fold concentrations in RL22 than the other varieties. In choice assays, oviposition deterrence efficacies of these candidate compounds were independently tested by their foliar application on SFB-susceptible varieties. Complementation of geraniol, which was exclusively found in RL22, reduced oviposition (>90%). To validate geraniol’s role in RL22’s SFB-deterrence, we silenced RL22’s geraniol synthase gene using virus-induced gene silencing. Geraniol biosynthesis suppression rendered RL22 SFB-susceptible; foliar geraniol application on the geraniol synthase-silenced plants restored oviposition deterrence.

We infer that geraniol is RL22’s SFB oviposition deterrent. The use of natural compounds like geraniol, which influence the chemical ecology of oviposition can reduce the load of hazardous larvicidal pesticides.
Causal associations between iron status and sepsis: a Mendelian randomisation analysis
Authors: Hamilton Fergus , Mitchell Ruth , Ahmed Haroon , Ghazal Peter , Timpson Nic
Published: May 2022

Iron deficiency is associated with a substantial burden of morbidity. However, supplementation of iron has been linked to increased rates of serious infection in randomised trials of children in sub-Saharan Africa. Randomised trials in other settings have been inconclusive and it is unknown if changes in levels of iron biomarkers – a mark of setpoint changes in iron homeostasis - are linked to sepsis in these other settings. We used genetic variants associated with levels of iron biomarkers as instrumental variables in a Mendelian randomisation (MR) analysis to test the hypothesis that increasing levels of iron biomarkers increase the risk of sepsis. In observational and MR analyses we found that increases in iron biomarkers increase the risk of sepsis. In stratified analyses, we show that this risk may be larger in those with iron deficiency and/or anaemia. Taken together, results here suggest a required caution in supplementation of iron and underline the role of iron homeostasis in severe infection.
Effectiveness of Covid-19 vaccines against SARS-CoV-2 Omicron variant (B.1.1.529): A systematic review with meta-analysis and meta-regression
Authors: Pratama Nando Reza , Wafa Ifan Ali , Budi David Setyo , Sutanto Henry , Asmarawati Tri Pudy , Wungu Citrawati Dyah Kencono
Published: May 2022

Background

There is a need for evaluation regarding vaccine effectiveness (VE) and the urgency of booster vaccination against Covid-19 B.1.1.529 (Omicron) variant.

Methods

Systematic search was conducted on April 6th, 2022, on databases (PubMed, ScienceDirect, CENTRAL, Web of Science, Scopus). VE difference (VED) estimates were assessed using random-effects model and DerSimonian-Laird tau estimators. Two models result, i.e., within 3 months and within 3 months or more, are compared. VE versus time meta-regression analysis was evaluated using mixed-effects model with Restricted-Maximum Likelihood tau estimators and Hartung-Knapp adjustments.

Findings

Ad26.COV2.S, BNT162b2, ChAdOx1 nCov-19, and mRNA-1273 vaccines were included in the analyses. Compared to full dose, booster dose of overall vaccines provided better protection against any (VED=22% (95%CI 15%-29%), p<0.001), severe (VED=20% (95%CI 8%-32%), p=0.001) and symptomatic (VED=22% (95%CI 11%-34%), p<0.001) Omicron infections within 3 months, as well as within 3 months or more (VED=30% (95%CI 24%-37%), p<0.001 for any, VED=18% (95%CI 13%-23%), p<0.001 for severe and VED=37% (95%CI 29%-46%), p<0.001 for symptomatic infections). The meta-regression analysis of overall vaccines revealed that the full dose VE against any and symptomatic Omicron infections were significantly reduced each month by 3.0% (95%CI 0.9%-4.8%, p=0.004) and 5.2% (95%CI 3.3%-7.1%, p=0.006), respectively; whereas booster dose effectiveness against severe and symptomatic Omicron infections were decreased by 3.7% (95%CI 5.1%-12.6%, p=0.030) and 3.9% (95%CI 1.2%-6.5%, p=0.006), respectively.

