The FAM13A Long Isoform Regulates Cilia Movement and Co-ordination in Airway Mucociliary Transport.

SNPs in the FAM13A locus are amongst the most commonly reported risk alleles associated with chronic obstructive pulmonary disease (COPD) and other respiratory diseases, however the physiological role of FAM13A is unclear. In humans, two major protein isoforms are expressed at the FAM13A locus: 'long' and 'short', but their functions remain unknown, partly due to a lack of isoform conservation in mice. We performed in-depth characterisation of organotypic primary human airway epithelial cell subsets and show that multiciliated cells predominantly express the FAM13A long isoform containing a putative N-terminal Rho GTPase activating protein (RhoGAP) domain. Using purified proteins, we directly demonstrate RhoGAP activity of this domain. In Xenopus laevis, which conserve the long isoform, Fam13a-deficiency impaired cilia-dependent embryo motility. In human primary epithelial cells, long isoform deficiency did not affect multiciliogenesis but reduced cilia co-ordination in mucociliary transport assays. This is the first demonstration that FAM13A isoforms are differentially expressed within the airway epithelium, with implications for the assessment and interpretation of SNP effects on FAM13A expression levels. We also show that the long FAM13A isoform co-ordinates cilia-driven movement, suggesting that FAM13A risk alleles may affect susceptibility to respiratory diseases through deficiencies in mucociliary clearance. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

Factors influencing the outcomes of non-pharmacological interventions for managing fatigue across the lifespan of people living with musculoskeletal (MSK) conditions: a scoping review protocol.

INTRODUCTION: Fatigue is an important and distressing symptom for many people living with chronic musculoskeletal (MSK) conditions. Many non-pharmacological interventions have been investigated in recent years and some have been demonstrated to be effective in reducing fatigue and fatigue impact, however, there is limited guidance for clinicians to follow regarding the most appropriate management options. The objective of this scoping review is to understand and map the extent of evidence in relation to the factors that relate to the outcome of non-pharmacological interventions on MSK condition-related fatigue across the lifespan. METHODS AND ANALYSIS: This scoping review will include evidence relating to people of all ages living with chronic MSK conditions who have been offered a non-pharmacological intervention with either the intention or effect of reducing fatigue and its impact. Databases including AMED, PsycINFO, CINAHLPlus, MEDLINE, EMBASE and Scopus will be searched for peer-reviewed primary research studies published after 1 January 2007 in English language. These findings will be used to identify factors associated with successful interventions and to map gaps in knowledge. ETHICS AND DISSEMINATION: Ethical approval was not required for this review. Findings will be disseminated by journal publications, conference presentations and by communicating with relevant healthcare and charity organisations.

An integrated approach to assess human health risk of neonicotinoid insecticides in surface water of the Yangtze River Basin, China.

Neonicotinoids are widely used insecticides that have raised considerable concerns for both environmental and human health. However, there lack of comprehensive evaluation of their accumulation in surface water ecosystems and exposure to various human groups. Additionally, there's a distinct lack of scientific evidence describing the carcinogenic and non-carcinogenic impacts of neonicotinoids from surface water. Using an integrated approach employing the Relative Potency Factor (RPF), Hazard Index (HI), and Monte Carlo Simulation (MCS), the study assessed neonicotinoid exposure and risk to four demographic groups via dermal contact and mistaken oral intake pathways in the Yangtze River Basin (YRB), China. Neonicotinoid concentrations range from 0.1 to 408.12 ng/L, indicating potential risk (10-3 to 10-1) across the studied demographic groups. The Incremental Lifetime Cancer Risk (ILCR) for dermal contact was within a moderate range of 2.00 × 10-3 to 1.67 × 10-2, while the mistaken oral intake was also within a moderate range of 3.07 × 10-3 to 7.05 × 10-3. The Hazard Index (HI) for dermal exposure ranged from 1.49 × 10-2 to 0.125, while for mistaken oral intake, it varied between 2.69 × 10-2 and 0.14. The findings highlight the importance of implementing specific interventions to address neonicotinoid exposure, especially among demographic groups that are more susceptible. This research underscores the urgent need for targeted strategies to address neonicotinoid risks to vulnerable populations within the YRB while contributing to insights for effective policies to mitigate neonicotinoid exposure in surface water ecosystems globally.

