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Rationale: Beryllium sensitization (BeS) and chronic beryllium disease (CBD) are determined by at least one genetic factor, a glutamic acid at position 69 (E69) of the HLA-DPB1 gene, and by exposure to beryllium. The relationship between exposure and the E69 genotype has not been well characterized.Objectives: The study goal was to define the relationship between beryllium exposure and E69 for CBD and BeS.Methods: Workers (n = 386) from a U.S. nuclear weapons facility were enrolled into a case-control study (70 BeS, 61 CBD, and 255 control subjects). HLA-DPB1 genotypes were determined by sequence-specific primer-polymerase chain reaction. Beryllium exposures were reconstructed on the basis of worker interviews and historical exposure measurements.Measurements and Main Results: Any E69 carriage increased odds for CBD (odds ratio [OR], 7.61; 95% confidence interval [CI], 3.66-15.84) and each unit increase in lifetime weighted average exposure increased the odds for CBD (OR, 2.27; 95% CI, 1.26-4.09). Compared with E69-negative genotypes, a single E69-positive *02 allele increased the odds for BeS (OR, 12.01; 95% CI, 4.28-33.71) and CBD (OR, 3.46; 95% CI, 1.42-8.43). A single non-*02 E69 allele further increased the odds for BeS (OR, 29.54; 95% CI, 10.33-84.53) and CBD (OR, 11.97; 95% CI, 5.12-28.00) and two E69 allele copies conferred the highest odds for BeS (OR, 55.68; 95% CI, 14.80-209.40) and CBD (OR, 22.54; 95% CI, 7.00-72.62).Conclusions: E69 and beryllium exposure both contribute to the odds of CBD. The increased odds for CBD and BeS due to E69 appear to be differentially distributed by genotype, with non-*02 E69 carriers and E69 homozygotes at higher odds than those with *02 genotypes. [ABSTRACT FROM AUTHOR]

Rationale: Occupational exposure to beryllium (Be) can result in chronic granulomatous inflammation characterized by the presence of Be-specific CD4+ T cells. Studies show that oxidative stress plays a role in the pathogenesis of chronic inflammatory disorders.Objectives: We hypothesized that Be-induced oxidative stress modulates the proliferation of Be-specific CD4+ T cells.Methods: Thirty-three subjects with chronic beryllium disease (CBD), 15 subjects with beryllium sensitization, and 28 healthy normal control subjects were consecutively enrolled from the Occupational and Environmental Health Clinic of the National Jewish Medical and Research Center.Measurements and Main Results: All studies were performed with Ficoll-Hypaque-isolated peripheral blood mononuclear cells from subsets of the study subjects. Decreased intracellular levels of the thiol antioxidants, glutathione and cysteine, were observed in peripheral blood mononuclear cells from subjects with beryllium sensitization and CBD, as compared with healthy control subjects. Beryllium stimulation decreased intracellular thiol antioxidants by more than 40%, accompanied by increased reactive oxygen species levels and the proliferation of Be-specific blood CD4+ T cells from subjects with CBD. Be-induced T-cell proliferation was inhibited by treatment with the thiol antioxidant N-acetylcysteine or the catalytic antioxidant manganese(III) 5,10,15,20-tetrakis(4-benzoic acid)porphyrin (MnTBAP). MnTBAP treatment also inhibited T-cell proliferation in response to the unrelated, MHC class II-restricted antigen tetanus toxoid. Treatment of CBD blood lymphocytes, but not antigen-presenting cells, with MnTBAP decreased Be-induced T-cell proliferation by more than 40%.Conclusions: Beryllium can mediate a thiol imbalance leading to oxidative stress that may modulate the proliferation and clonal expansion of Be-specific blood CD4+ T cells. These data suggest that Be-induced oxidative stress plays a role in the pathogenesis of granulomatous inflammation in CBD. [ABSTRACT FROM AUTHOR]

The blood beryllium lymphocyte proliferation test is used in medical surveillance to identify both beryllium sensitization and chronic beryllium disease. Approximately 50% of individuals with beryllium sensitization have chronic beryllium disease at the time of their initial clinical evaluation; however, the rate of progression from beryllium sensitization to chronic beryllium disease is unknown. We monitored a cohort of beryllium-sensitized patients at 2-year intervals, using bronchoalveolar lavage and repeated transbronchial lung biopsies to determine progression to chronic beryllium disease as evidenced by granulomatous inflammation in lung tissue. Fifty-five individuals with beryllium sensitization were monitored with a range of 2 to 5 clinical evaluations. Disease developed in 17 sensitized individuals (31%) within an average follow-up period of 3.8 years (range, 1.0-9.5 years). Thirty-eight of the 55 (69%) remained beryllium sensitized without disease after an average follow-up time of 4.8 years (range, 1.7-11.6 years). Progressors were more likely to have worked as machinists. We found no difference in average age, sex, race or ethnicity, smoking status, or beryllium exposure time between those who progressed to chronic beryllium disease and those who remained sensitized without disease. We conclude that beryllium sensitization is an adverse health effect in beryllium-exposed workers and merits medical follow-up. [ABSTRACT FROM AUTHOR]

Background: Sarcoidosis staging primarily has relied on the Scadding chest radiographic system, although chest CT imaging is finding increased clinical use., Research Question: Whether standardized chest CT scan assessment provides additional understanding of lung function beyond Scadding stage and demographics is unknown and the focus of this study., Study Design and Methods: We used National Heart, Lung, and Blood Institute study Genomics Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) cases of sarcoidosis (n = 351) with Scadding stage and chest CT scans obtained in a standardized manner. One chest radiologist scored all CT scans with a visual scoring system, with a subset read by another chest radiologist. We compared demographic features, Scadding stage and CT scan findings, and the correlation between these measures. Associations between spirometry and diffusing capacity of the lungs for carbon monoxide (Dlco) results and CT scan findings and Scadding stage were determined using regression analysis (n = 318). Agreement between readers was evaluated using Cohen's κ value., Results: CT scan features were inconsistent with Scadding stage in approximately 40% of cases. Most CT scan features assessed on visual scoring were associated negatively with lung function. Associations persisted for FEV 1 and Dlco when adjusting for Scadding stage, although some CT scan feature associations with FVC became insignificant. Scadding stage was associated primarily with FEV 1 , and inclusion of CT scan features reduced significance in association between Scadding stage and lung function. Multivariable regression modeling to identify radiologic measures explaining lung function included Scadding stage for FEV 1 and FEV 1 to FVC ratio (P < .05) and marginally for Dlco (P < .15). Combinations of CT scan measures accounted for Scadding stage for FVC. Correlations among Scadding stage and CT scan features were noted. Agreement between readers was poor to moderate for presence or absence of CT scan features and poor for degree and location of abnormality., Interpretation: In this study, CT scan features explained additional variability in lung function beyond Scadding stage, with some CT scan features obviating the associations between lung function and Scadding stage. Whether CT scan features, phenotypes, or endotypes could be useful for treating patients with sarcoidosis needs more study., Competing Interests: Financial/Nonfinancial Disclosures The authors have reported to CHEST the following: L. A. M. has received grants from the National Institutes of Health [Grants R01HL140357, R01HL142049, R01HL136681], Ann Theodore Foundation, the Foundation for Sarcoidosis Research, Mallinckrodt Pharmaceuticals, and the University of Cincinnati [Mallinckrodt Pharmaceuticals Foundation Grant] and serves on the Scientific Advisory Board for the Foundation for Sarcoidosis Research and Boehringer Ingelheim. B. S. B. has received a grant from Mallinckrodt Pharmaceuticals. E. S. C. has received grants from the National Institutes of Health, the Foundation for Sarcoidosis Research, American Thoracic Society, serves on the Scientific Advisory Board for the Foundation for Sarcoidosis Research, and has participated in clinical trials sponsored by aTyr Pharma and LabCorp Drug. L. L. K. has received grants from the National Institutes of Health [Grant R01HL157533], An Theodore Foundation, and Mallinckrodt Pharmaceuticals. D. A. L. was coinvestigator on a grant from the National Institutes of Health [Grant R01HL142049] and served on a Scientific Advisory Board for Boehringer Ingelheim, Inc. N. K. is a scientific founder at Thyron; served as a consultant to Boehringer Ingelheim, Pliant, Astra Zeneca, RohBar, Veracyte, Augmanity, CSL Behring, Splisense, Galapagos, Fibrogen, GSK, Merck, and Thyron over the last 3 years; reports equity in Pliant and Thyron; reports grants from Veracyte, Boehringer Ingelheim, and BMS; and reports nonfinancial support from Astra Zeneca. None declared (W. L. L., I. C., G. K. B., E. M. B., W. P. D., E. H., K. G., S. R. W., C. F.)., (Copyright © 2024 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.)