Interpretation

Compared to full dose only, a booster dose addition provides better protection against B.1.1.529 infection. Although the VE estimates of Ad26.COV2.S, BNT162b2, ChAdOx1 nCov-19, and mRNA-1273 vaccines against B.1.1.529 infection after both full and booster doses are generally moderate, and the booster dose provides excellent protection against severe infection, it is important to note that the VE estimates decline over time, suggesting the need for a regular Covid-19 booster injection after certain period of time to maintain VE.
Multi-center evaluation of baseline neutrophil:lymphocyte (NLR) ratio as an independent predictor of mortality and clinical risk stratifier in Idiopathic Pulmonary Fibrosis
Authors: Mikolasch Theresia A , George Peter M. , Sahota Jagdeep , Nancarrow Thomas , Barratt Shaney L , Woodhead Felix A. , Kouranos Vasilis , Cope Victoria S A , Creamer Andrew W , Fidan Silan , Ganeshan Balaji , Hoy Luke , Mackintosh John A , Shortman Robert , Duckworth Anna , Fallon Janet , Garthwaite Helen , Heightman Melissa , Adamali Huzaifa I , Lines Sarah , Win Thida , Wollerton Rebecca , Renzoni Elisabetta A , Steward Matthew , Wells Athol U. , Gibbons Michael , Groves Ashley M , Gooptu Bibek , Scotton Chris J. , Porter Joanna C.
Published: May 2022

Background

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal disorder with a variable disease trajectory. The aim of this study was to assess the potential of neutrophil-to-lymphocyte ratio (NLR) to predict outcomes for people with IPF.

Method

We adopted a two-stage discovery and validation design using patients from the UCL partners (UCLp) cohort. For the discovery analysis, we included 71 patients from UCLH. In the validation analysis, we included 928 people with IPF, using real-life data from UCLH and 5 other UK centres. Data were collected from patients presenting over a 13-year period with a mean follow up time of 3.7 years.

Findings

In the discovery analysis, we showed that values of NLR (<2.9 vs >/=2.9) were associated with increased risk of mortality (HR 2.04, 95% CI 1.09-3.81; p=0.025). In the validation cohort we confirmed this association of high NLR with mortality (HR 1.65, 95% CI 1.39-1.95; p<0·0001) and showed incorporation of baseline NLR in a modified GAP-stage/index (GAP/index)-plus improved predictive ability

Interpretation

We have identified NLR as a widely available test that significantly correlates with lung function, can predict outcomes in IPF and refines clinical GAP-staging. NLR may help ILD specialist centres prioritise at risk patients in a timely way, even in the absence of lung function.
Senescence-Induced Immune Remodeling Facilitates Metastatic Adrenal Cancer in a Sex-Dimorphic Manner
Authors: Warde Kate M. , Liu Lihua , Smith Lorenzo J. , Lohman Brian K. , Stubben Chris J. , Ekiz H. Atakan , Ammer Julia L. , Converso-Baran Kimber , Giordano Thomas J. , Hammer Gary D. , Basham Kaitlin J.
Published: May 2022

Aging is a carcinogen that markedly increases cancer risk, yet we have limited mechanistic understanding of cancer initiation in aged cells. Here, we demonstrate induction of the hallmark aging process cellular senescence, triggered by loss of Wnt inhibitor ZNRF3, remodels the tissue microenvironment and ultimately permits metastatic adrenal cancer. Detailed characterization reveals a striking sexual dimorphism. Males exhibit earlier senescence activation and a greater innate immune response. This results in high myeloid cell accumulation and lower incidence of malignancy. Conversely, females present a dampened immune response and are more prone to metastatic cancer. Senescence-recruited myeloid cells become increasingly depleted with advanced tumor progression, which is recapitulated in patients where a low myeloid signature is associated with worse outcome. Collectively, our study reveals a novel role for myeloid cells in restraining adrenal cancer progression with significant prognostic value, and provides a model for interrogating pleiotropic effects of cellular senescence in cancer.

