Dysregulation of COVID-19 related gene expression in the COPD lung

BACKGROUND

Chronic obstructive pulmonary disease (COPD) patients are at increased risk of poor outcome from Coronavirus disease (COVID-19). Early data suggest elevated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) receptor angiotensin converting enzyme 2 (ACE2) expression, but relationships to disease phenotype and downstream regulators of inflammation in the Renin-Angiotensin system (RAS) are unknown. We aimed to determine the relationship between RAS gene expression relevant to SARS-CoV-2 infection in the lung with disease characteristics in COPD, and the regulation of newly identified SARS-CoV-2 receptors and spike-cleaving proteases, important for SARS-CoV-2 infection.

METHODS

We quantified gene expression using RNA sequencing of epithelial brushings and bronchial biopsies from 31 COPD and 37 control subjects.

RESULTS

ACE2 gene expression (log2-fold change (FC)) was increased in COPD compared to ex-smoking (HV-ES) controls in epithelial brushings (0.25, p = 0.042) and bronchial biopsies (0.23, p = 0.050), and correlated with worse lung function (r = - 0.28, p = 0.0090). ACE2 was further increased in frequent exacerbators compared to infrequent exacerbators (0.51, p = 0.00045) and associated with use of ACE inhibitors (ACEi) (0.50, p = 0.0034), having cardiovascular disease (0.23, p = 0.048) or hypertension (0.34, p = 0.0089), and inhaled corticosteroid use in COPD subjects in bronchial biopsies (0.33, p = 0.049). Angiotensin II receptor type (AGTR)1 and 2 expression was decreased in COPD bronchial biopsies compared to HV-ES controls with log2FC of -0.26 (p = 0.033) and - 0.40, (p = 0.0010), respectively. However, the AGTR1:2 ratio was increased in COPD subjects compared with HV-ES controls, log2FC of 0.57 (p = 0.0051). Basigin, a newly identified potential SARS-CoV-2 receptor was also upregulated in both brushes, log2FC of 0.17 (p = 0.0040), and bronchial biopsies, (log2FC of 0.18 (p = 0.017), in COPD vs HV-ES. Transmembrane protease, serine (TMPRSS)2 was not differentially regulated between control and COPD. However, various other spike-cleaving proteases were, including TMPRSS4 and Cathepsin B, in both epithelial brushes (log2FC of 0.25 (p = 0.0012) and log2FC of 0.56 (p = 5.49E-06), respectively) and bronchial biopsies (log2FC of 0.49 (p = 0.00021) and log2FC of 0.246 (p = 0.028), respectively).

CONCLUSION

This study identifies key differences in expression of genes related to susceptibility and aetiology of COVID-19 within the COPD lung. Further studies to understand the impact on clinical course of disease are now required.

Human Lung Conventional Dendritic Cells Orchestrate Lymphoid Neogenesis during Chronic Obstructive Pulmonary Disease

Rationale: Emerging evidence supports a crucial role for tertiary lymphoid organs (TLOs) in chronic obstructive pulmonary disease (COPD) progression. However, mechanisms of immune cell activation leading to TLOs in COPD remain to be defined.Objectives: To examine the role of lung dendritic cells (DCs) in T follicular helper (Tfh)-cell induction, a T-cell subset critically implicated in lymphoid organ formation, in COPD.Methods: Myeloid cell heterogeneity and phenotype were studied in an unbiased manner via single-cell RNA sequencing on HLA-DR⁺ cells sorted from human lungs. We measured the in vitro capability of control and COPD lung DC subsets, sorted using a fluorescence-activated cell sorter, to polarize IL-21⁺CXCL13⁺ (IL-21-positive and C-X-C chemokine ligand type 13-positive) Tfh-like cells. In situ imaging analysis was performed on Global Initiative for Chronic Obstructive Lung Disease stage IV COPD lungs with TLOs.Measurements and Main Results: Single-cell RNA-sequencing analysis revealed a high degree of heterogeneity among human lung myeloid cells. Among these, conventional dendritic type 2 cells (cDC2s) showed increased induction of IL-21⁺CXCL13⁺ Tfh-like cells. Importantly, the capacity to induce IL-21⁺ Tfh-like cells was higher in cDC2s from patients with COPD than in those from control patients. Increased Tfh-cell induction by COPD cDC2s correlated with increased presence of Tfh-like cells in COPD lungs as compared with those in control lungs, and cDC2s colocalized with Tfh-like cells in TLOs of COPD lungs. Mechanistically, cDC2s exhibited a unique migratory signature and (transcriptional) expression of several pathways and genes related to DC-induced Tfh-cell priming. Importantly, blocking the costimulatory OX40L (OX40 ligand)-OX40 axis reduced Tfh-cell induction by control lung cDC2s.Conclusions: In COPD lungs, we found lung EBI2⁺ (Epstein-Barr virus-induced gene 2-positive) OX-40L-expressing cDC2s that induced IL-21⁺ Tfh-like cells, suggesting an involvement of these cells in TLO formation.

Differential gene expression in human tissue resident regulatory T cells from lung, colon, and blood

As we learn more about how immune responses occur in situ, it is becoming clear that each organ/tissue is characterized with its own anatomy and microenvironment which may affect and even determine the outcome of the immune responses. With emerging data from animal studies showing that regulatory T cells infiltrating non-lymphoid tissues exhibit unique phenotypes and transcriptional signatures and display functions beyond their well-established suppressive roles, there is an urgent need to explore the function of tissue Treg cells in humans. Here we characterized the transcriptome of Treg residing at the human mucosal tissue obtained from the normal area of cancer resections and their peripheral blood counterparts, identifying human lung and colon tissue Treg signature genes and their upstream regulators. Pathway analysis highlighted potential differences in the cross-talk between tissue Treg cells and other non-immune tissue-specific cell types. For example, genes associated with wnt pathway were differentially regulated in lung Treg cells compared to blood or colon indicating a potential role for lung Treg cells in epithelium repair and regeneration. Moreover, we identified several non-coding RNAs specifically expressed by tissue-resident Tregs. These results provide a comprehensive view of lung and colon tissue Treg transcriptional landscape.