Background: Sarcoidosis is a heterogeneous granulomatous disease with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential biomarkers., Methods: Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of sarcoidosis diagnosis and progression phenotype, adjusting for age, sex, smoking, and principal components of the data. We built a supervised multi-omics model using a subset of features from each dataset., Results: We identified 1,459 CpGs, 64 mRNAs, and five miRNAs associated with sarcoidosis versus controls and four mRNAs associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway, which is important in T cell and mTOR function. Novel immune related genes and miRNAs including LYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation of IL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis., Conclusions: Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing is required for confirmation., (© 2024. The Author(s).)

Objective: Sarcoidosis is a granulomatous disease affecting the lungs in over 90% of patients. Qualitative assessment of chest CT by radiologists is standard clinical practice and reliable quantification of disease from CT would support ongoing efforts to identify sarcoidosis phenotypes. Standard imaging feature engineering techniques such as radiomics suffer from extreme sensitivity to image acquisition and processing, potentially impeding generalizability of research to clinical populations. In this work, we instead investigate approaches to engineering variogram-based features with the intent to identify a robust, generalizable pipeline for image quantification in the study of sarcoidosis., Approach: For a cohort of more than 300 individuals with sarcoidosis, we investigated 24 feature engineering pipelines differing by decisions for image registration to a template lung, empirical and model variogram estimation methods, and feature harmonization for CT scanner model, and subsequently 48 sets of phenotypes produced through unsupervised clustering. We then assessed sensitivity of engineered features, phenotypes produced through unsupervised clustering, and sarcoidosis disease signal strength to pipeline., Main Results: We found that variogram features had low to mild association with scanner model and associations were reduced by image registration. For each feature type, features were also typically robust to all pipeline decisions except image registration. Strength of disease signal as measured by association with pulmonary function testing and some radiologist visual assessments was strong (optimistic AUC ≈ 0.9, p ≪ 0.0001 in models for architectural distortion, conglomerate mass, fibrotic abnormality, and traction bronchiectasis) and fairly consistent across engineering approaches regardless of registration and harmonization for CT scanner., Significance: Variogram-based features appear to be a suitable approach to image quantification in support of generalizable research in pulmonary sarcoidosis., Competing Interests: LAM received grants from the National Institute of Health (R01HL140357, R01HL142049, and R01HL136681), Ann Theodore Foundation, the FSR, Mallinckrodt Pharmaceuticals, and the University of Cincinnati (Mallinckrodt Pharmaceuticals Foundation Grant) and serves on the Scientific Advisory Board for FSR, and Boeringer Ingelheim. RY was a speaker at Boehringer Ingelhein and Omnicurus CME experts, and is a consultant with IMBIO. WLL, TEF, DAL, JR, ACH, SL, MMM, BQB, KJC, HJH, and NEC have nothing to declare.

Sarcoidosis is a multi-organ granulomatous inflammatory disease of unknown etiology. Over 50% of patients will require treatment at some point in their disease and 10%-30% will develop a chronic progressive disease with pulmonary fibrosis leading to significant morbidity and mortality. Recently published guidelines recommend immunosuppressive therapy for sarcoidosis patients at risk of increased disease-related morbidity and mortality, and in whom disease has negatively impacted quality of life. Prednisone the currently recommended first line therapy is associated with significant toxicity however none of the other guideline recommended steroid sparing therapy is approved by regulatory agencies for use in sarcoidosis, and data in support of their use is weak. For patients with severe refractory disease requiring prolonged therapy, treatment options are limited. The need for expanding treatment options in sarcoidosis has been emphasized. Well conducted large, randomized trials evaluating currently available therapeutic options as well as novel pathways for targeting disease are necessary to better guide treatment decisions. These trials will not be without significant challenges. Sarcoidosis is a rare disease with heterogenous presentation and variable progression and clinical outcome. There are no universally agreed upon biomarkers of disease activity and measurement of outcomes is confounded by the need to balance patient centric measures and objective measures of disease activity. Our paper provides an update on developmental drugs in sarcoidosis and outlines several novel pathways that may be targeted for future drug development. Currently available trials are highlighted and ongoing challenges to drug development and clinical trial design are briefly discussed., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

It is now common to have a modest to large number of features on individuals with complex diseases. Unsupervised analyses, such as clustering with and without preprocessing by Principle Component Analysis (PCA), is widely used in practice to uncover subgroups in a sample. However, in many modern studies features are often highly correlated and noisy (e.g. SNP's, -omics, quantitative imaging markers, and electronic health record data). The practical performance of clustering approaches in these settings remains unclear. Through extensive simulations and empirical examples applying Gaussian Mixture Models and related clustering methods, we show these approaches (including variants of kmeans, VarSelLCM, HDClassifier, and Fisher-EM) can have very poor performance in many settings. We also show the poor performance is often driven by either an explicit or implicit assumption by the clustering algorithm that high variance features are relevant while lower variance features are irrelevant, called the variance as relevance assumption. We develop practical pre-processing approaches that improve analysis performance in some cases. This work offers practical guidance on the strengths and limitations of unsupervised clustering approaches in modern data analysis applications., Competing Interests: Declaration of Interest Statement WL holds stock in SomaLogic. NEC owns stock in Illumina. LAM has NIH funding to support sarcoidosis research, has funding from the Foundation for Sarcoidosis Research (FSR), is a member of the FSR Scientific Advisory Board, and has served or will serve on advisory boards or as a consultant for aTYR Pharma Inc, Novartis Pharmaceutical, CSL Behring, and Boehringer Ingelheim. JA, TEF, and KK have no competing interests to declare.

Background: A limited pool of SNPs are linked to the development and severity of sarcoidosis, a systemic granulomatous inflammatory disease. By integrating genome-wide association studies (GWAS) data and expression quantitative trait loci (eQTL) single nuclear polymorphisms (SNPs), we aimed to identify novel sarcoidosis SNPs potentially influencing the development of complicated sarcoidosis., Methods: A GWAS (Affymetrix 6.0) involving 209 African-American (AA) and 193 European-American (EA, 75 and 51 complicated cases respectively) and publicly-available GWAS controls (GAIN) was utilized. Annotation of multi-tissue eQTL SNPs present on the GWAS created a pool of ~46,000 eQTL SNPs examined for association with sarcoidosis risk and severity (Logistic Model, Plink). The most significant EA/AA eQTL SNPs were genotyped in a sarcoidosis validation cohort (n=1034) and cross-validated in two independent GWAS cohorts., Results: No single GWAS SNP achieved significance (p<1x10-8), however, analysis of the eQTL/GWAS SNP pool yielded 621 eQTL SNPs (p<10-4) associated with 730 genes that highlighted innate immunity, MHC Class II, and allograft rejection pathways with multiple SNPs validated in an independent sarcoidosis cohort (105 SNPs analyzed) (NOTCH4, IL27RA, BTNL2, ANXA11, HLA-DRB1). These studies confirm significant association of eQTL/GWAS SNPs in EAs and AAs with sarcoidosis risk and severity (complicated sarcoidosis) involving HLA region and innate immunity., Conclusion: Despite the challenge of deciphering the genetic basis for sarcoidosis risk/severity, these results suggest that integrated eQTL/GWAS approaches may identify novel variants/genes and support the contribution of dysregulated innate immune responses to sarcoidosis severity., Competing Interests: Competing interests Joe GN Garcia MD is CEO and Founder of Aqualung Therapeutics Corporation. David R. Moller MD is Chairman and CTO of Sarcoidosis Diagnostic Testing, LLC. All other authors report no conflict of interest.

