bims-tralur 2021-08-15 papers

Issue of 2021–08–15
seven papers selected by
Willy Roque Barboza, Penn Medicine

Nat Aging. 2021 Feb;1(2): 205-217

Restoration of SIRT3 gene expression by airway delivery resolves age-associated persistent lung fibrosis in mice.

Mohammad Rehan, Deepali Kurundkar, Ashish R Kurundkar, Naomi J Logsdon, Samuel R Smith, Diptiman Chanda, Karen Bernard, Yan Y Sanders, Jessy S Deshane, Kevin G Dsouza, Sunad Rangarajan, Jaroslaw W Zmijewski, Victor J Thannickal.

Aging is a risk factor for progressive fibrotic disorders involving diverse organ systems, including the lung. Idiopathic pulmonary fibrosis, an age-associated degenerative lung disorder, is characterized by persistence of apoptosis-resistant myofibroblasts. In this report, we demonstrate that sirtuin-3 (SIRT3), a mitochondrial deacetylase, is downregulated in lungs of IPF human subjects and in mice subjected to lung injury. Over-expression of the SIRT3 cDNA via airway delivery restored capacity for fibrosis resolution in aged mice, in association with activation of the forkhead box transcription factor, FoxO3a, in fibroblasts, upregulation of pro-apoptotic members of the Bcl-2 family, and recovery of apoptosis susceptibility. While transforming growth factor-β1 reduced levels of SIRT3 and FoxO3a in lung fibroblasts, cell non-autonomous effects involving macrophage secreted products were necessary for SIRT3-mediated activation of FoxO3a. Together, these findings reveal a novel role of SIRT3 in pro-resolution macrophage functions that restore susceptibility to apoptosis in fibroblasts via a FoxO3a-dependent mechanism.

DOI: https://doi.org/10.1038/s43587-021-00027-5

Am J Respir Cell Mol Biol. 2021 Aug 09.

Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis (IPF).

Ankit Hanmandlu, Lisha Zhu, Tinne Cj Mertens, Scott Collum, Weizhen Bi, Feng Xiong, Ruoyu Wang, Rajarajan T Amirthalingam, Dewei Ren, Leng Han, Soma Sk Jyothula, Wenbo Li, W Jim Zheng, Harry Karmouty-Quintana.

Idiopathic pulmonary fibrosis (IPF), a devastating, fibro-proliferative chronic lung disorder, is associated with expansion of fibroblasts/myofibroblasts, which leads to excessive production and deposition of extracellular matrix (ECM). IPF is typically clinically identified as end-stage lung disease, after fibrotic processes are well-established and advanced. Fibroblasts have been shown to be critically important in the development and progression of IPF. We hypothesize that differential chromatin access can drive genetic differences in IPF fibroblasts relative to healthy fibroblasts. To this end, we performed Assay of Transposase-Accessible Chromatin (ATAC)-sequencing to identify differentially accessible regions within the genomes of fibroblasts from healthy and IPF lungs. Multiple motifs were identified to be enriched in IPF fibroblasts compared to healthy fibroblasts, including binding motifs for TWIST1 and FOXA1. RNA-sequencing identified 93 genes that could be annotated to differentially accessible regions. Pathway analysis of the annotated genes identified cellular adhesion, cytoskeletal anchoring, and cell differentiation as important biological processes. In addition, single nucleotide polymorphisms (SNPs) analysis showed that linkage disequilibrium (LD) blocks of IPF risk SNPs with IPF accessible regions that have been identified to be located in genes which are important in IPF, including MUC5B, TERT and TOLLIP. Validation studies in isolated lung tissue confirmed increased expression for TWIST1 and FOXA1 in addition to revealing SHANK2 and CSPR2 as novel targets. Thus, modulation of differential chromatin access may be an important mechanism in the pathogenesis of lung fibrosis.

Keywords: ATAC-seq; RNA-seq; epigenetics; lung fibrosis

DOI: https://doi.org/10.1165/rcmb.2020-0437OC

Front Immunol. 2021 ;12 721970

Extracellular CIRP Induces an Inflammatory Phenotype in Pulmonary Fibroblasts via TLR4.

Siavash Bolourani, Ezgi Sari, Max Brenner, Ping Wang.

