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1. Imaging Mass Cytometry Reveals Predominant Innate Immune Signature and Endothelial–Immune Cell Interaction in Juvenile Myositis Compared to Lupus Skin

   https://doi.org/10.1002/art.42283  

   Turnier, Jessica_L; Yee, Christine_M; Madison, Jacqueline_A; Rizvi, Syed_M; Berthier, Celine_C; Wen, Fei; Kahlenberg, J_Michelle (October 2022, Arthritis & Rheumatology)

   ObjectiveCutaneous inflammation can signal disease in juvenile dermatomyositis (DM) and childhood‐onset systemic lupus erythematosus (cSLE), but we do not fully understand cellular mechanisms of cutaneous inflammation. In this study, we used imaging mass cytometry to characterize cutaneous inflammatory cell populations and cell–cell interactions in juvenile DM as compared to cSLE. MethodsWe performed imaging mass cytometry analysis on skin biopsy samples from juvenile DM patients (n = 6) and cSLE patients (n = 4). Tissue slides were processed and incubated with metal‐tagged antibodies for CD14, CD15, CD16, CD56, CD68, CD11c, HLA–DR, blood dendritic cell antigen 2, CD20, CD27, CD138, CD4, CD8, E‐cadherin, CD31, pan‐keratin, and type I collagen. Stained tissue was ablated, and raw data were acquired using the Hyperion imaging system. We utilized the Phenograph unsupervised clustering algorithm to determine cell marker expression and permutation test by histoCAT to perform neighborhood analysis. ResultsWe identified 14 cell populations in juvenile DM and cSLE skin, including CD14+ and CD68+ macrophages, myeloid and plasmacytoid dendritic cells (pDCs), CD4+ and CD8+ T cells, and B cells. Overall, cSLE skin had a higher inflammatory cell infiltrate, with increased CD14+ macrophages, pDCs, and CD8+ T cells and immune cell–immune cell interactions. Juvenile DM skin displayed a stronger innate immune signature, with a higher overall percentage of CD14+ macrophages and prominent endothelial cell–immune cell interaction. ConclusionOur findings identify immune cell population differences, including CD14+ macrophages, pDCs, and CD8+ T cells, in juvenile DM skin compared to cSLE skin, and highlight a predominant innate immune signature and endothelial cell–immune cell interaction in juvenile DM, providing insight into candidate cell populations and interactions to better understand disease‐specific pathophysiology. 

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2. Whole blood transcriptomics identifies subclasses of pediatric septic shock

   https://doi.org/10.1186/s13054-023-04689-y  

   Yang, Jamie O.; Zinter, Matt S.; Pellegrini, Matteo; Wong, Man Yee; Gala, Kinisha; Markovic, Daniela; Nadel, Brian; Peng, Kerui; Do, Nguyen; Mangul, Serghei; et al (December 2023, Critical Care)

   Abstract BackgroundSepsis is a highly heterogeneous syndrome, which has hindered the development of effective therapies. This has prompted investigators to develop a precision medicine approach aimed at identifying biologically homogenous subgroups of patients with septic shock and critical illnesses. Transcriptomic analysis can identify subclasses derived from differences in underlying pathophysiological processes that may provide the basis for new targeted therapies. The goal of this study was to elucidate pathophysiological pathways and identify pediatric septic shock subclasses based on whole blood RNA expression profiles. MethodsThe subjects were critically ill children with cardiopulmonary failure who were a part of a prospective randomized insulin titration trial to treat hyperglycemia. Genome-wide expression profiling was conducted using RNA sequencing from whole blood samples obtained from 46 children with septic shock and 52 mechanically ventilated noninfected controls without shock. Patients with septic shock were allocated to subclasses based on hierarchical clustering of gene expression profiles, and we then compared clinical characteristics, plasma inflammatory markers, cell compositions using GEDIT, and immune repertoires using Imrep between the two subclasses. ResultsPatients with septic shock depicted alterations in innate and adaptive immune pathways. Among patients with septic shock, we identified two subtypes based on gene expression patterns. Compared with Subclass 2, Subclass 1 was characterized by upregulation of innate immunity pathways and downregulation of adaptive immunity pathways. Subclass 1 had significantly worse clinical outcomes despite the two classes having similar illness severity on initial clinical presentation. Subclass 1 had elevated levels of plasma inflammatory cytokines and endothelial injury biomarkers and demonstrated decreased percentages of CD4 T cells and B cells and less diverse T cell receptor repertoires. ConclusionsTwo subclasses of pediatric septic shock patients were discovered through genome-wide expression profiling based on whole blood RNA sequencing with major biological and clinical differences.Trial RegistrationThis is a secondary analysis of data generated as part of the observational CAF-PINT ancillary of the HALF-PINT study (NCT01565941). Registered March 29, 2012. 

