Am J Respir Crit Care Med. 2023 Sep 14. doi: 10.1164/rccm.202210-1881OC. Online ahead of print.

ABSTRACT

INTRODUCTION: IL-33 is a pro-inflammatory cytokine thought to play a role in the pathogenesis of asthma and COPD. A recent clinical trial using the anti-IL33 antibody showed a reduction in exacerbation and improved lung function in ex-smokers but not current smokers with COPD. In this study, we aimed to understand the effects of smoking status on IL-33.

METHODS: We investigated the association of smoking status with the level of gene expression of IL33 in the airways in eight independent transcriptomic studies of lung airways. Additionally, we performed western blot and immunohistochemistry for IL-33 in lung tissue to assess protein levels.

RESULTS: Across the bulk RNA-sequencing datasets, IL-33 gene expression and its signaling pathway were significantly lower in current- compared to ex- or never-smokers and increased upon smoking cessation (p<0.05). Single-cell sequencing showed that IL-33 is predominantly expressed in resting basal epithelial cells and decreases during the differentiation process triggered by smoke exposure. We also found a higher transitioning of this cellular sub-population into a more differentiated cell type during chronic smoking, potentially driving the reduction of IL-33. Protein analysis demonstrated lower IL-33 levels in lung tissue from COPD current- compared to ex-smokers and a lower proportion of IL-33 positive basal cells in current versus ex-smoking controls.

CONCLUSION: We provide strong evidence that cigarette smoke leads to an overall reduction in IL33 expression in both transcriptomic and protein level and this may be due to the decrease in resting basal cells. Together, these findings may explain the clinical observation that a recent antibody-based anti-IL-33 treatment is more effective in ex- than current smokers with COPD. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).

PMID:37708400 | DOI:10.1164/rccm.202210-1881OC

Cell Rep. 2023 Sep 13;42(9):113132. doi: 10.1016/j.celrep.2023.113132. Online ahead of print.

ABSTRACT

Uveal melanoma (UM) is a rare cancer resulting from the transformation of melanocytes in the uveal tract. Integrative analysis has identified four molecular and clinical subsets of UM. To improve our molecular understanding of UM, we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis using Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with the upregulation of PRAME, an independent prognostic biomarker in UM, and a potential therapeutic target. Our findings illustrate how multi-omics approaches can improve our understanding of tumorigenesis and reveal two distinct mechanisms of gene expression dysregulation in UM.

PMID:37708024 | DOI:10.1016/j.celrep.2023.113132

OMICS. 2023 Sep;27(9):434-443. doi: 10.1089/omi.2023.0098.

ABSTRACT

Systems biology tools offer new prospects for industrial strain selection. For bacteria that are significant for industrial applications, whole-genome sequencing coupled to flux balance analysis (FBA) can help unpack the complex relationships between genome mutations and carbon trafficking. This work investigates the l-tyrosine (l-Tyr) overproducing model system Corynebacterium glutamicum ATCC 21573 with an eye to more rational and precision strain development. Using genome-wide mutational analysis of C. glutamicum, we identified 27,611 single nucleotide polymorphisms and 479 insertion/deletion mutations. Mutations in the carbon uptake machinery have led to phosphotransferase system-independent routes as corroborated with FBA. Mutations within the central carbon metabolism of C. glutamicum impaired the carbon flux, as evidenced by the lower growth rate. The entry to and flow through the tricarboxylic acid cycle was affected by mutations in pyruvate and α-ketoglutarate dehydrogenase complexes, citrate synthase, and isocitrate dehydrogenase. FBA indicated that the estimated flux through the shikimate pathway became larger as the l-Tyr production rate increased. In addition, protocatechuate export was probabilistically impossible, which could have contributed to the l-Tyr accumulation. Interestingly, aroG and cg0975, which have received previous attention for aromatic amino acid overproduction, were not mutated. From the branch point molecule, prephenate, the change in the promoter region of pheA could be an influential contributor. In summary, we suggest that genome sequencing coupled with FBA is well poised to offer rational guidance for industrial strain development, as evidenced by these findings on carbon trafficking in C. glutamicum ATCC 21573.