Graphical abstract created with BioRender.com
Nanobodies identify an activated state of the TRIB2 pseudokinase
Authors: Jamieson Sam A , Pudjihartono Michael , Horne Christopher R , Day Robert C , Murphy James M , Mace Peter D
Published: May 2022

Tribbles proteins (TRIB1–3) are a pseudokinase-only branch of the human kinome, which recruit substrates to the COP1 ubiquitin-ligase for ubiquitination. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukaemia oncogene, by way of recruiting the C/EBPa transcription factor for degradation by COP1. Here we report selection and characterisation of nanobodies against the TRIB2 pseudokinase domain from a synthetic yeast surface-display library. We identified nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of Nb4.103 in complex with TRIB2 identified a mode of binding to the N-terminal lobe of the pseudokinase, in a manner that enables specific recognition of TRIB2 over TRIB1 and TRIB3. In the nanobody-stabilised state, TRIB2 adopts an activated conformation that is remarkably similar to the C/EBPa-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilise a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors, and nanobody tools for future investigation of TRIB2 function.
Shock or jump: deimatic behaviour is repeatable and polymorphic in a yellow-bellied toad
Authors: Chiocchio Andrea , Martino Giuseppe , Bisconti Roberta , Carere Claudio , Canestrelli Daniele
Published: May 2022

Inter-individual variation in antipredatory strategies has long attracted curiosity among scientists. Deimatisms is a complex and time-structured antipredatory strategy consisting in prey suddenly unleashing unexpected defences to frighten predators and stop their attack. Being deimatism traditionally considered as a stereotyped antipredatory response, the inter-individual variation in phenotypic traits related to deimatic displays is almost unexplored. In this study, we employed common garden experiments on 71 yellow-bellied toad Bombina pachypus to investigate the extent and pattern of inter-individual variation in the unken-reflex behaviour, a deimatic display performed by some amphibians. Results show that deimatic displays consistently differ among individuals. Only about half of the individuals reacted to the predation stimuli by exhibiting the display, which varied in responsiveness, duration and intensity. All the investigated descriptors were repeatable (R > 0.50, p < 0.01). Finally, we found significant correlations between the measured parameters, defining two alternative behavioural profiles: individuals quickly doing unken-reflex, with high intensity and long duration of the display, and individuals avoiding unken-reflex but rather escaping. Such dichotomy resembles respectively the proactive and reactive coping styles. Such an unexpected variation in deimatic behaviour raises intriguing questions on the evolutionary processes shaping multiple adaptive responses to predation within populations.
EndophilinA-dependent coupling between activity-dependent calcium influx and synaptic autophagy is disrupted by a Parkinson-risk mutation
Authors: Bademosi Adekunle T. , Decet Marianna , Kuenen Sabine , Calatayud Carles , Swerts Jef , Gallego Sandra F , Schoovaerts Nils , Louros Nikolaos , Martin Ella , Karamanou Spyridoula , Sibarita Jean-Baptiste , Vints Katlijn , Gounko Natalia V. , Meunier Frédéric A. , Economou Anastassios , Versées Wim , Rousseau Frederic , Schymkowitz Joost , Soukup Sandra-F. , Verstreken Patrik
Published: May 2022

Neuronal activity and neurotransmitter release cause use-dependent decline in protein function. However, it is unclear how this is coupled to local protein turnover and quality control mechanisms. Here we show that the endocytic protein Endophilin-A (EndoA/ENDOA1) couples activity-induced calcium influx to synaptic autophagy and neuronal survival. We identify single mutations in the EndoA flexible region that either increases EndoA diffusion and promotes autophagosome formation in the absence of calcium, or immobilizes EndoA and blocks autophagy, even in the presence of calcium. Hence, the EndoA flexible region is a switch that responds to calcium, regulating EndoA nanoscale synaptic organization and association with autophagosomes driving their formation. Interestingly, a pathogenic variant in the human ENDOA1 variable region that confers risk to Parkinson’s disease (PD), also confines ENDOA1 to the synaptic plasma membrane and equally blocks autophagy in flies in vivo and in induced human neurons. Thus, our work reveals a mechanism neurons use to connect neuronal activity to local protein turnover by autophagy, which is critical for neuronal survival.
INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease
Authors: Castranio EL , Hasel P , Haure-Mirande J-V , Ramirez Jimenez AV , Hamilton W , Kim RD , Wang M , Zhang B , Gandy S , Liddelow SA , Ehrlich ME
Published: May 2022

The dual specificity lipid/protein phosphatase SHIP1 (encoded by theINPP5Dgene) is enriched in myeloid cells. Single nucleotide polymorphisms (SNPs) inINPP5Dcoding and non-coding regions impact risk for developing late onset sporadic Alzheimer’s disease (LOAD). We present pathological analyses with spatial transcriptomics of mice with tamoxifen-sensitive microglial knockdown ofInpp5dand show exacerbated plaque pathology, plaque-associated microglial density, and altered gene expression around plaques, suggesting novel markers for plaque-associated reactive microglia.
Novel CRISPR-based detection of Leishmania species
Authors: Dueñas Eva , Nakamoto Jose A. , Cabrera-Sosa Luis , Huaihua Percy , Cruz María , Arévalo Jorge , Milón Pohl , Adaui Vanessa
Published: May 2022