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3. Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i

   https://doi.org/10.1128/AEM.00121-20  

   Glickman, Cody M.; Virdi, Ravleen; Hasan, Nabeeh A.; Epperson, L. Elaine; Brown, Leeza; Dawrs, Stephanie N.; Crooks, James L.; Chan, Edward D.; Strong, Michael; Nelson, Stephen T.; et al (October 2020, Applied and Environmental Microbiology)

   Alexandre, Gladys (Ed.)

   ABSTRACT Environmental nontuberculous mycobacteria (NTM), with the potential to cause opportunistic lung infections, can reside in soil. This might be particularly relevant in Hawai’i, a geographic hot spot for NTM infections and whose soil composition differs from many other areas of the world. Soil components are likely to contribute to NTM prevalence in certain niches as food sources or attachment scaffolds, but the particular types of soils, clays, and minerals that impact NTM growth are not well-defined. Hawai’i soil and chemically weathered rock (saprolite) samples were examined to characterize the microbiome and quantify 11 mineralogical features as well as soil pH. Machine learning methods were applied to identify important soil features influencing the presence of NTM. Next, these features were directly tested in vitro by incubating synthetic clays and minerals in the presence of Mycobacteroides abscessus and Mycobacterium chimaera isolates recovered from the Hawai'i environment, and changes in bacterial growth were determined. Of the components examined, synthetic gibbsite, a mineral form of aluminum hydroxide, inhibited the growth of both M. abscessus and M. chimaera , while other minerals tested showed differential effects on each species. For example, M. abscessus (but not M. chimaera ) growth was significantly higher in the presence of hematite, an iron oxide mineral. In contrast, M. chimaera (but not M. abscessus ) counts were significantly reduced in the presence of birnessite, a manganese-containing mineral. These studies shed new light on the mineralogic features that promote or inhibit the presence of Hawai’i NTM in Hawai’i soil. IMPORTANCE Globally and in the United States, the prevalence of NTM pulmonary disease—a potentially life-threatening but underdiagnosed chronic illness—is prominently rising. While NTM are ubiquitous in the environment, including in soil, the specific soil components that promote or inhibit NTM growth have not been elucidated. We hypothesized that NTM culture-positive soil contains minerals that promote NTM growth in vitro . Because Hawai’i is a hot spot for NTM and a unique geographic archipelago, we examined the composition of Hawai’i soil and identified individual clay, iron, and manganese minerals associated with NTM. Next, individual components were evaluated for their ability to directly modulate NTM growth in culture. In general, gibbsite and some manganese oxides were shown to decrease NTM, whereas iron-containing minerals were associated with higher NTM counts. These data provide new information to guide future analyses of soil-associated factors impacting persistence of these soil bacteria. 