PMID:37707996 | DOI:10.1089/omi.2023.0098

JAMA Netw Open. 2023 Sep 5;6(9):e2333618. doi: 10.1001/jamanetworkopen.2023.33618.

ABSTRACT

IMPORTANCE: Breast cancer mortality is complex and traditional approaches that seek to identify determinants of mortality assume that their effects on mortality are stationary across geographic space and scales.

OBJECTIVE: To identify geographic variation in the associations of population demographics, environmental, lifestyle, and health care access with breast cancer mortality at the US county-level.

DESIGN, SETTING, AND PARTICIPANTS: This geospatial cross-sectional study used data from the Surveillance, Epidemiology, and End Results (SEER) database on adult female patients with breast cancer. Statistical and spatial analysis was completed using adjusted mortality rates from 2015 to 2019 for 2176 counties in the US. Data were analyzed July 2022.

EXPOSURES: County-level population demographics, environmental, lifestyle, and health care access variables were obtained from open data sources.

MAIN OUTCOMES AND MEASURES: Model coefficients describing the association between 18 variables and age-adjusted breast cancer mortality rate. Compared with a multivariable linear regression (OLS), multiscale geographically weighted regression (MGWR) relaxed the assumption of spatial stationarity and allowed for the magnitude, direction, and significance of coefficients to change across geographic space.

RESULTS: Both OLS and MGWR models agreed that county-level age-adjusted breast cancer mortality rates were significantly positively associated with obesity (OLS: β, 1.21; 95% CI, 0.88 to 1.54; mean [SD] MGWR: β, 0.72 [0.02]) and negatively associated with proportion of adults screened via mammograms (OLS: β, -1.27; 95% CI, -1.70 to -0.84; mean [SD] MGWR: β, -1.07 [0.16]). Furthermore, the MGWR model revealed that these 2 determinants were associated with a stationary effect on mortality across the US. However, the MGWR model provided important insights on other county-level factors differentially associated with breast cancer mortality across the US. Both models agreed that smoking (OLS: β, -0.65; 95% CI, -0.98 to -0.32; mean [SD] MGWR: β, -0.75 [0.92]), food environment index (OLS: β, -1.35; 95% CI, -1.72 to -0.98; mean [SD] MGWR: β, -1.69 [0.70]), exercise opportunities (OLS: β, -0.56; 95% CI, -0.91 to -0.21; mean [SD] MGWR: β, -0.59 [0.81]), racial segregation (OLS: β, -0.60; 95% CI, -0.89 to -0.31; mean [SD] MGWR: β, -0.47 [0.41]), mental health care physician ratio (OLS: β, -0.93; 95% CI, -1.44 to -0.42; mean [SD] MGWR: β, -0.48 [0.92]), and primary care physician ratio (OLS: β, -1.46; 95% CI, -2.13 to -0.79; mean [SD] MGWR: β, -1.06 [0.57]) were negatively associated with breast cancer mortality, and that light pollution was positively associated (OLS: β, 0.48; 95% CI, 0.24 to 0.72; mean [SD] MGWR: β, 0.27 [0.04]). But in the MGWR model, the magnitude of effect sizes and significance varied across geographical regions. Inversely, the OLS model found that disability was not a significant variable for breast cancer mortality, yet the MGWR model found that it was significantly positively associated in some geographical locations.

CONCLUSIONS AND RELEVANCE: This cross-sectional study found that not all social determinants associated with breast cancer mortality are spatially stationary and provides spatially explicit insights for public health practitioners to guide geographically targeted interventions.

PMID:37707814 | DOI:10.1001/jamanetworkopen.2023.33618

Microbiol Spectr. 2023 Sep 14:e0078823. doi: 10.1128/spectrum.00788-23. Online ahead of print.