Tegumentary leishmaniasis, a disease caused by protozoan parasites of the genus Leishmania, is a major public health problem in many regions of Latin America. Its diagnosis is difficult given other conditions resembling leishmaniasis lesions and co-occurring in the same endemic areas. A combination of parasitological and molecular methods lead to accurate diagnosis, with the latter being traditionally performed in centralized reference and research laboratories as they require specialized infrastructure and operators. CRISPR-Cas systems have recently driven innovative tools for nucleic acid detection that combine high specificity, sensitivity and speed and are readily adaptable for point-of-care testing. Here, we harnessed the CRISPR-Cas12a system for molecular detection of Leishmania spp., emphasizing medically relevant parasite species circulating in Peru and other endemic areas in Latin America, with L. (Viannia) braziliensis being the main etiologic agent of cutaneous and mucosal leishmaniasis. We developed two assays targeting multi-copy targets commonly used in the molecular diagnosis of leishmaniasis: the 18S ribosomal RNA gene (18S rDNA), highly conserved across Leishmania species, and a region of kinetoplast DNA (kDNA) minicircles conserved in the L. (Viannia) subgenus. Our CRISPR-based assays were capable of detecting down to 5 × 10−2 (kDNA) or 5 × 100 (18S rDNA) parasite genome equivalents/reaction with PCR preamplification. The 18S PCR/CRISPR assay achieved pan-Leishmania detection, whereas the kDNA PCR/CRISPR assay was specific for L. (Viannia) detection. No cross-reaction was observed with Trypanosoma cruzi strain Y or human DNA. We evaluated the performance of the assays using 49 clinical samples compared to a kDNA real-time PCR assay as the reference test. The kDNA PCR/CRISPR assay performed equally well as the reference test, with positive and negative percent agreement of 100%. The 18S PCR/CRISPR assay had high positive and negative percent agreement of 82.1% and 100%, respectively. The findings support the potential applicability of the newly developed CRISPR-based molecular tools for first-line diagnosis of Leishmania infections at the genus and L. (Viannia) subgenus levels.
Nipsnap1—A Regulatory Factor Required For Long-Term Maintenance of Non-Shivering Thermogenesis
Authors: Liu Yang , Qu Yue , Cheng Chloe , Tsai Pei-Yin , Edwards Kaydine , Xue Siwen , Pandit Supriya , Eguchi Sakura , Sanghera Navneet , Barrow Joeva J
Published: May 2022

The molecular activation of non-shivering thermogenesis (NST) has strong potential to combat obesity and metabolic disease. However, the mechanisms surrounding the maintenance of NST once it is fully activated, remain unexplored. Here, we present 4-Nitrophenylphosphatase Domain and Non-Neuronal SNAP25-Like 1 (Nipsnap1) as a critical regulator of long-term thermogenic maintenance in brown adipose tissue (BAT). Nipsnap1 localizes to the mitochondrial matrix and increases its transcript and protein levels in response to both chronic cold and β3 adrenergic signaling. Through the generation of BAT-specific Nipsnap1 knockout mice (N1-KO), we show that these mice are unable to sustain activated energy expenditure and fail to protect their body temperature in the face of an extended cold challenge. Mechanistically, we demonstrate that Nipsnap1 integrates with lipid metabolism and BAT-specific ablation of Nipsnap1 leads to severe defects in β-oxidation capacity. Our findings identify Nipsnap1 as a potent regulator of long-term NST maintenance.
Questioning the association of the STMN2 dinucleotide repeat with ALS
Authors: Ross Jay P. , Akcimen Fulya , Liao Calwing , Spiegelman Dan , Weisburd Ben , Dupré Nicolas , Dion Patrick A. , Rouleau Guy A. , Farhan Sali M. K.
Published: May 2022

Lowered expression of STMN2 is associated with TDP-43 pathology in amyotrophic lateral sclerosis (ALS). Recently, the number of dinucleotide CA repeats in an intron of the STMN2 gene was reported to be associated with increased risk for ALS. Here, we used a case-control cohort of whole genome sequencing (WGS) as well as WGS from populations in the gnomAD cohort to attempt to replicate this proposed association. We find that repeats well above the previously reported pathogenic threshold of 19 are commonly observed in unaffected individuals across different populations. Further, we did not observe an association between longer STMN2 CA repeats and ALS phenotype. In summary, our results do not support a role of STMN2 CA repeats towards ALS risk.