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4. Genomic and microbiological analyses of iron acquisition pathways among respiratory and environmental nontuberculous mycobacteria from Hawai’i

   https://doi.org/10.3389/fmicb.2023.1268963  

   Tan, Cara G.; Oberlag, Nicole M.; McGowan, Acelyn E.; Dawrs, Stephanie N.; Chan, Yvonne L.; Strong, Michael; Hasan, Nabeeh A.; Honda, Jennifer R. (November 2023, Frontiers in Microbiology)

   As environmental opportunistic pathogens, nontuberculous mycobacteria (NTM) can cause severe and difficult to treat pulmonary disease. In the United States, Hawai’i has the highest prevalence of infection. Rapid growing mycobacteria (RGM) such asMycobacterium abscessusandM. porcinumand the slow growing mycobacteria (SGM) includingM. intracellularesubspecieschimaeraare common environmental NTM species and subspecies in Hawai’i. Although iron acquisition is an essential process of many microorganisms, iron acquisition via siderophores among the NTM is not well-characterized. In this study, we apply genomic and microbiological methodologies to better understand iron acquisition via siderophores for environmental and respiratory isolates ofM. abscessus,M. porcinum, andM. intracellularesubspecieschimaerafrom Hawai’i. Siderophore synthesis and transport genes, including mycobactin(mbt), mmpL/S, andesx-3were compared among 47 reference isolates, 29 respiratory isolates, and 23 environmental Hawai’i isolates. Among all reference isolates examined, respiratory isolates showed significantly more siderophore pertinent genes compared to environmental isolates. Among the Hawai’i isolates, RGMM. abscessusandM. porcinumhad significantly lessesx-3 andmbtgenes compared to SGMM. chimaerawhen stratified by growth classification. However, no significant differences were observed between the species when grown on low iron culture agar or siderophore production by the chrome azurol S (CAS) assayin vitro. These results indicate the complex mechanisms involved in iron sequestration and siderophore activity among diverse NTM species. 

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5. Varying conjunctival immune response adaptations of house finch populations to a rapidly evolving bacterial pathogen

   https://doi.org/10.3389/fimmu.2024.1250818  

   Kuttiyarthu Veetil, Nithya; Henschen, Amberleigh E.; Hawley, Dana M.; Melepat, Balraj; Dalloul, Rami A.; Beneš, Vladimír; Adelman, James S.; Vinkler, Michal (February 2024, Frontiers in Immunology)

   Pathogen adaptations during host-pathogen co-evolution can cause the host balance between immunity and immunopathology to rapidly shift. However, little is known in natural disease systems about the immunological pathways optimised through the trade-off between immunity and self-damage. The evolutionary interaction between the conjunctival bacterial infectionMycoplasma gallisepticum(MG) and its avian host, the house finch (Haemorhous mexicanus), can provide insights into such adaptations in immune regulation. Here we use experimental infections to reveal immune variation in conjunctival tissue for house finches captured from four distinct populations differing in the length of their co-evolutionary histories with MG and their disease tolerance (defined as disease severity per pathogen load) in controlled infection studies. To differentiate contributions of host versus pathogen evolution, we compared house finch responses to one of two MG isolates: the original VA1994 isolate and a more evolutionarily derived one, VA2013. To identify differential gene expression involved in initiation of the immune response to MG, we performed 3’-end transcriptomic sequencing (QuantSeq) of samples from the infection site, conjunctiva, collected 3-days post-infection. In response to MG, we observed an increase in general pro-inflammatory signalling, as well as T-cell activation and IL17 pathway differentiation, associated with a decrease in the IL12/IL23 pathway signalling. The immune response was stronger in response to the evolutionarily derived MG isolate compared to the original one, consistent with known increases in MG virulence over time. The host populations differed namely in pre-activation immune gene expression, suggesting population-specific adaptations. Compared to other populations, finches from Virginia, which have the longest co-evolutionary history with MG, showed significantly higher expression of anti-inflammatory genes and Th1 mediators. This may explain the evolution of disease tolerance to MG infection in VA birds. We also show a potential modulating role of BCL10, a positive B- and T-cell regulator activating the NFKB signalling. Our results illuminate potential mechanisms of house finch adaptation to MG-induced immunopathology, contributing to understanding of the host evolutionary responses to pathogen-driven shifts in immunity-immunopathology trade-offs. 

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