Extracellular cold-inducible RNA-binding protein (eCIRP), a new damage-associated molecular pattern (DAMP), has been recently shown to play a critical role in promoting the development of bleomycin-induced pulmonary fibrosis. Although fibroblast activation is a critical component of the fibrotic process, the direct effects of eCIRP on fibroblasts have never been examined. We studied eCIRP's role in the induction of inflammatory phenotype in pulmonary fibroblasts and its connection to bleomycin-induced pulmonary fibrosis in mice. We found that eCIRP causes the induction of proinflammatory cytokines and differentially expression-related pathways in a TLR4-dependent manner in pulmonary fibroblasts. Our analysis further showed that the accessory pathways MD2 and Myd88 are involved in the induction of inflammatory phenotype. In order to study the connection of the enrichment of these pathways in priming the microenvironment for pulmonary fibrosis, we investigated the gene expression profile of lung tissues from mice subjected to bleomycin-induced pulmonary fibrosis collected at various time points. We found that at day 14, which corresponds to the inflammatory-to-fibrotic transition phase after bleomycin injection, TLR4, MD2, and Myd88 were induced, and the transcriptome was differentially enriched for genes in those pathways. Furthermore, we also found that inflammatory cytokines gene expressions were induced, and the cellular responses to these inflammatory cytokines were differentially enriched on day 14. Overall, our results show that eCIRP induces inflammatory phenotype in pulmonary fibroblasts in a TLR4 dependent manner. This study sheds light on the mechanism by which eCIRP induced inflammatory fibroblasts, contributing to pulmonary fibrosis.

Keywords: bleomicyn; eCIRP; fibroblast; fibrosis; inflammation

DOI: https://doi.org/10.3389/fimmu.2021.721970

JCI Insight. 2021 Aug 10. pii: 144575. [Epub ahead of print]

Hedgehog interacting protein-expressing lung fibroblasts suppress lymphocytic inflammation in mice.

Jeong H Yun, ChangHee Lee, Tao Liu, Siqi Liu, Edy Y Kim, Shuang Xu, Jeffrey L Curtis, Luca Pinello, Russell P Bowler, Edwin K Silverman, Craig P Hersh, Xiaobo Zhou.

Chronic obstructive pulmonary disease (COPD) is mainly caused by cigarette smoking, characterized by chronic inflammation in vulnerable individuals. However, it is unknown how genetic factors may shape chronic inflammation in COPD. To understand how hedgehog interacting protein, encoded by HHIP gene identified in the genome-wide association study in COPD, plays a role in inflammation, we utilized Hhip+/- mice that resemble persistent inflammation and emphysema observed in human COPD upon aging. By performing single cell RNA sequencing of the whole lung from mice at different ages, we found that Hhip+/- mice develop a cytotoxic immune response with a specific increase in Klrg1+CD8+T cells with upregulated Ifnγ expression recapitulating human COPD. Hhip expression was restricted to a lung fibroblast subpopulation that has increased interaction with CD8+T lymphocytes in Hhip+/- compared to Hhip+/+ during aging. Hhip-expressing lung fibroblasts have upregulated IL-18 pathway genes in Hhip+/- lung fibroblasts, which was sufficient to drive increased levels of IFNγ in CD8+T cells ex vivo. Our finding provides insight into how a common genetic variation contributes to the amplified lymphocytic inflammation in COPD.

Keywords: COPD; Inflammation; Mouse models; Pulmonology

DOI: https://doi.org/10.1172/jci.insight.144575

BMJ Open Respir Res. 2021 08;pii: e000969. [Epub ahead of print]8(1):

Patients with idiopathic pulmonary fibrosis have poor clinical outcomes with COVID-19 disease: a propensity matched multicentre research network analysis.

Syeda Fatima Naqvi, Dhairya A Lakhani, Amir Humza Sohail, James Maurer, Sarah Sofka, Arif Sarwari, Yousaf B Hadi.

INTRODUCTION: Outcomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with pre-existing idiopathic pulmonary fibrosis (IPF) remain understudied, and it is unknown if IPF is an independent predictor of worse disease course. Herein, we report the clinical outcomes in a large cohort of 251 patients with COVID-19 in the setting of known IPF. Outcomes were compared with a propensity matched cohort of patients with COVID-19 without IPF.
METHODS: Analysis of a federated multicentre research network TriNetX was performed including patients more than 16 years of age diagnosed with SARS-CoV-2 infection. Outcomes in patients diagnosed as positive for SARS-CoV-2 infection with concurrent IPF were compared with a propensity matched cohort of patients without IPF.
RESULTS: A total of 311 060 patients with SARS-CoV-2 infection on the research network were identified, 251 patients (0.08%) carried a diagnosis of IPF. Mean age of patients with IPF was 68.30±12.20 years, with male predominance (n=143, 56.97%). Comorbidities including chronic lower respiratory diseases, diabetes mellitus, ischaemic heart disease and chronic kidney disease were more common in patients with IPF when compared with the non-IPF cohort. After propensity matching, higher rates of composite primary outcome (death or mechanical ventilation) at 30 and 60 days, as well as need for hospitalisation, critical care, and acute kidney injury were observed in the IPF cohort.
CONCLUSION: Poor outcomes of COVID-19 disease were observed in patients with IPF after robust matching of confounders. Our data confirm that patients with IPF constitute a high-risk cohort for poor outcomes related to COVID-19 disease.