Disclosures

None to disclose
The mutational landscape of single neurons and oligodendrocytes reveals evidence of inflammation-associated DNA damage in multiple sclerosis
Authors: Motyer Allan , Jackson Stacey , Yang Bicheng , Harliwong Ivon , Tian Wei , Shiu Wingin , Shao Yunchang , Wang Bo , McLean Catriona , Barnett Michael , Kilpatrick Trevor J. , Leslie Stephen , Rubio Justin P.
Published: May 2022

Neuroinflammation has been linked to DNA damage in multiple sclerosis (MS), but its impact on neural cell genomes at nucleotide resolution is unknown. To address this question, we performed single nucleus whole genome sequencing to determine the landscape of somatic mutation in 172 neurons and oligodendrocytes (OLs) extracted from post-mortem brain tissue from 5 MS cases and three controls. We identified two cases with a significant excess of somatic single nucleotide variants (sSNV) in neurons and OLs from MS inflammatory demyelinated lesions. For a case with primary progressive MS, this translated to a 68% increase in sSNV frequency and 32-year equivalent increase in biological age of lesion-resident cells. Mutational signature analysis conducted on all cells revealed that defective DNA repair and transcription-associated DNA damage are important mutagenic mechanism in both neurons and OLs in MS. Our findings provide the first evidence that inflammation in the brains of people with MS is associated with DNA damage, which may have implications for other neurodegenerative diseases and future drug development.
Insecticide Resistance Surveillance of Malaria and Arbovirus Vectors in Papua New Guinea 2017-2022
Authors: Katusele Michelle , Lagur Solomon , Endersby-Harshman Nancy , Demok Samuel , Goi Joelyn , Vincent Naomi , Sakur Muker , Dau Absalom , Kilepak Lemen , Gideon Stephen , Pombreaw Christine , Makita Leo , Hoffmann Ary , Robinson Leanne J , Laman Moses , Karl Stephan
Published: May 2022

Background

Insecticide resistance monitoring is key for evidence-based control of Anopheles and Aedes disease vectors in particular, since the vast majority of insecticide-based public health adult vector control tools are reliant on pyrethroids. While widespread pyrethroid resistance in Anopheles species and Aedes aegypti has been described in many countries, data for Papua New Guinea are scarce. Available data indicate the local Anopheles populations remain pyrethroid-susceptible, making regular insecticide resistance monitoring even more important. Knowledge on Aedes insecticide resistance in PNG is very limited, however, high levels of Aedes aegypti resistance have been described. Here we present insecticide resistance monitoring data from across PNG generated between 2017 and 2022.

Methods

Mosquito larvae were collected in larval habitat surveys and through ovitraps. Mosquitoes were reared to adults and subjected to insecticide treated filter papers in WHO insecticide susceptibility bioassays. Subsets of Aedes mosquitoes were subjected to sequencing of the voltage-sensitive sodium channel (Vssc) region to identify resistance mutations.

Results

Overall, nearly 20,000 adult female mosquitoes from nine PNG provinces were used in the tests. We show that in general, Anopheline mosquitoes in PNG remain susceptible to pyrethroids but with worrying signs of reduced 24 h mortality in some areas. In addition, some Anopheles populations were indicated to be resistant against DDT. We show that Ae. aegypti in PNG are pyrethroid, DDT and likely bendiocarb resistant with a range of Vssc resistance mutations identified. We demonstrate that Ae. albopictus is DDT resistant and is likely developing pyrethroid resistance based on finding a low frequency of Vssc mutations.