ABSTRACT

Anaerobic fungi (AF) inhabit the gastrointestinal tract of ruminants and play an important role in the degradation of fiber feed. However, limited knowledge is available on seasonal dynamics and inter-species differences in rumen AF community in yak and cattle under natural grazing systems. Using the random forests model, the null model, and structural equation model, we investigated the seasonal dynamics and key driving factors of fiber-associated rumen AF in grazing yak and cattle throughout the year on the Qinghai-Tibet Plateau (QTP). We found that the richness and diversity of rumen AF of grazing yak and cattle in cold season were significantly higher than those in warm season (P < 0.05). We identified 12 rumen AF genera, among which , Cyllamyces, and Orpinomyces were predominant in the rumen of both grazing yak and cattle. LEfSe and random forest analysis showed that Feramyces, Tahromyces, and Buwchfawromyces were important seasonal indicator of rumen AF in grazing yak (P < 0.05), and Caecomyces, Cyllamyces, and Piromyces in grazing cattle (P < 0.05). Null model analysis revealed that the dynamic changes of rumen AF community structure were mainly affected by deterministic factors. Notably, mantel test and structural equation model revealed that forage physical-chemical properties, including dry matter (DM), neutral detergent fiber (NDF), and hemicellulose contents (HC) were the key factors driving the seasonal variations of the rumen AF community (P < 0.05). The results revealed that forage lignocellulose was probably an important factor affecting the seasonal dynamics and inter-species differences of the rumen AF community under natural grazing conditions. IMPORTANCE The seasonal dynamics of rumen anaerobic fungi in nature grazing yak and cattle were determined during cold and warm seasons based on pasture nutritional quality and environmental data sets. The main driving factors of anaerobic fungi in yak and cattle rumen were explored by combining random forest and structural equation models. In addition, the dynamic differences in the composition of the anaerobic fungi community in the yak and cattle in different seasons were characterized. It was found that some rumen anaerobic fungi have contributed to high fiber degradation rate in yak. These novel findings improve our understanding of the association of environmental and dietary seasonal variations with anaerobic fungal community, facilitating yak adaptation to high altitude.

PMID:37707448 | DOI:10.1128/spectrum.00788-23

Biotechnol Bioeng. 2023 Sep 14. doi: 10.1002/bit.28556. Online ahead of print.

ABSTRACT

In this study, eight nonconserved residues with exposed surfaces and flexible conformations of the homotetrameric PGUS (β-glucuronidase from Aspergillus oryzae Li-3) were identified. Single-point mutation into cysteine enabled the thiol-maleimide reaction and site-specific protein assembly using a two-arm polyethylene glycol (PEG)-maleimide crosslinker (Mal2 ). The Mal2 (1k) (with 1 kDa PEG spacer)-crosslinked PGUS assemblies showed low crosslinking efficiency and unimproved thermostability except for G194C-Mal2 (1k). To improve the crosslinking efficiency, a lengthened crosslinker Mal2 (2k) (with 2 kDa PEG spacer) was used to produce PGUS assembly and a highly improved thermostability was achieved with a half-life of 47.2-169.2 min at 70°C, which is 1.04-3.74 times that of wild type PGUS. It is found that the thermostability of PGUS assembly was closely associated with the formation of inter-tetramer assembly and intratetramer crosslinking, rather than the PEGylation of the enzyme. Therefore, the four-arm PEG-maleimide crosslinker Mal4 (2k) (with 2 kDa PEG spacer) was employed to simultaneously increase the inter-tetramer assembly and intratetramer crosslinking, and the resulting PGUS assemblies showed further improved thermostabilities compared with Mal2 (2k)-crosslinked assemblies. Finally, the application of PGUS assemblies with significantly improved thermostability to the bioconversion of GL proved that the PGUS assembly is a strong catalyst for glycyrrhizin (GL) hydrolysis in industrial applications.

PMID:37707439 | DOI:10.1002/bit.28556

J Virol. 2023 Sep 14:e0039623. doi: 10.1128/jvi.00396-23. Online ahead of print.