Assessing neonicotinoid accumulation and ecological risks in the aquatic environment of Yangtze River Basin, China.

Neonicotinoids (NNIs) constitute commonly used pesticides across various regions, however, the lack of research and data on its long-term effects and threshold levels within specific ecosystems have left an important knowledge gap. This study aimed to comprehensively examine NNI concentrations and their potential impacts on human health and aquatic organisms in the region of the Yangtze River Basin (YRB). The study employed datasets on seven commonly applied NNIs across 244 surface water samples collected from 12 distinct geographic sites within the YRB. The relative potency factor was used to evaluate human exposure risks, while the species sensitivity distribution could estimate acute and chronic hazardous concentrations for 5% of species (HC5) for NNIs impacting aquatic organisms. Analysis revealed varying NNI concentrations across the sampled sites, with thiacloprid recording the lowest concentration at 0.1 ng L-1, and dinotefuran recording a high concentration of 408 ng L-1. The observation indicated NNI concentration declined at sampling sites downstream of the YRB. Infants were identified as the most vulnerable to NNI exposure, with an estimated daily intake of 40.8 ng kg-1 bw d-1. The acute HC5 was determined at 946 ng L-1 and a chronic HC5 at 338 ng L-1, to NNI hazards. These findings highlight the urgent need for a more comprehensive understanding of the ecological implications and hazards posed by NNIs within the YRB. Variations in NNI concentrations across sites, potential risks to human health, and increased vulnerability of aquatic organisms from this study underscore the necessity for further research and concerted efforts to mitigate these ecological threats in the region.

The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes.

Most cancer types exhibit aberrant transcriptional activity, including derepression of retrotransposable elements (RTEs). However, the degree, specificity and potential consequences of RTE transcriptional activation may differ substantially among cancer types and subtypes. Representing one extreme of the spectrum, we characterize the transcriptional activity of RTEs in cohorts of esophageal adenocarcinoma (EAC) and its precursor Barrett's esophagus (BE) from the OCCAMS (Oesophageal Cancer Clinical and Molecular Stratification) consortium, and from TCGA (The Cancer Genome Atlas). We found exceptionally high RTE inclusion in the EAC transcriptome, driven primarily by transcription of genes incorporating intronic or adjacent RTEs, rather than by autonomous RTE transcription. Nevertheless, numerous chimeric transcripts straddling RTEs and genes, and transcripts from stand-alone RTEs, particularly KLF5- and SOX9-controlled HERVH proviruses, were overexpressed specifically in EAC. Notably, incomplete mRNA splicing and EAC-characteristic intronic RTE inclusion was mirrored by relative loss of the respective fully-spliced, functional mRNA isoforms, consistent with compromised cellular fitness. Defective RNA splicing was linked with strong transcriptional activation of a HERVH provirus on Chr Xp22.32 and defined EAC subtypes with distinct molecular features and prognosis. Our study defines distinguishable RTE transcriptional profiles of EAC, reflecting distinct underlying processes and prognosis, thus providing a framework for targeted studies.

Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin.

Increased levels and diversity of human endogenous retrovirus (HERV) transcription characterize most cancer types and are linked with disease outcomes. However, the underlying processes are incompletely understood. Here, we show that elevated transcription of HERVH proviruses predicted survival of lung squamous cell carcinoma (LUSC) and identified an isoform of CALB1, encoding calbindin, ectopically driven by an upstream HERVH provirus under the control of KLF5, as the mediator of this effect. HERVH-CALB1 expression was initiated in preinvasive lesions and associated with their progression. Calbindin loss in LUSC cell lines impaired in vitro and in vivo growth and triggered senescence, consistent with a protumor effect. However, calbindin also directly controlled the senescence-associated secretory phenotype (SASP), marked by secretion of CXCL8 and other neutrophil chemoattractants. In established carcinomas, CALB1-negative cancer cells became the dominant source of CXCL8, correlating with neutrophil infiltration and worse prognosis. Thus, HERVH-CALB1 expression in LUSC may display antagonistic pleiotropy, whereby the benefits of escaping senescence early during cancer initiation and clonal competition were offset by the prevention of SASP and protumor inflammation at later stages.