Keywords: COVID-19; interstitial fibrosis; viral infection

DOI: https://doi.org/10.1136/bmjresp-2021-000969

Cell Stem Cell. 2021 Aug 06. pii: S1934-5909(21)00294-0. [Epub ahead of print]

Hsf1 promotes hematopoietic stem cell fitness and proteostasis in response to ex vivo culture stress and aging.

Miriama Kruta, Mary Jean Sunshine, Bernadette A Chua, Yunpeng Fu, Ashu Chawla, Christopher H Dillingham, Lorena Hidalgo San Jose, Bijou De Jong, Fanny J Zhou, Robert A J Signer.

Maintaining proteostasis is key to resisting stress and promoting healthy aging. Proteostasis is necessary to preserve stem cell function, but little is known about the mechanisms that regulate proteostasis during stress in stem cells, and whether disruptions of proteostasis contribute to stem cell aging is largely unexplored. We determined that ex-vivo-cultured mouse and human hematopoietic stem cells (HSCs) rapidly increase protein synthesis. This challenge to HSC proteostasis was associated with nuclear accumulation of Hsf1, and deletion of Hsf1 impaired HSC maintenance ex vivo. Strikingly, supplementing cultures with small molecules that enhance Hsf1 activation partially suppressed protein synthesis, rebalanced proteostasis, and supported retention of HSC serial reconstituting activity. Although Hsf1 was dispensable for young adult HSCs in vivo, Hsf1 deficiency increased protein synthesis and impaired the reconstituting activity of middle-aged HSCs. Hsf1 thus promotes proteostasis and the regenerative activity of HSCs in response to culture stress and aging.

Keywords: Hsf1; aging; heat shock response; hematopoiesis; hematopoietic stem cell; protein synthesis; proteostasis; stem cell; stress; translation

DOI: https://doi.org/10.1016/j.stem.2021.07.009

mBio. 2021 Aug 10. e0157221

Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury.

Amy C Sims, Hugh D Mitchell, Lisa E Gralinski, Jennifer E Kyle, Kristin E Burnum-Johnson, Mariam Lam, M Leslie Fulcher, Ande West, Richard D Smith, Scott H Randell, Thomas O Metz, Timothy P Sheahan, Katrina M Waters, Ralph S Baric.

Tissue- and cell-specific expression patterns are highly variable within and across individuals, leading to altered host responses after acute virus infection. Unraveling key tissue-specific response patterns provides novel opportunities for defining fundamental mechanisms of virus-host interaction in disease and the identification of critical tissue-specific networks for disease intervention in the lung. Currently, there are no approved therapeutics for Middle East respiratory syndrome coronavirus (MERS-CoV) patients, and little is understood about how lung cell types contribute to disease outcomes. MERS-CoV replicates equivalently in primary human lung microvascular endothelial cells (MVE) and fibroblasts (FB) and to equivalent peak titers but with slower replication kinetics in human airway epithelial cell cultures (HAE). However, only infected MVE demonstrate observable virus-induced cytopathic effect. To explore mechanisms leading to reduced MVE viability, donor-matched human lung MVE, HAE, and FB were infected, and their transcriptomes, proteomes, and lipidomes were monitored over time. Validated functional enrichment analysis demonstrated that MERS-CoV-infected MVE were dying via an unfolded protein response (UPR)-mediated apoptosis. Pharmacologic manipulation of the UPR in MERS-CoV-infected primary lung cells reduced viral titers and in male mice improved respiratory function with accompanying reductions in weight loss, pathological signatures of acute lung injury, and times to recovery. Systems biology analysis and validation studies of global kinetic transcript, protein, and lipid data sets confirmed that inhibition of host stress pathways that are differentially regulated following MERS-CoV infection of different tissue types can alleviate symptom progression to end-stage lung disease commonly seen following emerging coronavirus outbreaks. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe atypical pneumonia in infected individuals, but the underlying mechanisms of pathogenesis remain unknown. While much has been learned from the few reported autopsy cases, an in-depth understanding of the cells targeted by MERS-CoV in the human lung and their relative contribution to disease outcomes is needed. The host response in MERS-CoV-infected primary human lung microvascular endothelial (MVE) cells and fibroblasts (FB) was evaluated over time by analyzing total RNA, proteins, and lipids to determine the cellular pathways modulated postinfection. Findings revealed that MERS-CoV-infected MVE cells die via apoptotic mechanisms downstream of the unfolded protein response (UPR). Interruption of enzymatic processes within the UPR in MERS-CoV-infected male mice reduced disease symptoms, virus-induced lung injury, and time to recovery. These data suggest that the UPR plays an important role in MERS-CoV infection and may represent a host target for therapeutic intervention.

Keywords: MERS-CoV; acute lung injury; apoptosis; fibroblasts; microvascular endothelial cells; primary human lung cells; unfolded protein response

DOI: https://doi.org/10.1128/mBio.01572-21