ABSTRACT

RNA processing plays a key role in gene expression, allowing for increased protein diversity and functional complexity. Consequently, modulating RNA processing can impact gene function. Given HIV-1's reliance on host RNA processing machinery for viral protein production/replication, modulators of this process could serve as novel anti-virals to complement and/or enhance existing therapies. In this study, screening of several serine-arginine-rich (SR) kinase inhibitors for their impact on HIV-1 gene expression identified harmine as an inhibitor of HIV-1 gene expression in several cell lines and primary CD4+ T cells/macrophages at low micromolar concentrations with limited cell toxicity. Harmine induced a loss of viral structural protein expression associated with reduced HIV-1 unspliced and singly-spliced HIV-1 RNA levels but limited impact on multiply spliced RNAs. Although harmine is a known inhibitor of both DYRK1A and monoaminoxidase A (MAO A), neither DYRK1A depletion nor other MAO A inhibitors had any effect on HIV-1 expression. However, the compound altered the expression of several other SR kinases in primary CD4+ T cells, increasing CLK1 and reducing CLK2 kinase levels, effects known to regulate HIV-1 expression. Harmine was also unique among the SR kinase inhibitors tested for its ability to suppress replication of a seasonal coronavirus, human coronavirus (HCoV)-229E, and multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, reducing viral protein expression and virus release. Harmine acts post-entry, arresting virus replication even after the onset of viral protein production. At doses required to suppress HIV-1 replication, harmine had limited impact on the host transcriptome, alternative splicing, or alterative polyadenylation as assessed by RNA-Seq. Together, our study demonstrates the feasibility of targeting host RNA processing to inhibit a range of viruses with minimal impact on the host cell. IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4+ T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.

PMID:37706687 | DOI:10.1128/jvi.00396-23

Cardiovasc Res. 2023 Sep 14:cvad147. doi: 10.1093/cvr/cvad147. Online ahead of print.

ABSTRACT

AIMS: Myocardial infarction (MI) is a major cause of death and disability worldwide. Most metabolomics studies investigating metabolites predicting MI are limited by the participant number and/or the demographic diversity. We sought to identify biomarkers of incident MI in the Consortium of Metabolomics Studies (COMETS).

METHODS AND RESULTS: We included 7,897 individuals aged on average 66 years from six intercontinental cohorts with blood metabolomic profiling (n = 1,428 metabolites, of which 168 were present in at least 3 cohorts with over 80% prevalence) and MI information (1,373 cases). We performed a two-stage Individual Patients Data meta-analysis. We first assessed the associations between circulating metabolites and incident MI for each cohort adjusting for traditional risk factors, and then performed a fixed effect inverse-variance meta-analysis to pull the results together. Finally, we conducted a pathway enrichment analysis to identify potential pathways linked to MI.On meta-analysis, 56 metabolites including 21 lipids and 17 amino acids were associated with incident MI after adjusting for multiple testing (false discovery rate, FDR < 0.05), and 10 were novel. The largest increased risk was observed for the carbohydrate mannitol/sorbitol (HR [95% CI] = 1.40[1.26-1.56], p-value < 0.001), whereas the largest decrease in risk was found for glutamine (HR [95% CI] = 0.74[0.67-0.82], p-value < 0.001). Moreover, the identified metabolites were significantly enriched (corrected p-value < 0.05) in pathways previously linked with cardiovascular diseases, including aminoacyl-tRNA biosynthesis.

CONCLUSIONS: In the most comprehensive metabolomics study of incident MI to date, 10 novel metabolites were associated with MI. Metabolite profiles might help to identify high-risk individuals before disease onset. Further research is needed to fully understand the mechanisms of action and elaborate pathway findings.

TRANSLATIONAL PERSPECTIVE: In the largest meta-analyses covering six international cohorts, we identify 10 novel and 46 known metabolites associated with incident MI, that can be used to identify at-risk individuals before disease onset. Our results improve our understanding of the molecular changes that take place in MI development and provide potential novel targets for clinical prediction and a deeper understanding of causal mechanisms.

PMID:37706562 | DOI:10.1093/cvr/cvad147

Elife. 2023 Sep 14;12:e85530. doi: 10.7554/eLife.85530. Online ahead of print.

