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Alveolar macrophages (AMs) derived from embryonic precursors seed the lung before birth and self-maintain locally throughout adulthood, but are regenerated by bone marrow (BM) under stress conditions. However, the regulation of AM development and maintenance remains poorly understood. Here, we show that histone deacetylase 3 (HDAC3) is a key epigenetic factor required for AM embryonic development, postnatal homeostasis, maturation, and regeneration from BM. Loss of HDAC3 in early embryonic development affects AM development starting at E14.5, while loss of HDAC3 after birth affects AM homeostasis and maturation. Single-cell RNA sequencing analyses reveal four distinct AM sub-clusters and a dysregulated cluster-specific pathway in the HDAC3-deficient AMs. Moreover, HDAC3-deficient AMs exhibit severe mitochondrial oxidative dysfunction and deteriorative cell death. Mechanistically, HDAC3 directly binds to Pparg enhancers, and HDAC3 deficiency impairs Pparg expression and its signaling pathway. Our findings identify HDAC3 as a key epigenetic regulator of lung AM development and homeostasis. Alveolar macrophages are known to derive from embryonic precursors although the regulation of this process is poorly understood. Here the authors propose a key role for histone deacetylase 3 as an epigenetic regulator of lung alveolar macrophage development.

Idiopathic pulmonary fibrosis is a progressive lung disease with a poor prognosis. Alveolar macrophages (AMs) are essential for maintaining lung homeostasis and play a significant role in the development of lung fibrosis. Tissue-Resident Alveolar Macrophages (TR-AMs), which originate from embryonic progenitors, can self-renew locally in a steady state, independent of hematopoiesis. During fibrogenesis, circulating monocytes rapidly migrate into the lungs and differentiate into monocyte-derived AMs (Mo-AMs). MicroRNAs (miRNAs), small non-coding RNAs, are critical for regulating gene expression. Our recent study found that the loss of miRNAs in embryonic progenitors significantly decreased the number of TR-AMs in late-stage embryos, indicating that miRNAs are necessary for TR-AM development. However, the role of miRNAs in the postnatal maintenance of TR-AMs and Mo-AMs, as well as their function in pulmonary fibrosis, remains unclear. Here, we demonstrate that deleting miRNAs after birth severely disrupts TR-AM homeostasis and Mo-AM repopulation from the bone marrow following irradiation. The deficiency of miRNAs in TR-AMs and Mo-AMs was linked to diminished bleomycin-induced experimental lung fibrosis. Mechanistically, the absence of miRNAs increased TR-AM apoptosis under both normal and fibrotic conditions. RNA sequencing (RNA-seq) analysis revealed distinct transcriptomic and pathway changes in miRNA-deficient AM subgroups after lung injury. The integration of RNA-seq and miRNA array analyses identified miRNA-mRNA networks in TR-AMs and Mo-AMs in response to bleomycin injury. Ingenuity Pathway Analysis further predicted let-7a, miR-155, and miR-125 as unique upstream regulators of Mo-AM responses to lung fibrosis. Our findings suggest that miRNAs are key epigenetic mediators that differentially regulate the maintenance and function of TR-AMs and Mo-AMs in the pathogenesis of pulmonary fibrosis.

Sarcoidosis is a multisystem disease of unknown cause. Löfgren's syndrome (LS) is a characteristic subgroup of sarcoidosis that is associated with a good prognosis in sarcoidosis. However, little is known about its genetic architecture or its broader phenotype, non-LS sarcoidosis. To address the genetic architecture of sarcoidosis phenotypes, LS and non-LS. An association study in a white Swedish cohort of 384 LS, 664 non-LS, and 2,086 control subjects, totaling 3,134 subjects using a fine-mapping genotyping platform was conducted. Replication was performed in four independent cohorts, three of white European descent (Germany, n = 4,975; the Netherlands, n = 613; and Czech Republic, n = 521), and one of black African descent (United States, n = 1,657), totaling 7,766 subjects. A total of 727 LS-associated variants expanding throughout the extended major histocompatibility complex (MHC) region and 68 non-LS-associated variants located in the MHC class II region were identified and confirmed. A shared overlap between LS and non-LS defined by 17 variants located in the MHC class II region was found. Outside the MHC region, two LS-associated loci, in ADCY3 and between CSMD1 and MCPH1, were observed and replicated. Comprehensive and integrative analyses of genetics, transcription, and pathway modeling on LS and non-LS indicates that these sarcoidosis phenotypes have different genetic susceptibility, genomic distributions, and cellular activities, suggesting distinct molecular mechanisms in pathways related to immune response with a common region.

Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition that can manifest with abscesses, sinus tracts, and scarring in the intertriginous areas of the body. HS is characterized by immune dysregulation, featuring elevated levels of myeloid cells, T helper (Th) cells, and pro-inflammatory cytokines, particularly those involved in Th1- and Th17-mediated immunity. In most epidemiological studies, HS shows a strong female sex bias, with reported female-to-male ratios estimated at roughly 3:1, suggesting that sex-related factors contribute to HS pathophysiology. In this article, we review the role of intrinsic and extrinsic factors that contribute to immunological differences between the sexes and postulate their role in the female sex bias observed in HS. We discuss the effects of hormones, X chromosome dosage, genetics, the microbiome, and smoking on sex-related differences in immunity to postulate potential immunological mechanisms in HS pathophysiology. Future studies are required to better characterize sex-biased factors that contribute to HS disease presentations.