The study provides insights into proteins that may be relevant in BeS and CBD. It provides a framework to investigate the global changes in lung compartment-specific inflammatory cells to better understand the potential interplay of proteins in CBD. https://bit.ly/3PLNTXC., Competing Interests: Conflict of interest: L. Li received support for the present manuscript from NIH HHS/USA grants R01ES023826, R01ES033678, R01ES025722, R01ES034767 and K01ES020857. Conflict of interest: I.V. Yang received support for the present manuscript from NIH HHS/USA grants R01ES023826, R01ES033678 and R01ES025722; consulting fees were received from Eleven P15, outside the submitted work; and she is an unpaid Chair for the American Thoracic Society Section on Genetics and Genomics, outside the submitted work. Conflict of interest: L.A. Maier received support for the present manuscript from NIH HHS/USA grants R01ES023826, R01ES033678 and R01ES025722. Conflict of interest: M. Bhargava received support for the present manuscript from NIH HHS/USA grant R01ES025722; and grants or contracts from R01HL153613 (Comprehensive Proteomic Classifier for the Molecular Characterization of Pulmonary Sarcoidosis; PI M. Bhargava, MPI Maier), KIN-1902-2001 (A Randomized, Double-blind, Placebo-controlled Phase 2 Study with Open Label Extension to Assess the Efficacy and Safety of Namilumab in Subjects with Chronic Pulmonary Sarcoidosis; Site PI M. Bhargava); FSR Pilot Grant (Comprehensive Assessment Of Signal Transduction Pathways in Sarcoidosis; PI M. Bhargava) ATYR1923-C-004 (A Phase 3, Randomized, Double-Blind, Placebo-Controlled Study to Evaluate the Efficacy and Safety of Intravenous Efzofitimod in Patients with Pulmonary Sarcoidosis; Site PI M. Bhargava), Chest Foundation (Inflammatory Protein Panel for Sarcoidosis Diagnosis and Prognosis; PI M. Bhargava), outside the submitted work; and has patents planned, issued or pending (Ingbar D, Rich T, Schumacher R, et al. (2022). Composition and Methods for Treating Pulmonary Edema or Lung Inflammation. American Inventors), outside the submitted work. Conflict of interest: The remaining authors have nothing to disclose., (Copyright ©The authors 2023.)

Sarcoidosis is a complex systemic disease. Our study aimed to (1) identify novel alleles associated with sarcoidosis susceptibility; (2) provide an in-depth evaluation of HLA alleles and sarcoidosis susceptibility and (3) integrate genetic and transcription data to identify risk loci that may more directly impact disease pathogenesis. We report a genome-wide association study of 1335 sarcoidosis cases and 1264 controls of European descent (EA) and investigate associated alleles in a study of African Americans (AA: 1487 cases and 1504 controls). The EA and AA cohort was recruited from multiple United States sites. HLA alleles were imputed and tested for association with sarcoidosis susceptibility. Expression quantitative locus and colocalization analysis were performed using a subset of subjects with transcriptome data. Forty-nine SNPs in the HLA region in HLA-DRA, -DRB9, -DRB5, -DQA1 and BRD2 genes were significantly associated with sarcoidosis susceptibility in EA, rs3129888 was also a risk variant for sarcoidosis in AA. Classical HLA alleles DRB1*0101, DQA1*0101 and DQB1*0501, which are highly correlated, were also associated with sarcoidosis. rs3135287 near HLA-DRA was associated with HLA-DRA expression in peripheral blood mononuclear cells and bronchoalveolar lavage from subjects and lung tissue and whole blood from GTEx. We identified six novel SNPs (out of the seven SNPs representing the 49 significant SNPs) and nine HLA alleles associated with sarcoidosis susceptibility in the largest EA population. We also replicated our findings in an AA population. Our study reiterates the potential role of antigen recognition and/or presentation HLA class II genes in sarcoidosis pathogenesis., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Pulmonary sarcoidosis is characterized by the accumulation of immune cells that form granulomas affecting the lungs. Efzofitimod (ATYR1923), a novel immunomodulator, selectively binds neuropilin 2, which is upregulated on immune cells in response to lung inflammation., Research Question: What is the tolerability, safety, and effect on outcomes of efzofitimod in pulmonary sarcoidosis?, Study Design and Methods: In this randomized, double-blind, placebo-controlled study evaluating multiple ascending doses of efzofitimod administered intravenously every 4 weeks for 24 weeks, randomized patients (2:1) underwent a steroid taper to 5 mg/d by week 8 or < 5 mg/d after week 16. The primary end point was the incidence of adverse events (AEs); secondary end points included steroid reduction, change in lung function, and patient-reported outcomes on health-related quality-of-life scales., Results: Thirty-seven patients received at least one dose of study medication. Efzofitimod was well tolerated at all doses, with no new or unexpected AEs and no dose-dependent AE incidence. Average daily steroid doses through end of study were 6.8 mg, 6.5 mg, and 5.6 mg for the 1 mg/kg, 3 mg/kg, and 5 mg/kg groups compared with 7.2 mg for placebo, resulting in a baseline-adjusted relative steroid reduction of 5%, 9%, and 22%, respectively. Clinically meaningful improvements were achieved across several patient-reported outcomes, several of which reached statistical significance in the 5 mg/kg dose arm. A dose-dependent but nonsignificant trend toward improved lung function also was observed for 3 and 5 mg/kg., Interpretation: Efzofitimod was safe and well tolerated and was associated with dose-dependent improvements of several clinically relevant end points compared with placebo. The results of this study support further evaluation of efzofitimod in pulmonary sarcoidosis., Trial Registry: ClinicalTrials.gov; No.: NCT03824392; URL: www., Clinicaltrials: gov., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The contribution and regulation of various CD4+ T cell lineages that occur with remitting vs progressive courses in sarcoidosis are poorly understood. We developed a multiparameter flow cytometry panel to sort these CD4+ T cell lineages followed by measurement of their functional potential using RNA-sequencing analysis at six-month intervals across multiple study sites. To obtain good quality RNA for sequencing, we relied on chemokine receptor expression to identify and sort lineages. To minimize gene expression changes induced by perturbations of T cells and avoid protein denaturation caused by freeze/thaw cycles, we optimized our protocols using freshly isolated samples at each study site. To accomplish this study, we had to overcome significant standardization challenges across multiple sites. Here, we detail standardization considerations for cell processing, flow staining, data acquisition, sorting parameters, and RNA quality control analysis that were performed as part of the NIH-sponsored, multi-center study, BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints (BRITE). After several rounds of iterative optimization, we identified the following aspects as critical for successful standardization: 1) alignment of PMT voltages across sites using CS&T/rainbow bead technology; 2) a single template created in the cytometer program that was used by all sites to gate cell populations during data acquisition and cell sorting; 3) use of standardized lyophilized flow cytometry staining cocktails to reduce technical error during processing; 4) development and implementation of a standardized Manual of Procedures. After standardization of cell sorting, we were able to determine the minimum number of sorted cells necessary for next generation sequencing through analysis of RNA quality and quantity from sorted T cell populations. Overall, we found that implementing a multi-parameter cell sorting with RNA-seq analysis clinical study across multiple study sites requires iteratively tested standardized procedures to ensure comparable and high-quality results., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Magallon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Chronic beryllium disease (CBD) is a Th1 granulomatous lung disease preceded by sensitization to beryllium (BeS). We profiled the methylome, transcriptome, and selected proteins in the lung to identify molecular signatures and networks associated with BeS and CBD. BAL cell DNA and RNA were profiled using microarrays from CBD ( n  = 30), BeS ( n  = 30), and control subjects ( n  = 12). BAL fluid proteins were measured using Olink Immune Response Panel proteins from CBD ( n  = 22) and BeS ( n  = 22) subjects. Linear models identified features associated with CBD, adjusting for covariation and batch effects. Multiomic integration methods identified correlated features between datasets. We identified 1,546 differentially expressed genes in CBD versus control subjects and 204 in CBD versus BeS. Of the 101 shared transcripts, 24 have significant cis relationships between gene expression and DNA methylation, assessed using expression quantitative trait methylation analysis, including genes not previously identified in CBD. A multiomic model of top DNA methylation and gene expression features demonstrated that the first component separated CBD from other samples and the second component separated control subjects from remaining samples. The top features on component one were enriched for T-lymphocyte function, and the top features on component two were enriched for innate immune signaling. We identified six differentially abundant proteins in CBD versus BeS, with two (SIT1 and SH2D1A) selected as important RNA features in the multiomic model. Our integrated analysis of DNA methylation, gene expression, and proteins in the lung identified multiomic signatures of CBD that differentiated it from BeS and control subjects.