ABSTRACT

Tissue fibrosis affects multiple organs and involves a master-regulatory role of macrophages which respond to an initial inflammatory insult common in all forms of fibrosis. The recently unravelled multi-organ heterogeneity of macrophages in healthy and fibrotic human disease suggests that macrophages expressing osteopontin (SPP1), associate with lung and liver fibrosis. However, the conservation of this SPP1+ macrophage population across different tissues, and its specificity to fibrotic diseases with different etiologies remain unclear. Integrating 15 single cell RNA-sequencing datasets to profile 235,930 tissue macrophages from healthy and fibrotic heart, lung, liver, kidney, skin and endometrium, we extended the association of SPP1+ macrophages with fibrosis to all these tissues. We also identified a subpopulation expressing matrisome-associated genes (e.g., matrix metalloproteinases and their tissue inhibitors), functionally enriched for ECM remodelling and cell metabolism, representative of a matrisome-associated macrophage (MAM) polarization state within SPP1+ macrophages. Importantly, the MAM polarization state follows a differentiation trajectory from SPP1+ macrophages and is associated with a core set of regulon activity. SPP1+ macrophages without the MAM polarization state (SPP1+MAM-) show a positive association with ageing lung in mice and humans. These results suggest an advanced and conserved polarization state of SPP1+ macrophages in fibrotic tissues resulting from prolonged inflammatory cues within each tissue microenvironment.

PMID:37706477 | DOI:10.7554/eLife.85530

Aging Cell. 2023 Sep 14:e13969. doi: 10.1111/acel.13969. Online ahead of print.

ABSTRACT

Aging is a natural process associated with declined organ function and higher susceptibility to developing chronic diseases. A systemic single-cell type-based study provides a unique opportunity to understand the mechanisms behind age-related pathologies. Here, we use single-cell gene expression analysis comparing healthy young and aged human lungs from nonsmoker donors to investigate age-related transcriptional changes. Our data suggest that aging has a heterogenous effect on lung cells, as some populations are more transcriptionally dynamic while others remain stable in aged individuals. We found that monocytes and alveolar macrophages were the most transcriptionally affected populations. These changes were related to inflammation and regulation of the immune response. Additionally, we calculated the LungAge score, which reveals the diversity of lung cell types during aging. Changes in DNA damage repair, fatty acid metabolism, and inflammation are essential for age prediction. Finally, we quantified the senescence score in aged lungs and found that the more biased cells toward senescence are immune and progenitor cells. Our study provides a comprehensive and systemic analysis of the molecular signatures of lung aging. Our LungAge signature can be used to predict molecular signatures of physiological aging and to detect common signatures of age-related lung diseases.

PMID:37706427 | DOI:10.1111/acel.13969

Histopathology. 2023 Sep 14. doi: 10.1111/his.15040. Online ahead of print.

ABSTRACT

AIMS: Malignant tumours of the lacrimal apparatus are rare and frequently show a poor prognosis, with no clear therapeutic standards. Characterisation of the genetic landscape of these rare tumours is sparse, and therefore therapeutics generally follow those of their common salivary gland counterparts. To further clarify the pathophysiology and discover potential therapeutic targets, we investigated the genetic landscape of eight tumours of the lacrimal apparatus.

METHODS AND RESULTS: DNA and RNA sequencing were performed to identify genetic mutations and gene fusions. Immunohistochemistry, fluorescence in-situ hybridisation and reverse transcription-polymerase chain reaction followed by Sanger sequencing were performed to confirm the identified molecular alterations. Genetic alterations were detected in six tumours. Among five adenoid cystic carcinomas (ACC), four had confirmed alterations of MYB or MYBL1 genes, including a MYB::NFIB fusion, a MYBL1::NFIB fusion, a MYB amplification and a novel NFIB::THSD7B fusion. Mutations in genes encoding epigenetic modifiers, as well as NOTCH1, FGFR2 and ATM mutations, were also identified in ACCs. A carcinoma ex pleomorphic adenoma showed TP53 and CIC mutations and an amplification of ERBB2. A transitional cell carcinoma was associated with HPV16 infection. No genetic alteration was found for one adenocarcinoma, not otherwise specified.

CONCLUSIONS: Our study highlights the variety of molecular alterations associated with lacrimal system tumours and emphasises the importance of molecular testing in these tumours, which can reveal potentially targetable mutations. Our results also reinforce the hypothesis of a common physiopathology of all ACCs, regardless of their primary location.

PMID:37706251 | DOI:10.1111/his.15040

NAR Genom Bioinform. 2023 Sep 11;5(3):lqad081. doi: 10.1093/nargab/lqad081. eCollection 2023 Sep.