Conclusion

This study represents the largest overview of insecticide resistance in PNG. While Ae. aegypti is highly pyrethroid resistant, the Anopheline and Ae. albopictus populations exhibit low levels of resistance in some areas. It is important to continue to monitor insecticide resistance in PNG and prepare for the widespread emergence of pyrethroid resistance in major disease vectors.
Structure of V-ATPase from citrus fruit
Authors: Tan Yong Zi , Keon Kristine A. , Abdelaziz Rana , Imming Peter , Schulze Waltraud , Schumacher Karin , Rubinstein John L
Published: May 2022

Vacuolar-type ATPases (V-ATPases) are rotary proton pumps involved in numerous essential cellular processes in all eukaryotes. Difficulty in obtaining preparations of purified V-ATPase from plants in sufficient quantities for structural analysis has hindered determining the 3D structure of the plant V-ATPase. We used the Legionella pneumophila effector SidK to affinity-purify the endogenous V-ATPase from lemon fruit. The preparation was sufficient to partially cover an electron microscopy specimen grid, allowing structure determination for the enzyme in two rotational states. The structure defines the ATP:H+ ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared to the yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme.
Temporal changes in the microglial proteome of male and female mice after a diffuse brain injury using label-free quantitative proteomics
Authors: Doust Yasmine V. , Bindoff Aidan , Holloway Olivia G. , Wilson Richard , King Anna E. , Ziebell Jenna M.
Published: May 2022

Traumatic brain injury (TBI) triggers neuroinflammatory cascades mediated by microglia, which promotes tissue repair in the short-term. These cascades may exacerbate TBI-induced tissue damage and symptoms in the months to years post-injury. However, the progression of the microglial function across time post-injury and whether this differs between biological sexes is not well understood. In this study, we examined the microglial proteome in the days (3- and 7-days) to 1 month (28 days) after a midline fluid percussion injury (mFPI) in male and female mice using label-free quantitative proteomics. We identified a reduction in microglial proteins involved with clearance of neuronal debris via phagocytosis at 3- and 7-days post-injury. At 28 days post-injury pro-inflammatory proteins were decreased and anti-inflammatory proteins were increased in microglia. These results indicate a reduction in microglial clearance of neuronal debris in the days post-injury with a shift to anti-inflammatory function by 1 month. The changes in the microglial proteome that occurred across time post-injury did not differ between biological sexes. However, we did identify an increase in microglial proteins related to pro-inflammation as well as insulin and estrogen signalling in males compared with female mice that occurred with or without a brain injury. Although microglial response was similar between males and females up to 1 month following TBI, biological sex differences in the basal microglial proteome has implications for the efficacy of treatment strategies targeting the microglial response post-injury.
MITE infestation of germline accommodated by genome editing in Blepharisma
Authors: Seah Brandon Kwee Boon , Singh Minakshi , Emmerich Christiane , Singh Aditi , Woehle Christian , Huettel Bruno , Byerly Adam , Stover Naomi , Sugiura Mayumi , Harumoto Terue , Swart Estienne Carl
Published: May 2022

During a sophisticated developmental process, ciliates excise numerous internally eliminated sequences (IESs) from a germline genome copy, producing a functional somatic genome. Most IESs ultimately originate from transposons but homology is obscured by sequence decay. To obtain more representative perspectives on ciliate genome editing, we assembled forty thousand IESs of Blepharisma stoltei, from a much earlier-diverging lineage than existing models. Short IESs (< 115 bp) were largely non-repetitive, with a pronounced ~10 bp length periodicity, whereas longer IESs (max 7 kbp) were non-periodic and contained abundant interspersed repeats. Contrary to current models, the Blepharisma germline genome encodes few transposases. Instead, its most abundant repeat (8000 copies) was a Miniature Inverted-repeat Transposable Element (MITE), apparently a deletion derivative of a germline-limited Pogo-family transposon. We propose MITEs as an important and eventually self-limiting IES source. Rather than defending germline genomes against mobile elements, we argue that transposase domestication actually facilitates junk DNA accumulation.
Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
Authors: Zhang Minjie , Hwang Irena T. , Li Kongpan , Bai Jianhui , Chen Jian-Fu , Weissman Tsachy , Zou James Y. , Lu Zhipeng
Published: May 2022