Background: Sarcoidosis, a multi-systemic granulomatous disease, is a predominantly T-cell disease but evidence for a role for humoral immunity in disease pathogenesis is growing. Utilizing samples from the Genomic Research in Alpha-1 anti-trypsin Deficiency and Sarcoidosis (GRADS) study, we examined the prevalence of autoantibodies in sarcoidosis patients with pulmonary-only and extra-pulmonary organ involvement compared to normal controls., Study Design and Methods: We analyzed serum samples from sarcoidosis patients who participated in the GRADS study utilizing an autoantigen microarray platform for both IgM and IgG antibodies. The cohort included sarcoidosis patients with pulmonary-only disease (POS, n = 106), sarcoidosis patients with extra-pulmonary disease (EPS, n = 120) and a normal control cohort (NC, n = 101). Organ involvement was assessed following a standardized format across all GRADS participating centers., Results: Sarcoidosis patients overall had increased levels of IgM and IgG autoantibodies compared to normal controls. In addition, several autoantibodies were elevated in the POS and EPS cohorts compared to the NC cohort. Differences in autoantibody levels were also noted between the POS and the EPS cohorts. When comparing organ involvement with sarcoidosis, bone, spleen and ear, nose and throat involvement had higher IgM expression than other organs., Conclusion: Sarcoidosis patients have elevated IgM and IgG autoantibody levels compared to normal controls. In addition, individuals with pulmonary as well as additional organ involvement had higher IgM expression. Further research is needed focusing on specific organ-autoantibody pairs and role of autoantibodies in disease pathogenesis., Competing Interests: The authors have declared that no competing interests exist in relationship to this work.

Purpose: Exposures related to beryllium (Be) are an enduring concern among workers in the nuclear weapons and other high-tech industries, calling for regular and rigorous biological monitoring. Conventional biomonitoring of Be in urine is not informative of cumulative exposure nor health outcomes. Biomarkers of exposure to Be based on non-invasive biomonitoring could help refine disease risk assessment. In a cohort of workers with Be exposure, we employed blood plasma extracellular vesicles (EVs) to discover novel biomarkers of exposure to Be., Methods: EVs were isolated from plasma using size-exclusion chromatography and subjected to mass spectrometry-based proteomics. A protein-based classifier was developed using LASSO regression and validated by ELISA., Results: We discovered a dual biomarker signature comprising zymogen granule protein 16B and putative protein FAM10A4 that differentiated between Be-exposed and -unexposed subjects. ELISA-based quantification of the biomarkers in an independent cohort of samples confirmed higher expression of the signature in the Be-exposed group, displaying high predictive accuracy (AUROC = 0.919). Furthermore, the biomarkers efficiently discriminated high- and low-exposure groups (AUROC = 0.749)., Conclusions: This is the first report of EV biomarkers associated with Be exposure and exposure levels. The biomarkers could be implemented in resource-limited settings for Be exposure assessment., (© 2022. The Author(s).)

Introduction: Sarcoidosis is a granulomatous disorder thought to be caused by exposures in genetically susceptible individuals. This study investigated whether specific exposures were associated with different sarcoidosis phenotypes., Methods: Extensive demographic, occupational and environmental exposure data was analyzed from subjects enrolled in the NHLBI Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study., Results: In patients with sarcoidosis, radiation exposure was significantly associated with an increased risk of cardiac sarcoidosis versus non-cardiac sarcoidosis. No exposures were significantly associated with pulmonary only disease versus extrapulmonary disease with or without pulmonary involvement, Scadding Stage II/III/IV versus Scadding Stage 0/I, acute or remitting disease versus non-acute or non-remitting disease, nor chronic versus non-chronic disease. Although not reaching statistically significance after adjustment for multiple comparisons, there were a number of exposures associated with specific disease phenotypes, including exposures where relationships to sarcoidosis have previously been described such as rural exposures and pesticide exposures., Conclusions: Radiation exposure may be a risk factor for cardiac sarcoidosis. Other exposures may also be associated with specific phenotypes and should be further explored. The study was limited by small groups of exposed subjects for individual exposures and multiple comparisons. The development of novel and innovative exposure assessment tools is needed., (Copyright © 2022. Published by Elsevier Ltd.)

Introduction: Respiratory infections are ubiquitous. The COVID-19 pandemic has refocused our attention on how morbid and potentially fatal they can be, and how host factors have an impact on the clinical course and outcomes. Due to a range of vulnerabilities, patients with sarcoidosis may be at higher risk of poor outcomes from respiratory infections. The objective of the SARCoidosis Outcomes in all respiratory Viral Infectious Diseases (SARCOVID) Study is to determine the short-term and long-term impacts of respiratory viral illnesses (COVID-19 and non-COVID-19) in sarcoidosis., Methods and Analysis: Up to 20 clinical sites across the USA are participating in the recruitment of 2000 patients for this observational, prospective study. To ensure that the study cohort is representative of the general population with sarcoidosis, participating sites include those dedicated to reaching under-represented minorities or patients from non-urban areas. Baseline data on demographic features, comorbidities, sarcoidosis characteristics and pre-enrolment lung function will be captured at study entry. During this 3-year study, all acute respiratory infectious events (from SARS-CoV-2 and any other respiratory pathogen) will be assessed and recorded at quarterly intervals. The level of required medical care and survival outcomes determine infection severity, and the impact of infection on quality of life measures will be recorded. Post-infection lung function and imaging results will measure the long-term impact on the trajectory of sarcoidosis. Patients will be analysed according to the clinical phenotypes of cardiac and fibrotic pulmonary sarcoidosis. Control groups include non-infected patients with sarcoidosis and patients with non-sarcoidosis interstitial lung disease., Ethics and Dissemination: Each site received local institutional review board approval prior to enrolling patients, with the consent process determined by local institution standards. Data will be published in a timely manner (goal <12 months) at the conclusion of the 3-year follow-up period and will be made available upon request., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Sex-specific differences in fetal lung maturation have been well described; however, little is known about the sex-specific differences in microRNA (miRNA) expression during human fetal lung development. Interestingly, many adult chronic lung diseases also demonstrate sex-specific differences in prevalence. The developmental origins of health and disease hypothesis suggests that these sex-specific differences in fetal lung development may influence disease susceptibility later in life. In this study, we performed miRNA sequencing on human fetal lung tissue samples to investigate differential expression of miRNAs between males and females in the pseudoglandular stage of lung development. We hypothesized that differences in miRNA expression are present between sexes in early human lung development and may contribute to the sex-specific differences seen in pulmonary diseases later in life. Methods: RNA was isolated from human fetal lung tissue samples for miRNA sequencing. The count of each miRNA was modeled by sex using negative binomial regression models in DESeq2, adjusting for post-conception age, age 2 , smoke exposure, batch, and RUV factors. We tested for differential expression of miRNAs by sex, and for the presence of sex-by-age interactions to determine if miRNA expression levels by age were distinct between males and females. Results: miRNA expression profiles were generated on 298 samples (166 males and 132 females). Of the 809 miRNAs expressed in human fetal lung tissue during the pseudoglandular stage of lung development, we identified 93 autosomal miRNAs that were significantly differentially expressed by sex and 129 miRNAs with a sex-specific pattern of miRNA expression across the course of the pseudoglandular period. Conclusion: Our study demonstrates differential expression of numerous autosomal miRNAs between the male and female developing human lung. Additionally, the expression of some miRNAs are modified by age across the pseudoglandular stage in a sex-specific way. Some of these differences in miRNA expression may impact susceptibility to pulmonary disease later in life. Our results suggest that sex-specific miRNA expression during human lung development may be a potential mechanism to explain sex-specific differences in lung development and may impact subsequent disease susceptibility., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Lin, Liu, Yang, Maier, DeMeo, Wood, Ye, Cruse, Smith, Vyhlidal, Kechris and Sharma.)