ABSTRACT

MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. Through alternative splicing, transcripts might lose the exon with the miRNA target site and become unresponsive to miRNA regulation. To check this hypothesis, we studied the role of miRNA target sites in both coding and non-coding regions using six cancer data sets from The Cancer Genome Atlas (TCGA) and Parkinson's disease data from PPMI. First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. To check whether alternative splicing interferes with this regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites in the coding regions to that of transcripts without target sites. Models containing transcripts with target sites perform significantly better. We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.

PMID:37705830 | PMC:PMC10495541 | DOI:10.1093/nargab/lqad081

NAR Genom Bioinform. 2023 Sep 11;5(3):lqad079. doi: 10.1093/nargab/lqad079. eCollection 2023 Sep.

ABSTRACT

Alternative polyadenylation is a main driver of transcriptome diversity in mammals, generating transcript isoforms with different 3' ends via cleavage and polyadenylation at distinct polyadenylation (poly(A)) sites. The regulation of cell type-specific poly(A) site choice is not completely resolved, and requires quantitative poly(A) site usage data across cell types. 3' end-based single-cell RNA-seq can now be broadly used to obtain such data, enabling the identification and quantification of poly(A) sites with direct experimental support. We propose SCINPAS, a computational method to identify poly(A) sites from scRNA-seq datasets. SCINPAS modifies the read deduplication step to favor the selection of distal reads and extract those with non-templated poly(A) tails. This approach improves the resolution of poly(A) site recovery relative to standard software. SCINPAS identifies poly(A) sites in genic and non-genic regions, providing complementary information relative to other tools. The workflow is modular, and the key read deduplication step is general, enabling the use of SCINPAS in other typical analyses of single cell gene expression. Taken together, we show that SCINPAS is able to identify experimentally-supported, known and novel poly(A) sites from 3' end-based single-cell RNA sequencing data.

PMID:37705828 | PMC:PMC10495540 | DOI:10.1093/nargab/lqad079

NAR Cancer. 2023 Sep 11;5(3):zcad047. doi: 10.1093/narcan/zcad047. eCollection 2023 Sep.

ABSTRACT

Cancer cells often experience large-scale alterations in genome architecture because of DNA damage and replication stress. Whether mutations in core regulators of chromosome structure can also lead to cancer-promoting loss in genome stability is not fully understood. To address this question, we conducted a systematic analysis of mutations affecting a global regulator of chromosome biology -the SMC5/6 complex- in cancer genomics cohorts. Analysis of 64 959 cancer samples spanning 144 tissue types and 199 different cancer genome studies revealed that the SMC5/6 complex is frequently altered in breast cancer patients. Patient-derived mutations targeting this complex associate with strong phenotypic outcomes such as loss of ploidy control and reduced overall survival. Remarkably, the phenotypic impact of several patient mutations can be observed in a heterozygous context, hence providing an explanation for a prominent role of SMC5/6 mutations in breast cancer pathogenesis. Overall, our findings suggest that genes encoding global effectors of chromosome architecture can act as key contributors to cancer development in humans.

PMID:37705607 | PMC:PMC10495288 | DOI:10.1093/narcan/zcad047

EMBO Rep. 2023 Sep 14:e55506. doi: 10.15252/embr.202255506. Online ahead of print.

ABSTRACT

N6 -methyladenosine (m6 A), the most abundant internal modification in eukaryotic mRNA, plays important roles in many physiological and pathological processes, including the development and progression of cancer. RNA modification by m6 A is regulated by methyltransferases, demethylases, and m6 A-binding proteins that function in large part by regulating mRNA expression and function. Here, we investigate the expression of m6 A regulatory proteins in breast cancer. We find that expression of KIAA1429/VIRMA, a component of the m6 A methyltransferase complex, is upregulated in breast cancer tissue and correlates positively with poor survival. KIAA1429/VIRMA is mislocalized to the cytosol of breast cancer tissues and cell lines, and shRNA-mediated knockdown inhibits breast cancer cell proliferation, migration, and invasion. Mechanistically, KIAA1429/VIRMA is shown to bind to the m6 A-dependent RNA-binding protein insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), leading to recruitment and stabilization of m6 A-modified hyaluronan synthase 2 (HAS2) mRNA. HAS2 mRNA and KIAA1429/VIRMA mRNA levels correlate positively in breast cancer tissues, suggesting that the KIAA1429/VIRMA-IGF2BP3-HAS2 axis promotes breast cancer growth and contributes to poor prognosis.