The recent development and application of methods based on the general principle of “crosslinking and proximity ligation” (crosslink-ligation) are revolutionizing RNA structure studies in living cells. However, extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new strategy to map short reads with irregular gaps at high sensitivity and specificity. Analysis of previously published data reveals distinct properties and bias caused by the crosslinking reactions. We perform rigorous and exhaustive classification of alignments and discover eight types of arrangements that provide distinct information on RNA structures and interactions. To deconvolve the dense and intertwined gapped alignments, we develop a network/graph-based tool Crosslinked RNA Secondary Structure Analysis using Network Techniques (CRSSANT), which enables clustering of gapped alignments and discovery of new alternative and dynamic conformations. We discover that multiple crosslinking and ligation events can occur on the same RNA, generating multisegment alignments to report complex high-level RNA structures and multi-RNA interactions. We find that alignments with overlapped segments are produced from potential homodimers and develop a new method for their de novo identification. Analysis of overlapping alignments revealed potential new homodimers in cellular noncoding RNAs and RNA virus genomes in the Picornaviridae family. Together, this suite of computational tools enables rapid and efficient analysis of RNA structure and interaction data in living cells.
Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
Authors: St. Pierre Celine L. , Macias-Velasco Juan F. , Wayhart Jessica P. , Yin Li , Semenkovich Clay F. , Lawson Heather A.
Published: May 2022

Allele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's product, leading to expression imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute to this cross talk remains understudied. Here, we explored how genotype, parent-of-origin, tissue, sex, and dietary fat simultaneously influence ASE biases. Male and female mice from a F1 reciprocal cross of the LG/J and SM/J strains were fed a high or low fat diet. We harnessed strain-specific variants to distinguish between two ASE classes: parent-of-origin-dependent (unequal expression based on parental origin) and sequence-dependent (unequal expression based on nucleotide identity). We present a comprehensive map of ASE patterns in 2853 genes across three tissues and nine environmental contexts. We found that both ASE classes are highly dependent on tissue and environmental context. They vary across metabolically relevant tissues, between males and females, and in response to dietary fat. We also found 45 genes with inconsistent ASE biases that switched direction across tissues and/or environments. Finally, we integrated ASE and QTL data from published intercrosses of the LG/J and SM/J strains. Our ASE genes are often enriched in QTLs for metabolic and musculoskeletal traits, highlighting how this orthogonal approach can prioritize candidate genes. Together, our results provide novel insights into how genetic, epigenetic, and environmental mechanisms govern allele-specific expression, which is an essential step toward deciphering the genotype-to-phenotype map.
A tunable broadband THz absorber using periodic arrays of graphene disks
Authors: Mohamad Khani Amir Ali , Aghaee Toktam , Mazloum Jalil , Jamali Morteza
Published: May 2022

Purpose

A wide band perfect THz absorber is presented in this work. The structure includes two layers of graphene disks on the silicon dioxide dielectric layer while a golden plate is placed at the bottom to act as a fully reflecting mirror against THz waves. According to the simulations, the device is robust enough to show independent operation versus layers thicknesses variations, chemical potentials mismatches and changing of electron relaxation time. The designed THz absorber in this work is an appropriate basic block for several applications in THz optical systems such as sensors, detectors and modulators.

Design/methodology/approach

The layers in the proposed device are modeled via passive circuit elements and consequently, the equivalent circuit of the device is calculated. Leveraging the developed equivalent circuit model (ECM) and impedance matching concept, the proposed device is designed to perfect absorption with 4.7 THz bandwidth that possesses over 90% absorption. Ample simulations are performed using MATLAB (ECM) and CST (finite element method) to verify the superior performance of the device. According to the simulations, the device is robust enough to show independent operation versus layers thicknesses variations, chemical potentials mismatches and changing of electron relaxation time.

Findings

This work reports a wideband THz absorber, composed of two graphene layers. This paper considers the circuit model representation for two different layers of the device. For a unique structure, a highly tunable response versus chemical potential is obtained. The circuit model approach and impedance matching theory are exploited to reduce computational time regarding conventional approaches.

Originality/value

A wide band absorber in THz band is presented. Leveraging circuit model approach and impedance matching theory, the design procedure is simplified regarding CPU time and memory requirements compared to conventional methods. Detailed calculations and ample simulations verify the performance excellency of the device to absorb THz incident waves in 2–6.5 THz frequencies. Also, the robustness of the device is investigated versus parameters mismatches like layers thicknesses and chemical potentials values. According to the simulations and absorption response, the proposed device is an appropriate block to be used in THz optical systems such as detectors, imaging systems and optical modulators.