Antibodies against endogenous retroviruses promote lung cancer immunotherapy.

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)1,2. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive1,2. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma3. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response.

Biodegradation of cefalexin by two bacteria strains from sewage sludge.

Bioremediation has been used as an environmentally-friendly, energy-saving and efficient method for removing pollutants. However, there have been very few studies focusing on the specific antibiotic-degrading microorganisms in the activated sludge and their degradation mechanism. Two strains of cefalexin-degrading bacteria (Rhizobium sp. (CLX-2) and Klebsiella sp. (CLX-3)) were isolated from the activated sludge in this study. They were capable of rapidly eliminating over 99% of cefalexin at an initial concentration of 10 mg l-1 within 12 h. The exponential phase of cefalexin degradation happened a little earlier than that of bacterial growth. The first-order kinetic model could elucidate the biodegradation process of cefalexin. The optimized environmental temperature and pH values for rapid biodegradation by these two strains were found to be 30°C and 6.5-7, respectively. Furthermore, two major biodegradation metabolites of CLX-3, 7-amino-3-cephem-4-carboxylic acid and 2-hydroxy-3-phenyl pyrazine were identified using UHPLC-MS and the biodegradation pathway of cefalexin was proposed. Overall, the results showed that Rhizobium sp. (CLX-2) and Klebsiella sp. (CLX-3) could possibly be useful resources for antibiotic pollution remediation.

SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export.

SARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis.

ADAR1 averts fatal type I interferon induction by ZBP1.

Mutations of the ADAR1 gene encoding an RNA deaminase cause severe diseases associated with chronic activation of type I interferon (IFN) responses, including Aicardi-Goutières syndrome and bilateral striatal necrosis1-3. The IFN-inducible p150 isoform of ADAR1 contains a Zα domain that recognizes RNA with an alternative left-handed double-helix structure, termed Z-RNA4,5. Hemizygous ADAR1 mutations in the Zα domain cause type I IFN-mediated pathologies in humans2,3 and mice6-8; however, it remains unclear how the interaction of ADAR1 with Z-RNA prevents IFN activation. Here we show that Z-DNA-binding protein 1 (ZBP1), the only other protein in mammals known to harbour Zα domains9, promotes type I IFN activation and fatal pathology in mice with impaired ADAR1 function. ZBP1 deficiency or mutation of its Zα domains reduced the expression of IFN-stimulated genes and largely prevented early postnatal lethality in mice with hemizygous expression of ADAR1 with mutated Zα domain (Adar1mZα/- mice). Adar1mZα/- mice showed upregulation and impaired editing of endogenous retroelement-derived complementary RNA reads, which represent a likely source of Z-RNAs activating ZBP1. Notably, ZBP1 promoted IFN activation and severe pathology in Adar1mZα/- mice in a manner independent of RIPK1, RIPK3, MLKL-mediated necroptosis and caspase-8-dependent apoptosis, suggesting a novel mechanism of action. Thus, ADAR1 prevents endogenous Z-RNA-dependent activation of pathogenic type I IFN responses by ZBP1, suggesting that ZBP1 could contribute to type I interferonopathies caused by ADAR1 mutations.

Optimization, equilibrium, adsorption behaviour of Cu/Zn/Fe LDH and LDHBC composites towards atrazine reclamation in an aqueous environment.