PMID:37705505 | DOI:10.15252/embr.202255506

Microb Pathog. 2023 Sep 11:106344. doi: 10.1016/j.micpath.2023.106344. Online ahead of print.

ABSTRACT

Increasing evidence demonstrated that Enterohemorrhagic Escherichia coli (EHEC) and Shigella dysenteriae type 1 (S. dysenteriae1) are considered pathogens, that are connected with diarrhea and are still the greatest cause of death in children under the age of five years, worldwide. EHEC and S. dysenteriae 1 infections can be prevented and managed using a vaccination strategy against pathogen attachment stages. In this study, the chitosan nanostructures were loaded with recombinant EIT and STX1B-IpaD polypeptides. The immunogenic properties of this nano-vaccine candidate were investigated. The EIT and STX1B-IpaD recombinant proteins were heterologous expressed, purified, and confirmed by western blotting. The chitosan nanoparticles, were used to encapsulate the purified proteins. The immunogenicity of recombinant nano vaccine candidate, was examined in three groups of BalB/c mice by injection, oral delivery, and combination of oral-injection. ELISA and antibody titer, evaluated the humoral immune response. Finally, all three mice groups were challenged by two pathogens to test the ability of the nano-vaccine candidate to protect against bacterial infection. The Sereny test in guinea pigs was used to confirm the neutralizing effect of immune sera in controlling S. dysenteriae 1, infections. SDS-PAGE and western blotting, confirmed the presence and specificity of 63 and 27 kDa recombinant EIT and STX1B-IpaD, respectively. The results show that the nanoparticles containing recombinant proteins could stimulate the systemic and mucosal immune systems by producing IgG and IgA, respectively. The challenge test showed that, the candidate nano-vaccine could protect the animal model from bacterial infection. The combination of multiple recombinant proteins, carrying several epitopes and natural nanoparticles could evocate remarkable humoral and mucosal responses and improve the protection properties of synthetic antigens. Furthermore, compared with other available antigen delivery methods, using oral delivery as immune priming and injection as a booster method, could act as combinatorial methods to achieve a higher level of immunity. This approach could present an appropriate vaccine candidate against both EHEC and S. dysenteriae 1.

PMID:37704060 | DOI:10.1016/j.micpath.2023.106344

Neurobiol Dis. 2023 Sep 11:106287. doi: 10.1016/j.nbd.2023.106287. Online ahead of print.

ABSTRACT

In Parkinson's disease (PD), post-mortem studies in affected brain regions have demonstrated a decline in mitochondrial number and function. This combined with many studies in cell and animal models suggest that mitochondrial dysfunction is central to PD pathology. We and others have shown that the mitochondrial protein deacetylase, SIRT3 has neurorestorative effects in PD models. In this study, to determine whether there is a link between PD pathology and SIRT3, we analysed SIRT3 levels in human subjects with PD, and compared to age-matched controls. In the SNc of PD subjects, SIRT3 was reduced by 56.8 ± 15.5% compared to control, regardless of age (p < 0.05, R = 0.6539). Given that age is the primary risk factor for PD, this finding suggests that reduced SIRT3 may contribute to PD pathology. Next, we measured whether there was a correlation between α-synuclein and SIRT3. In a parallel study, we assessed the disease-modifying potential of SIRT3 over-expression in a seeding model of α-synuclein. In PFF rats, infusion of rAAV1.SIRT3-myc reduced abundance of α-synuclein inclusions by 30.1 ± 18.5%. This was not observed when deacetylation deficient SIRT3H248Y was transduced, demonstrating the importance of SIRT3 deacetylation in reducing α-synuclein aggregation. These studies confirm show the that there is a clear difference in SIRT3 levels in subjects with Parkinson's disease compared age-matched controls, suggesting a link between SIRT3 and the progression of PD. We also demonstrate that over-expression of SIRT3 reduces α-synuclein aggregation, further validating AAV.SIRT3-myc as a potential disease-modifying solution for PD.