Background: Most phenotyping paradigms in sarcoidosis are based on expert opinion; however, no paradigm has been widely adopted because of the subjectivity in classification. We hypothesized that cluster analysis could be performed on common clinical variables to define more objective sarcoidosis phenotypes., Methods: We performed a retrospective cohort study of 554 sarcoidosis cases to identify distinct phenotypes of sarcoidosis based on 29 clinical features. Model-based clustering was performed using the VarSelLCM R package and the Integrated Completed Likelihood (ICL) criteria were used to estimate number of clusters. To identify features associated with cluster membership, features were ranked based on variable importance scores from the VarSelLCM model, and additional univariate tests (Fisher's exact test and one-way ANOVA) were performed using q-values correcting for multiple testing. The Wasfi severity score was also compared between clusters., Results: Cluster analysis resulted in 6 sarcoidosis phenotypes. Salient characteristics for each cluster are as follows: Phenotype (1) supranormal lung function and majority Scadding stage 2/3; phenotype (2) supranormal lung function and majority Scadding stage 0/1; phenotype (3) normal lung function and split Scadding stages between 0/1 and 2/3; phenotype (4) obstructive lung function and majority Scadding stage 2/3; phenotype (5) restrictive lung function and majority Scadding stage 2/3; phenotype (6) mixed obstructive and restrictive lung function and mostly Scadding stage 4. Although there were differences in the percentages, all Scadding stages were encompassed by all of the phenotypes, except for phenotype 1, in which none were Scadding stage 4. Clusters 4, 5, 6 were significantly more likely to have ever been on immunosuppressive treatment and had higher Wasfi disease severity scores., Conclusions: Cluster analysis produced 6 sarcoidosis phenotypes that demonstrated less severe and severe phenotypes. Phenotypes 1, 2, 3 have less lung function abnormalities, a lower percentage on immunosuppressive treatment and lower Wasfi severity scores. Phenotypes 4, 5, 6 were characterized by lung function abnormalities, more parenchymal abnormalities, an increased percentage on immunosuppressive treatment and higher Wasfi severity scores. These data support using cluster analysis as an objective and clinically useful way to phenotype sarcoidosis subjects and to empower clinicians to identify those with more severe disease versus those who have less severe disease, independent of Scadding stage., (© 2022. The Author(s).)

Purpose: An open question in deep clustering is how to explain what in the image is driving the cluster assignments. This is especially important for applications in medical imaging when the derived cluster assignments may inform decision-making or create new disease subtypes. We develop cluster activation mapping (CLAM), which is methodology to create localization maps highlighting the image regions important for cluster assignment. Approach: Our approach uses a linear combination of the activation channels from the last layer of the encoder within a pretrained autoencoder. The activation channels are weighted by a channelwise confidence measure, which is a modification of score-CAM. Results: Our approach performs well under medical imaging-based simulation experiments, when the image clusters differ based on size, location, and intensity of abnormalities. Under simulation, the cluster assignments were predicted with 100% accuracy when the number of clusters was set at the true value. In addition, applied to computed tomography scans from a sarcoidosis population, CLAM identified two subtypes of sarcoidosis based purely on CT scan presentation, which were significantly associated with pulmonary function tests and visual assessment scores, such as ground-glass, fibrosis, and honeycombing. Conclusions: CLAM is a transparent methodology for identifying explainable groupings of medical imaging data. As deep learning networks are often criticized and not trusted due to their lack of interpretability, our contribution of CLAM to deep clustering architectures is critical to our understanding of cluster assignments, which can ultimately lead to new subtypes of diseases., (© 2022 Society of Photo-Optical Instrumentation Engineers (SPIE).)

Purpose of Review: Sarcoidosis is an idiopathic granulomatous disease that primarily affects the lungs. Several lines of evidence suggest that occupational exposures are associated with disease risk. This review critically evaluates studies using the Bradford Hill criteria for causation to determine if a causal relationship can be established between occupational exposure and sarcoidosis., Recent Findings: Large epidemiological studies have proposed multiple occupational exposures associated with sarcoidosis but lack consistency of results. Many convincing studies demonstrate an association between World Trade Center (WTC) dust and sarcoidosis, which illustrates a causal relationship based on the fulfillment of the Bradford Hill criteria. Studies describing an association between silica/metals and sarcoidosis are intriguing but fulfill a limited number of the Bradford Hill criteria and warrant further investigation before a causal relationship can be determined. Finally, we also discuss preliminary studies associating sarcoidosis phenotypes with specific occupational exposures., Summary: Using the Bradford Hill criteria for causation, we demonstrate that WTC dust has a causative relationship with sarcoidosis, which reinforces the theory that sarcoidosis is an exposure-related disease. More research is needed to determine other specific occupational exposures causing disease., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Multiple overlapping pathways are identified in tissue, BAL cells, PBMCs and a sarcoidosis in vitro granuloma model. Inferences from omic studies are constrained by small sample sizes. Studies comparing differences between sarcoidosis phenotypes are needed. https://bit.ly/30NaHz4., Competing Interests: Conflict of interest: M. Bhargava has nothing to disclose. Conflict of interest: S-Y. Liao has nothing to disclose. Conflict of interest: E.D. Crouser has nothing to disclose. Conflict of interest: L.A. Maier has nothing to disclose. Conflict of interest: S.M. Leach has nothing to disclose., (Copyright ©The authors 2022.)

Objectives: Human leukocyte antigen-DP beta 1 (HLA-DPB1) with a glutamic acid at the 69th position of the ß chain (E69) genotype and inhalational beryllium exposure individually contribute to risk of chronic beryllium disease (CBD) and beryllium sensitisation (BeS) in exposed individuals. This retrospective nested case-control study assessed the contribution of genetics and exposure in the development of BeS and CBD., Methods: Workers with BeS (n=444), CBD (n=449) and beryllium-exposed controls (n=890) were enrolled from studies conducted at nuclear weapons and primary beryllium manufacturing facilities. Lifetime-average beryllium exposure estimates were based on workers' job questionnaires and historical and industrial hygienist exposure estimates, blinded to genotype and case status. Genotyping was performed using sequence-specific primer-PCR. Logistic regression models were developed allowing for over-dispersion, adjusting for workforce, race, sex and ethnicity., Results: Having no E69 alleles was associated with lower odds of both CBD and BeS; every additional E69 allele increased odds for CBD and BeS. Increasing exposure was associated with lower odds of BeS. CBD was not associated with exposure as compared to controls, yet the per cent of individuals with CBD versus BeS increased with increasing exposure. No evidence of a gene-by-exposure interaction was found for CBD or BeS., Conclusions: Risk of CBD increases with E69 allele frequency and increasing exposure, although no gene by environment interaction was found. A decreased risk of BeS with increasing exposure and lack of exposure response in CBD cases may be due to the limitations of reconstructed exposure estimates. Although reducing exposure may not prevent BeS, it may reduce CBD and the associated health effects, especially in those carrying E69 alleles., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. No commercial re-use. See rights and permissions. Published by BMJ.)

The prognostic value of peripheral blood mononuclear cell (PBMC) expression profiles, when used in patients with chronic hypersensitivity pneumonitis (CHP), as an adjunct to traditional clinical assessment is unknown. RNA-seq analysis on PBMC from 37 patients with CHP at initial presentation determined that (1) 74 differentially expressed transcripts at a 10% false discovery rate distinguished those with (n=10) and without (n=27) disease progression, defined as absolute FVC and/or diffusing capacity of the lungs for carbon monoxide (DLCO) decline of ≥10% and increased fibrosis on chest CT images within 24 months, and (2) classification models based on gene expression and clinical factors strongly outperform models based solely on clinical factors (baseline FVC%, DLCO% and chest CT fibrosis)., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. No commercial re-use. See rights and permissions. Published by BMJ.)