Cu-Zn-Fe Layered double hydroxides (LDH) and LDH dispersed on bamboo biochar (LDHBC) was used to study the adsorption of Atrazine by characterizing the adsorption kinetics, isotherms and response surface methodology (RSM) to reveal interactive effects of pH, adsorbent dosage and adsorbate initial concentration towards LDH optimum performance. The estimate of parameters determined for Langmuir isotherm quantities were in the range (21.84-37.91 mg/g) for LDH and (63.64-87.04 mg/g) for LDHBC. Regeneration and reusability after five cycles detected that the adsorption efficiencies of the adsorbents were reduced to 36% for LDH and 66% for LDHBC. Box Behnken design analysis could further reveal optimized conditions for higher Atrazine removal by LDH up to 74.8%. The adsorption mechanisms could be determined by π-π interactions occurring at the interfaces by hydrogen bonding and pore filling effects.

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses.

Nucleic acids are powerful triggers of innate immunity and can adopt the Z-conformation, an unusual left-handed double helix. Here, we studied the biological function(s) of Z-RNA recognition by the adenosine deaminase ADAR1, mutations in which cause Aicardi-Goutières syndrome. Adar1mZα/mZα mice, bearing two point mutations in the Z-nucleic acid binding (Zα) domain that abolish Z-RNA binding, displayed spontaneous induction of type I interferons (IFNs) in multiple organs, including in the lung, where both stromal and hematopoietic cells showed IFN-stimulated gene (ISG) induction. Lung neutrophils expressed ISGs induced by the transcription factor IRF3, indicating an initiating role for neutrophils in this IFN response. The IFN response in Adar1mZα/mZα mice required the adaptor MAVS, implicating cytosolic RNA sensing. Adenosine-to-inosine changes were enriched in transposable elements and revealed a specific requirement of ADAR1's Zα domain in editing of a subset of RNAs. Thus, endogenous RNAs in Z-conformation have immunostimulatory potential curtailed by ADAR1, with relevance to autoinflammatory disease in humans.

Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control.

Excessive replication of Saccharomyces cerevisiae Ty1 retrotransposons is regulated by Copy Number Control, a process requiring the p22/p18 protein produced from a sub-genomic transcript initiated within Ty1 GAG. In retrotransposition, Gag performs the capsid functions required for replication and re-integration. To minimize genomic damage, p22/p18 interrupts virus-like particle function by interaction with Gag. Here, we present structural, biophysical and genetic analyses of p18m, a minimal fragment of Gag that restricts transposition. The 2.8 Å crystal structure of p18m reveals an all α-helical protein related to mammalian and insect ARC proteins. p18m retains the capacity to dimerise in solution and the crystal structures reveal two exclusive dimer interfaces. We probe our findings through biophysical analysis of interface mutants as well as Ty1 transposition and p18m restriction in vivo. Our data provide insight into Ty1 Gag structure and suggest how p22/p18 might function in restriction through a blocking-of-assembly mechanism.

E3 ubiquitin ligase HECTD2 mediates melanoma progression and immune evasion.

The ubiquitin-proteasome system maintains protein homoeostasis, underpins the cell cycle, and is dysregulated in cancer. However, the role of individual E3 ubiquitin ligases, which mediate the final step in ubiquitin-mediated proteolysis, remains incompletely understood. Identified through screening for cancer-specific endogenous retroviral transcripts, we show that the little-studied E3 ubiquitin ligase HECTD2 exerts dominant control of tumour progression in melanoma. HECTD2 cell autonomously drives the proliferation of human and murine melanoma cells by accelerating the cell cycle. HECTD2 additionally regulates cancer cell production of immune mediators, initiating multiple immune suppressive pathways, which include the cyclooxygenase 2 (COX2) pathway. Accordingly, higher HECTD2 expression is associated with weaker anti-tumour immunity and unfavourable outcome of PD-1 blockade in human melanoma and counteracts immunity against a model tumour antigen in murine melanoma. This central, multifaceted role of HECTD2 in cancer cell-autonomous proliferation and in immune evasion may provide a single target for a multipronged therapy of melanoma.