ObjectiveThe objective of this study is to assess the effects of social determinants of health (SDOH) and race-ethnicity on readmission and to investigate the potential for geospatial clustering of patients with a greater burden of SDOH that could lead to a higher risk of readmission.DesignA retrospective study of inpatients at five hospitals within Henry Ford Health (HFH) in Detroit, Michigan from November 2015 to December 2018 was conducted.SettingThis study used an adult inpatient registry created based on HFH electronic health record data as the data source. A subset of the data elements in the registry was collected for data analyses that included readmission index, race-ethnicity, six SDOH variables and demographics and clinical-related variables.ParticipantsThe cohort was composed of 248 810 admission patient encounters with 156 353 unique adult patients between the study time period. Encounters were excluded if they did not qualify as an index admission for all payors based on the Centers for Medicare and Medicaid Service definition.Main outcome measureThe primary outcome was 30-day all-cause readmission. This binary index was identified based on HFH internal data supplemented by external validated readmission data from the Michigan Health Information Network.ResultsRace-ethnicity and all SDOH were significantly associated with readmission. The effect of depression on readmission was dependent on race-ethnicity, with Hispanic patients having the strongest effect in comparison to either African Americans or non-Hispanic whites. Spatial analysis identified ZIP codes in the City of Detroit, Michigan, as over-represented for individuals with multiple SDOH.ConclusionsThere is a complex relationship between SDOH and race-ethnicity that must be taken into consideration when providing healthcare services. Insights from this study, which pinpoint the most vulnerable patients, could be leveraged to further improve existing models to predict risk of 30-day readmission for individuals in future work.

Sarcoidosis is a systemic inflammatory disease characterized by the formation of granulomas in affected organs. Genome-wide association studies (GWASs) of this disease have been conducted only in European population. We present the first sarcoidosis GWAS in African Americans (AAs, 818 cases and 1,088 related controls) followed by replication in independent sets of AAs (455 cases and 557 controls) and European Americans (EAs, 442 cases and 2,284 controls). We evaluated >6 million SNPs either genotyped using the Illumina Omni1-Quad array or imputed from the 1000 Genomes Project data. We identified a novel sarcoidosis-associated locus, NOTCH4, that reached genome-wide significance in the combined AA samples (rs715299, P(AA-meta) = 6.51 × 10(-10)) and demonstrated the independence of this locus from others in the MHC region in the same sample. We replicated previous European GWAS associations within HLA-DRA, HLA-DRB5, HLA-DRB1, BTNL2, and ANXA11 in both our AA and EA datasets. We also confirmed significant associations to the previously reported HLA-C and HLA-B regions in the EA but not AA samples. We further identified suggestive associations with several other genes previously reported in lung or inflammatory diseases.

Vα24-invariant human natural killer T (NKT) cells comprise a unique subset of CD1d-restricted T cells with potent immune regulatory function and are involved in the development of a variety of human diseases. However, the lack of comprehensive molecular subset identities limits their objective classification and clinical application. Using unbiased single-cell RNA sequencing (scRNA-seq) of over 4000 unstimulated and 7000 stimulated human peripheral blood NKT cells, we identified four and five clusters of NKT cells from each NKT group, respectively. Our study uncovers multiple previously unrecognized NKT subsets with potential functional specificities, including a cluster of NKT cells with regulatory T cell property. Flow cytometry and Ingenuity Pathway Analysis confirmed the existence of these NKT populations and indicated the related functional capacities. Our study provides the unbiased and more comprehensive molecular identities of human NKT subsets, which will eventually lead the way to tailored therapies targeting selected NKT subsets.

Excessive use of animal manure as fertilizers can lead to pollution through the introduction of nitrogen, phosphorus, and other mineral compounds to the environment. Wet chemical analytical methods are traditionally used to determine the precise chemical composition of manure to manage the application of animal waste to the soil. However, such methods require significant resources to carry out the processes. Affordable, rapid, and accurate methods of analyses of various chemical components present in animal manure, therefore, are valuable in managing soil and mitigating water pollution. In this study, a stacked regression ensemble approach using near-infrared spectroscopy was developed to simultaneously determine the amount of dry matter, total ammonium nitrogen, total nitrogen, phosphorus pentoxide, calcium oxide, magnesium oxide, and potassium oxide contents in both cattle and poultry manure collected from livestock production areas in France and Reunion Island. The performance of the stacked regression, an ensemble learning algorithm that is formed by collating the well-performing models for prediction was then compared with that of various other machine learning techniques, including support vector regression (linear, polynomial, and radial), least absolute shrinkage and selection operator, ridge regression, elastic net, partial least squares, random forests, recursive partitioning and regression trees, and boosted trees. Results show that stack regression performed optimally well in predicting the seven abovementioned chemical constituents in the testing set and may provide an alternative to the traditional partial least squares method for a more accurate and simultaneous method in determining the chemical properties of animal manure.