Introduction: The Borg and Modified Medical Research Council (mMRC) dyspnea scales have been used to evaluate dyspnea in sarcoidosis. The Baseline Dyspnea Index (BDI) and Transitional Dyspnea Index (TDI) are useful for the assessment of dyspnea in COPD. It is not known if the BDI-TDI accurately assesses dyspnea in sarcoidosis patients., Methods: Data was analyzed from the Registry for Advanced Sarcoidosis (ReAS), a multi-national database enrolling patients with advanced sarcoidosis and a comparison group of sarcoidosis patients with non-advanced disease. At baseline, patients completed a BDI questionnaire along with spirometry, 6-min walk distance (6MWD), mMRC, Borg score, fatigue assessment score (FAS) and HRQoL assessments using Kings Sarcoidosis Questionnaire (KSQ) and St Georges Respiratory Questionnaire (SGRQ). At 12-months, patients with advanced disease completed a TDI questionnaire along with the other measures. Correlations between BDI and baseline variables, and between TDI and changes in baseline variables were evaluated., Results: There was significant correlation (p < 0.001 for all) between BDI and baseline 6MWD (rho = 0.336), FVC% (rho = 0.387), FEV1% (rho = 0.285), DLCO% (rho = 0.355), mMRC (rho = -0.721), Borg score (rho = -0.389), FAS (rho = -0.669), SGRQ (rho = -0.785), and KSQ (rho = 0.318 to 0.724). At follow-up, TDI correlated with BDI, but not with changes in pulmonary function or other dyspnea measures., Conclusion: BDI scores correlated with pulmonary function, 6MWD, and other dyspnea measures. TDI scores did not correlate with changes in pulmonary function or other dyspnea measures. BDI may be a useful independent measure of dyspnea in sarcoidosis patients. The role of TDI needs further evaluation in longitudinal studies associated with changes in clinical parameters., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits., Methods: RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50)., Results: Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg., Conclusion: Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes., Competing Interests: Conflict of interest: M. Vukmirovic has nothing to disclose. Conflict of interest: X. Yan has nothing to disclose. Conflict of interest: K.F. Gibson has nothing to disclose. Conflict of interest: M. Gulati reports grants from NIH, during the conduct of the study; personal fees for advisory board work and other (PI/publication committee) from Boehringer Ingelheim, other (lectures) from France Foundation, other (PI/centre director) from Pulmonary Fibrosis Foundation, grants from NIH and Sarcoidosis Research Foundation, outside the submitted work. Conflict of interest: J.C. Schupp has nothing to disclose. Conflict of interest: G. DeIuliis has nothing to disclose. Conflict of interest: T.S. Adams has nothing to disclose. Conflict of interest: B. Hu has nothing to disclose. Conflict of interest: A. Mihaljinec has nothing to disclose. Conflict of interest: T.N. Woolard has nothing to disclose. Conflict of interest: H. Lynn has nothing to disclose. Conflict of interest: N. Emeagwali has nothing to disclose. Conflict of interest: E.L Herzog reports grants from NIH, Sanofi, Bristol Myers and Promedior, personal fees for consultancy from Boehringer Ingelheim and Pfizer, outside the submitted work. Conflict of interest: E.S. Chen has nothing to disclose. Conflict of interest: A. Morris reports grants from NIH, during the conduct of the study. Conflict of interest: J.K. Leader has nothing to disclose. Conflict of interest: Y. Zhang has nothing to disclose. Conflict of interest: J.G.N. Garcia has nothing to disclose. Conflict of interest: L.A. Maier grants from NIH (1U01 HL112695-01, U01 HL112707-03) and NIH/NCRR (UL1TRR002535), during the conduct of the study; grants from National Institutes of Health (1R01 HL127461-01A1, R01HL136681-01A1, 1R01 HL140357-01A1, R01HL136681-01A1), FSR, University of Cinncinati under a Mallinckrodt foundation, MNK14344100, ATYR1923-C-002, outside the submitted work; and is a member of the FSR scientific advisory board, for which no compensation is received. Conflict of interest: R.G. Collman reports grants from National Institutes of Health, during the conduct of the study. Conflict of interest: W.P. Drake has nothing to disclose. Conflict of interest: M.J. Becich reports grants from NCATS, NCI, PCORI, NHLBI and CDC NIOSH, other (startup) from SpIntellx, during the conduct of the study; other (startup) from SpIntellx, outside the submitted work; and has patents SpIntellx (multiple) pending. Conflict of interest: H. Hochheiser has nothing to disclose. Conflict of interest: S.R. Wisniewski has nothing to disclose. Conflict of interest: P.V. Benos has nothing to disclose. Conflict of interest: D.R. Moller reports grants from NHLBI (1U01HL112708), during the conduct of the study; personal fees for consultancy from Merck, aTYR and Roivant, personal fees for advisory board work from SarcoMed, personal fees for consultancy/witness from Legal Expert, other (royalties) from Hodder Education and Taylor & Francis Group, outside the submitted work; has patents number 9,683,999 B2 issued, and number 9,977,029 B2 issued; is Chairman and Chief Technical Officer of Sarcoidosis Diagnostic Testing, LLC (a company whose goal is to develop a diagnostic blood test for sarcoidosis) and has received funding including past salary support under the NHLBI STTR programme, grant R41 HL129728 more than 3 years ago; and is a former member of the Scientific Advisory Board of the Foundation for Sarcoidosis Research. Conflict of interest: A. Prasse reports personal fees for lectures and consultancy and non-financial support for meeting attendance from Boehringer Ingelheim and Roche, personal fees for lectures from Novartis and AstraZeneca, personal fees for consultancy from Amgen, Pliant and Nitto Denko, outside the submitted work. Conflict of interest: L.L. Koth has nothing to disclose. Conflict of interest: N. Kaminski reports personal fees for consultancy and/or advisory board work from Biogen Idec, Boehringer Ingelheim, Third Rock, Samumed, NuMedii, Indaloo, Theravance, LifeMax, Three Lake Partners, RohBar and Pliant, non-financial support from Miragen, equity with Pliant, a grant from Veracyte; all outside the submitted work; and has a patent New Therapies in Pulmonary Fibrosis and on Peripheral Blood Gene Expression that have been licensed to Biotech., (Copyright ©The authors 2021. For reproduction rights and permissions contact permissions@ersnet.org.)

Sarcoidosis is a multisystem disease of unknown cause with heterogeneous clinical manifestations and variable course. Spontaneous remissions occur in some patients, whereas others have progressive disease impacting survival, organ function, and quality of life. Four high-risk sarcoidosis phenotypes associated with chronic inflammation have recently been identified as high-priority areas for research. These include treatment-refractory pulmonary disease, cardiac sarcoidosis, neurosarcoidosis, and multiorgan sarcoidosis. Significant gaps currently exist in the understanding of these high-risk manifestations of sarcoidosis, including their natural history, diagnostic criteria, biomarkers, and the treatment strategy, such as the ideal agent, optimal dose, and treatment duration. The use of registries with well-phenotyped patients is a critical first step to study high-risk sarcoidosis manifestations systematically. We review the diagnostic and treatment approach to high-risk sarcoidosis manifestations. Appropriately identifying these disease subgroups will help enroll well-phenotyped patients in sarcoidosis registries and clinical trials, a necessary step to narrow existing gaps in understanding of this enigmatic disease.