Gv1, a Zinc Finger Gene Controlling Endogenous MLV Expression.

The genomes of inbred mice harbor around 50 endogenous murine leukemia virus (MLV) loci, although the specific complement varies greatly between strains. The Gv1 locus is known to control the transcription of endogenous MLVs and to be the dominant determinant of cell-surface presentation of MLV envelope, the GIX antigen. Here, we identify a single Krüppel-associated box zinc finger protein (ZFP) gene, Zfp998, as Gv1 and show it to be necessary and sufficient to determine the GIX+ phenotype. By long-read sequencing of bacterial artificial chromosome clones from 129 mice, the prototypic GIX+ strain, we reveal the source of sufficiency and deficiency as splice-acceptor variations and highlight the varying origins of the chromosomal region encompassing Gv1. Zfp998 becomes the second identified ZFP gene responsible for epigenetic suppression of endogenous MLVs in mice and further highlights the prominent role of this gene family in control of endogenous retroviruses.

Permissive selection followed by affinity-based proliferation of GC light zone B cells dictates cell fate and ensures clonal breadth.

Affinity maturation depends on how efficiently germinal centers (GCs) positively select B cells in the light zone (LZ). Positively selected GC B cells recirculate between LZs and dark zones (DZs) and ultimately differentiate into plasmablasts (PBs) and memory B cells (MBCs). Current understanding of the GC reaction presumes that cMyc-dependent positive selection of LZ B cells is a competitive affinity-dependent process; however, this cannot explain the production of GC-derived lower-affinity MBCs or retention of GC B cells with varied affinities. Here, by combining single-cell/bulk RNA sequencing and flow cytometry, we identified and characterized temporally and functionally distinct positively selected cMyc+ GC B cell subpopulations. cMyc+ LZ B cell subpopulations enriched with either higher- or lower-affinity cells diverged soon after permissive positive selection. The former subpopulation contained PB precursors, whereas the latter comprised less proliferative MBC precursors and future DZ entrants. The overall affinity of future DZ entrants was enhanced in the LZ through preferential proliferation of higher-affinity cells. Concurrently, lower-affinity cells were retained in GCs and protected from apoptosis. These findings redefine positive selection as a dynamic process generating three distinct B cell fates and elucidate how positive selection ensures clonal diversity for broad protection.

Photodegradation of pesticides using compound-specific isotope analysis (CSIA): a review.

Pesticides are commonly applied in agriculture to protect crops from pests, weeds, and harmful pathogens. However, chronic, low-level exposure to pesticides can be toxic to humans. Photochemical degradation of pesticides in water, soil, and other environmental media can alter their environmental fate and toxicity. Compound-specific isotope analysis (CSIA) is an advanced diagnostic tool to quantify the degradation of organic pollutants and provide insight into reaction mechanisms without the need to identify transformation products. CSIA allows for the direct quantification of organic degradation, including pesticides. This review summarizes the recent developments observed in photodegradation studies on different categories of pesticides using CSIA technology. Only seven pesticides have been studied using photodegradation, and these studies have mostly occurred in the last five years. Knowledge gaps in the current literature, as well as potential approaches for CSIA technology for pesticide monitoring, are discussed in this review. Furthermore, the CSIA analytical method is challenged by chemical element types, the accuracy of instrument analysis, reaction conditions, and the stability of degradation products. Finally, future research applications and the operability of this method are also discussed.

Remediation with Semicoke-Preparation, Characterization, and Adsorption Application.

Development of low-cost contaminant sorbents from industrial waste is now an essential aspect of the circular economy since their disposal continues to threaten ecological integrity. Semicoke (SC), a by-product generated in large quantities and described as solid waste from gasification of low-rank coal (LRC), is gaining popularity in line with its reuse capacity in the energy industry but is less explored as a contaminant adsorbent despite its physical and elemental carbon properties. This paper summarizes recent information on SC, sources and production, adsorption mechanism of polluting contaminants, and summarizes regeneration methods capable of yielding sustainability for the material reuse.