PMID:37704058 | DOI:10.1016/j.nbd.2023.106287

Cell Rep Methods. 2023 Sep 5:100580. doi: 10.1016/j.crmeth.2023.100580. Online ahead of print.

ABSTRACT

Human biology is rooted in highly specialized cell types programmed by a common genome, 98% of which is outside of genes. Genetic variation in the enormous noncoding space is linked to the majority of disease risk. To address the problem of linking these variants to expression changes in primary human cells, we introduce ExPectoSC, an atlas of modular deep-learning-based models for predicting cell-type-specific gene expression directly from sequence. We provide models for 105 primary human cell types covering 7 organ systems, demonstrate their accuracy, and then apply them to prioritize relevant cell types for complex human diseases. The resulting atlas of sequence-based gene expression and variant effects is publicly available in a user-friendly interface and readily extensible to any primary cell types. We demonstrate the accuracy of our approach through systematic evaluations and apply the models to prioritize ClinVar clinical variants of uncertain significance, verifying our top predictions experimentally.

PMID:37703883 | DOI:10.1016/j.crmeth.2023.100580

J Innate Immun. 2023 Sep 13. doi: 10.1159/000533898. Online ahead of print.

ABSTRACT

Insect humoral immune responses are regulated in part by protease cascades, whose components circulate as zymogens in the hemolymph. In mosquitoes, these cascades consist of clip domain serine proteases (cSPs) and/or their non-catalytic homologs (cSPHs), which form a complex network, whose molecular make-up is not fully understood. Using a systems biology approach, based on a co-expression network of gene family members that function in melanization and co-immunoprecipitation using the serine protease inhibitor (SRPN)2, a key negative regulator of the melanization response in mosquitoes, we identify the cSP CLIPB4 from the African malaria mosquito Anopheles gambiae as a central node in this protease network. CLIPB4 is tightly co-expressed with SRPN2 and forms protein complexes with SRPN2 in the hemolymph of immune-challenged female mosquitoes. Genetic and biochemical approaches validate our network analysis and show that CLIPB4 is required for melanization and antibacterial immunity, acting as a prophenoloxidase (proPO)-activating protease, which is inhibited by SRPN2. In addition, we provide novel insight into the structural organization of the cSP network in An. gambiae, by demonstrating that CLIPB4 is able to activate proCLIPB8, a cSP upstream of the proPO-activating protease CLIPB9. These data provide the first evidence that, in mosquitoes, cSPs provide branching points in immune protease networks and deliver positive reinforcement in proPO activation cascades.

PMID:37703846 | DOI:10.1159/000533898

Cytokine. 2023 Sep 11;171:156352. doi: 10.1016/j.cyto.2023.156352. Online ahead of print.

ABSTRACT

Chronic obstructive pulmonary disease (COPD) is a common chronic inflammatory disease with high morbidity and mortality rates worldwide. Cytokines, which are the main regulators of immune responses, play crucial roles in inflammatory diseases such as COPD. Moreover, certain genetic variations can alter cytokine expression, and changes in cytokine level or function can affect disease susceptibility. Therefore, investigating the association between genetic variations and disease progression can be useful for prevention and treatment. Several studies have explored the association between common genetic variations in cytokine genes and COPD susceptibility. In this study, we summarized the reported studies and, where possible, conducted a systematic review and meta-analysis to evaluate the genetic association between various cytokines and COPD pathogenesis. We extracted relevant articles from PubMed and Google Scholar databases using a standard systematic search strategy. We included a total of 183 studies from 78 separate articles that evaluated 50 polymorphisms in 12 cytokine genes in this study. Our analysis showed that among all reported cytokine polymorphisms (including TNF-α, TGF-β, IL1, IL1RN, IL4, IL4R, IL6, IL10, IL12, IL13, IL17, IL18, IL27, and IL33), only four variants, including TNF-α-rs1800629, TGF-β1-rs6957, IL13-rs1800925, and IL6-rs1800796, were associated with the risk of COPD development. This updated meta-analysis strongly supports the association of TNF-α-rs1800629, TGF-β1-rs6957, IL13-rs1800925, and IL6-rs1800796 variants with a high risk of COPD.

PMID:37703677 | DOI:10.1016/j.cyto.2023.156352