Introduction: Sarcoidosis is a multiorgan granulomatous disorder thought to be triggered and influenced by gene-environment interactions. Sarcoidosis affects 45-300/100 000 individuals in the USA and has an increasing mortality rate. The greatest gap in knowledge about sarcoidosis pathobiology is a lack of understanding about the underlying immunological mechanisms driving progressive pulmonary disease. The objective of this study is to define the lung-specific and blood-specific longitudinal changes in the adaptive immune response and their relationship to progressive and non-progressive pulmonary outcomes in patients with recently diagnosed sarcoidosis., Methods and Analysis: The BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints study is a US-based, NIH-sponsored longitudinal blood and bronchoscopy study. Enrolment will occur over four centres with a target sample size of 80 eligible participants within 18 months of tissue diagnosis. Participants will undergo six study visits over 18 months. In addition to serial measurement of lung function, symptom surveys and chest X-rays, participants will undergo collection of blood and two bronchoscopies with bronchoalveolar lavage separated by 6 months. Freshly processed samples will be stained and flow-sorted for isolation of CD4 +T helper (Th1, Th17.0 and Th17.1) and T regulatory cell immune populations, followed by next-generation RNA sequencing. We will construct bioinformatic tools using this gene expression to define sarcoidosis endotypes that associate with progressive and non-progressive pulmonary disease outcomes and validate the tools using an independent cohort., Ethics and Dissemination: The study protocol has been approved by the Institutional Review Boards at National Jewish Hospital (IRB# HS-3118), University of Iowa (IRB# 201801750), Johns Hopkins University (IRB# 00149513) and University of California, San Francisco (IRB# 17-23432). All participants will be required to provide written informed consent. Findings will be disseminated via journal publications, scientific conferences, patient advocacy group online content and social media platforms., Competing Interests: Competing interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Löfgren's syndrome (LS) is an acute form of sarcoidosis characterized by a genetic association with HLA-DRB1*03 (HLA-DR3) and an accumulation of CD4+ T cells of unknown specificity in the bronchoalveolar lavage (BAL). Here, we screened related LS-specific TCRs for antigen specificity and identified a peptide derived from NAD-dependent histone deacetylase hst4 (NDPD) of Aspergillus nidulans that stimulated these CD4+ T cells in an HLA-DR3-restricted manner. Using ELISPOT analysis, a greater number of IFN-γ- and IL-2-secreting T cells in the BAL of DR3+ LS subjects compared with DR3+ control subjects was observed in response to the NDPD peptide. Finally, increased IgG antibody responses to A. nidulans NDPD were detected in the serum of DR3+ LS subjects. Thus, our findings identify a ligand for CD4+ T cells derived from the lungs of LS patients and suggest a role of A. nidulans in the etiology of LS., Competing Interests: Disclosures: L.A. Maier reported grants from NIH (1R01HL114587-01A1; 1R01 HL140357-01A1; R01HL136681-01A1; 1R01 HL142049-01A1; R01 HL127461), FSR, Clinical Studies Network, and MNK14344100 outside the submitted work; in addition, L.A. Maier is a member of the FSR Scientific Advisory Board. She does not receive any compensation for this activity. No other disclosures were reported., (© 2021 Greaves et al.)

Background Previous gene expression studies have identified genes IFNγ, TNFα, RNase 3, CXCL9, and CD55 as potential biomarkers for sarcoidosis and/or chronic beryllium disease (CBD). We hypothesized that differential expression of these genes could function as diagnostic biomarkers for sarcoidosis and CBD, and prognostic biomarkers for sarcoidosis. Study Design/Methods We performed RT-qPCR on whole blood samples from CBD (n = 132), beryllium sensitized (BeS) (n = 109), and sarcoidosis (n = 99) cases and non-diseased controls (n = 97) to determine differential expression of target genes. We then performed logistic regression modeling and generated ROC curves to determine which genes could most accurately differentiate: 1) CBD versus sarcoidosis 2) CBD versus BeS 3) sarcoidosis versus controls 4) non-progressive versus progressive sarcoidosis. Results CD55 and TNFα were significantly upregulated, while CXCL9 was significantly downregulated in CBD compared to sarcoidosis (p < 0.05). The ROC curve from the logistic regression model demonstrated high discriminatory ability of the combination of CD55, TNFα, and CXCL9 to distinguish between CBD and sarcoidosis with an AUC of 0.98. CD55 and TNFα were significantly downregulated in sarcoidosis compared to controls (p < 0.05). The ROC curve from the model showed a reasonable discriminatory ability of CD55 and TNFα to distinguish between sarcoidosis and controls with an AUC of 0.86. There was no combination of genes that could accurately differentiate between CBD and BeS or sarcoidosis phenotypes. Interpretation CD55, TNFα and CXCL9 expression levels can accurately differentiate between CBD and sarcoidosis, while CD55 and TNFα expression levels can accurately differentiate sarcoidosis and controls., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Purpose of Review: Epidemiological and clinical observations as well as familial clustering support the existence of a genetic predisposition to sarcoidosis. In this article, we review the most recent findings in genetics of sarcoidosis and discuss how the identification of risk alleles may help advancing our understanding of disease etiology and development., Recent Findings: Genetic studies of sarcoidosis phenotypes have identified novel and ancestry-specific associations. Gene-environment interaction studies highlighted the importance of integrating genetic information when assessing the relationship between sarcoidosis and environmental exposures. A case-control-family study revealed that the heritability of sarcoidosis is only 49%, suggesting the existence of additional important contributors to disease risk. The application of whole-exome sequencing has identified associations with disease activity and prognosis. Finally, gene expression studies of circulating immune cells have identified shared and unique pathways between sarcoidosis and other granulomatous diseases., Summary: Sarcoidosis genetic research has led to the identification of a number of associations with both sarcoidoses per se and disease phenotypes. Newer sequencing technologies are likely to increase the number of genetic variants associated with sarcoidosis. However, studying phenotypically and ethnically homogeneous patient subsets remains critically important regardless of the genetic approach used., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Over 90% of one million annual US joint replacements are highly successful. Nonetheless, 10% do poorly owing to infection or mechanical issues. Many implant components are sensitizers, and sensitization could also contribute to implant failure., Objective: To determine the prevalence of implant sensitization in joint failure patients, their clinical characteristics, and implant revision outcomes. We hypothesized that sensitized patients would improve when revised with nonallergenic materials., Methods: We prospectively enrolled 105 joint failure patients referred by orthopedic surgeons who had already excluded infection or mechanical causes. Patients provided informed consent, completed a history and physical examination, patch testing to metals and bone cement, and a nickel lymphocyte proliferation test. A study coordinator was able to contact 64% of patients (n = 67) 9 to 12 months later to evaluate outcomes., Results: A total of 59% were sensitized to an implant component: 32% to metal and 37% to bone cement. The nickel lymphocyte proliferation test was 60% sensitive and 96% specific in diagnosing nickel sensitization. Most sensitized subjects reported no or uncertain histories of reactions to a specific material. Implant sensitized patients were younger and reported previous eczema, joint itching, and implant loosening. By 9 to 12 months later, most patients with a revised implant (revised) described significant improvement (16 of 22 revised for sensitization [P = .0003] vs 9 of 13 revised without sensitization [P = .047]) compared with patients without implant revision). All revised patients with sensitization used components to which they were not sensitized. Pain (P = .001), swelling (P = .035), and instability (P = .006) were significantly reduced in the revised sensitized group., Conclusions: Sensitization to implant components is an important cause of unexplained joint replacement failure. Joint revisions based on sensitization information resulted in significant improvements., (Copyright © 2021 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.)

Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis., Competing Interests: Conflict of interest: I.R. Konigsberg has nothing to disclose. Conflict of interest: L.A. Maier reports grants from National Institutes of Health, during the conduct of the study; and grants from National Institutes of Health, University of Cincinnati under a Mallinckrodt Foundation, MNK14344100 and ATYR1923-C-002, outside the submitted work. L.A. Maier is a member of the FSR Scientific Advisory Board. She does not receive any compensation for this activity. Conflict of interest: I.V. Yang reports grants from NIH, during the conduct of the study; and personal fees from Eleven P15, outside the submitted work. I.V. Yang has a patent “Circulating Biomarkers of Preclinical Pulmonary Fibrosis” pending., (Copyright ©The authors 2021.)

Discovering dominant epitopes for T cells, particularly CD4+ T cells, in human immune-mediated diseases remains a significant challenge. Here, we used bronchoalveolar lavage (BAL) cells from HLA-DP2-expressing patients with chronic beryllium disease (CBD), a debilitating granulomatous lung disorder characterized by accumulations of beryllium-specific (Be-specific) CD4+ T cells in the lung. We discovered lung-resident CD4+ T cells that expressed a disease-specific public CDR3β T cell receptor motif and were specific to Be-modified self-peptides derived from C-C motif ligand 4 (CCL4) and CCL3. HLA-DP2-CCL/Be tetramer staining confirmed that these chemokine-derived peptides represented major antigenic targets in CBD. Furthermore, Be induced CCL3 and CCL4 secretion in the lungs of mice and humans. In a murine model of CBD, the addition of LPS to Be oxide exposure enhanced CCL4 and CCL3 secretion in the lung and significantly increased the number and percentage of CD4+ T cells specific for the HLA-DP2-CCL/Be epitope. Thus, we demonstrate a direct link between Be-induced innate production of chemokines and the development of a robust adaptive immune response to those same chemokines presented as Be-modified self-peptides, creating a cycle of innate and adaptive immune activation.

Little is known about the prevalence, clinical characteristics and impact of hypothyroidism in patients with sarcoidosis. We aimed to determine the prevalence and clinical features of hypothyroidism and its relation to organ involvement and other clinical manifestations in patients with sarcoidosis. We conducted a national registry-based study investigating 3835 respondents to the Sarcoidosis Advanced Registry for Cures Questionnaire between June 2014 and August 2019. This registry is based on a self-reported, web-based questionnaire that provides data related to demographics, diagnostics, sarcoidosis manifestations and treatment. We compared sarcoidosis patients with and without self-reported hypothyroidism. We used multivariable logistic regression and adjusted for potential confounders to determine the association of hypothyroidism with nonorgan-specific manifestations. 14% of the sarcoidosis patients self-reported hypothyroidism and were generally middle-aged white women. Hypothyroid patients had more comorbid conditions and were more likely to have multiorgan sarcoidosis involvement, especially with cutaneous, ocular, joints, liver and lacrimal gland involvement. Self-reported hypothyroidism was associated with depression (adjusted odds ratio (aOR) 1.3, 95% CI 1.01-1.6), antidepressant use (aOR 1.3, 95% CI 1.1-1.7), obesity (aOR 1.7, 95% CI 1.4-2.1), sleep apnoea (aOR 1.7, 95% CI 1.3-2.2), chronic fatigue syndrome (aOR 1.5, 95% CI 1.2-2) and was borderline associated with fibromyalgia (aOR 1.3, 95% CI 1-1.8). Physical impairment was more common in patients with hypothyroidism. Hypothyroidism is a frequent comorbidity in sarcoidosis patients that might be a potentially reversible contributor to fatigue, depression and physical impairment in this population. We recommend considering routine screening for hypothyroidism in sarcoidosis patients especially in those with multiorgan sarcoidosis, fatigue and depression., Competing Interests: Conflict of interest: B.N. Alzghoul has nothing to disclose. Conflict of interest: F.N. Amer has nothing to disclose. Conflict of interest: D. Barb has nothing to disclose. Conflict of interest: A. Innabi has nothing to disclose. Conflict of interest: M.T. Mardini has nothing to disclose. Conflict of interest: C. Bai has nothing to disclose. Conflict of interest: B. Alzghoul has nothing to disclose. Conflict of interest: T. Al-Hakim reports helping with the FSR-SARC registry design and enrollment. Conflict of interest: N. Singh reports helping with the FSR-SARC registry design and enrollment. Conflict of interest: M. Buchanan reports helping with the FSR-SARC registry design and enrollment. Conflict of interest: L. Serchuck reports helping with the FSR-SARC registry design and enrollment. Conflict of interest: D. Gomez Manjarres has nothing to disclose. Conflict of interest: W.W. Woodmansee has nothing to disclose. Conflict of interest: L.A. Maier reports being a nonpaid member of the Scientific Advisory Board of the FSR, and receives grant funding for research as a member of the FSR-Clinical Studies Network. She helped with the FSR-SARC registry design and enrolment. Conflict of interest: D.C. Patel has nothing to disclose., (Copyright ©The authors 2021.)

Rationale: Improvement of quality of life (QoL) in patients with sarcoidosis is an important goal of management. The King's Sarcoidosis Questionnaire (KSQ) and Patient Global Assessment (PGA) are instruments that have been used in sarcoidosis. Objectives: We defined the minimal clinically important difference (MCID) as the within-patient clinically meaningful change threshold and determined the MCID of KSQ general health (KSQ GH), KSQ lung, and PGA using both anchor and distribution methods. The discriminatory properties of these MCIDs relative to other QoL instruments were then determined. Methods: Patients with sarcoidosis recruited from six centers in the United States were prospectively studied. Initially and at 6 months, patients completed a series of QoL questionnaires, including the St. George's Respiratory Questionnaire (SGRQ), Short Form 36 (SF-36), Fatigue Assessment Scale (FAS), Sarcoidosis Assessment Tool (SAT), KSQ, and PGA, and spirometry. For the anchor method, receiver operator characteristic curves were used to determine the MCID for improvement or worsening. The distribution method using half of the standard deviation was calculated for KSQ GH, KSQ lung, and PGA. Results: Of the 325 patients enrolled in the study, 271 completed the 6-month evaluation. At 6 months, approximately half of patients were worse and 30% were improved based on previously established MCID values for the SGRQ, SF-36, and FAS. There were no discordant cases. There were significant correlations between the KSQ GH, KSQ lung, and PGA and most parameters assessed. The best correlations were with the SGRQ, SF-36, and FAS, which have established MCID values. Using anchor analysis, we found that most of the domains of SGRQ and SF-36 were able to determine the significant MCIDs for all three variables. These MCIDs were similar to those determined by the half least square method. We propose an MCID of 8 for the KSQ GH, an MCID of 4 for the KSQ lung, and an MCID of 2 for the PGA because these values captured >90% of parameters studied. These MCID values discriminated between changes in other QoL instruments. Conclusions: The determination of MCID values for KSQ lung, KSQ GH, and PGA may prove useful for clinical practice as well as clinical trials.

Objective: Cardiac sarcoidosis is difficult to diagnose, often requiring expensive and inconvenient advanced imaging techniques. Circulating exosomes contain genetic material, such as microRNA (miRNA), that are derived from diseased tissues and may serve as potential disease-specific biomarkers. We thus sought to determine whether circulating exosome-derived miRNA expression patterns would distinguish cardiac sarcoidosis (CS) from acute myocardial infarction (AMI)., Methods: Plasma and serum samples conforming to CS, AMI or disease-free controls were procured from the Biologic Specimen and Data Repository Information Coordinating Center repository and National Jewish Health. Next generation sequencing (NGS) was performed on exosome-derived total RNA (n = 10 for each group), and miRNA expression levels were compared after normalization using housekeeping miRNA. Quality assurance measures excluded poor quality RNA samples. Differentially expressed (DE) miRNA patterns, based upon >2-fold change (p < 0.01), were established in CS compared to controls, and in CS compared to AMI. Relative expression of several DE-miRNA were validated by qRT-PCR., Results: Despite the advanced age of the stored samples (~5-30 years), the quality of the exosome-derived miRNA was intact in ~88% of samples. Comparing plasma exosomal miRNA in CS versus controls, NGS yielded 18 DE transcripts (12 up-regulated, 6 down-regulated), including miRNA previously implicated in mechanisms of myocardial injury (miR-92, miR-21) and immune responses (miR-618, miR-27a). NGS further yielded 52 DE miRNA in serum exosomes from CS versus AMI: 5 up-regulated in CS; 47 up-regulated in AMI, including transcripts previously detected in AMI patients (miR-1-1, miR-133a, miR-208b, miR-423, miR-499). Five miRNAs with increased DE in CS included two isoforms of miR-624 and miR-144, previously reported as markers of cardiomyopathy., Conclusions: MiRNA patterns of exosomes derived from CS and AMI patients are distinct, suggesting that circulating exosomal miRNA patterns could serve as disease biomarkers. Further studies are required to establish their specificity relative to other cardiac disorders., Competing Interests: The authors have declared that no competing interests exist.