System control of auto-reactive T cells

Potentially auto-reactive T cells routinely escape thymic negative selection, but rarely elicit peripheral autoimmunity. We investigated the fate of these cells in murine secondary lymphoid organs using quantitative imaging approaches. During steady state, a small number of seemingly auto-reactive CD4+ T cells were detected along the T cell zone border. These cells displayed clear signs of antigenic stimulation, specifically plasmalemma expression of PD-1, in the absence of foreign bacteria or host commensals. Remarkably, high densities of regulatory T cells routinely converged on the auto-reactive CD4+ T cells, which in turn, exhibited compromised plasma membrane integrity consistent with cell death. Acute depletion of regulatory T cells resulted in uncontrolled expansion of the auto-reactive cells and correlated with reduced death. Collectively, these results suggest that regulatory T cells may not only suppress, but also prune the repertoire of dangerous clones, thereby minimizing the risk of autoimmunity.

Computational modeling of signaling networks for eukaryotic chemosensing

The task of developing and simulating computational models of signaling networks for eukaryotic chemosensing confronts the modeler with several challenges: (1) The stimuli that initiate the cellular responses one wishes to study are provided by extracellular concentration gradients. This means that the computational model must have a spatially resolved representation of extracellular molecular concentrations. (2) The intracellular responses consist of the generation of intracellular accumulations and/or translocations of signaling molecules, requiring spatially resolved computational representations of the simulated cells. (3) The signaling networks responsible for eukaryotic chemosensing comprise a multitude of components acting as receptors, adaptors, (lipid- and protein-) kinases (including GTPases), (lipid- and protein-) phosphatases, and molecule types used by others for membrane attachment. Models of such signaling networks may become quite complicated, unless one wishes to rely on abstract functional modules with certain input-output characteristics as modeling "shortcuts" replacing subnetworks of biological signaling molecules. In this chapter, we describe how modelers can use a modeling tool ("simmune") developed to facilitate the design and simulation of detailed computational models of signaling pathways (for eukaryotic chemosensing here), thereby avoiding the technical difficulties typically associated with building and simulating such quantitative models.

Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method

The signaling network underlying eukaryotic chemosensing is a complex combination of receptor-mediated transmembrane signals, lipid modifications, protein translocations, and differential activation/deactivation of membrane-bound and cytosolic components. As such, it provides particularly interesting challenges for a combined computational and experimental analysis. We developed a novel detailed molecular signaling model that, when used to simulate the response to the attractant cyclic adenosine monophosphate (cAMP), made nontrivial predictions about Dictyostelium chemosensing. These predictions, including the unexpected existence of spatially asymmetrical, multiphasic, cyclic adenosine monophosphate–induced PTEN translocation and phosphatidylinositol-(3,4,5)P₃ generation, were experimentally verified by quantitative single-cell microscopy leading us to propose significant modifications to the current standard model for chemoattractant-induced biochemical polarization in this organism. Key to this successful modeling effort was the use of “Simmune,” a new software package that supports the facile development and testing of detailed computational representations of cellular behavior. An intuitive interface allows user definition of complex signaling networks based on the definition of specific molecular binding site interactions and the subcellular localization of molecules. It automatically translates such inputs into spatially resolved simulations and dynamic graphical representations of the resulting signaling network that can be explored in a manner that closely parallels wet lab experimental procedures. These features of Simmune were critical to the model development and analysis presented here and are likely to be useful in the computational investigation of many aspects of cell biology.

Cells can orient their migration in response to small local differences in the concentration of extracellular chemicals (chemoattractants). Understanding this process (chemosensing) requires analyzing the time and position-dependent behavior of the signaling molecules within the responding cell, making it an especially interesting challenge for both experimental and computational investigation. Here, the authors report the development and testing of a new detailed molecular model of the chemosensing apparatus of the amoeba Dictyostelium discoidium reacting to the chemoattractant cyclic adenosine monophosphate. Computer simulations performed using this model predicted unexpected and previously unreported patterns of changes in the concentration and location of two important intracellular signaling molecules. These predictions were experimentally verified using microscopy, suggesting the need for modifications to the current “standard” model of eukaryotic chemosensing. The high degree of detail in their model was made possible by a new software suite called “Simmune,” which allows biologists to enter information about molecular interactions using a graphical interface. Without requiring the user to write any equations, the software automatically constructs the overall reaction network, simulates the model, and provides several ways to view the biochemistry of simulated cells. This new tool should help biologists to translate qualitative representations of cell biological processes into quantitative, predictive models.

[Subsequent rehabilitation treatment after aortocoronary bypass--how often is reintegration into occupational life successful?]

Investigated was the insurance course of 184 insurants of the Landesversicherungsanstalt Oberfranken und Mittelfranken who, in 1986 and 1987, had participated in in-patient rehabilitation procedures immediately following the post-acute stage, i.e. Anschlussheilbehandlung (AHB), after aortocoronary bypass surgery. Nearly 60% of these insurants were granted a pension within the first two years after AHB, half of them on a permanent basis. The pensioning rate is substantially influenced by beneficiary age: all of the 60 to 64 year-olds and almost every second of the 50 to 54 year-olds were granted a pension. Insurants with formal vocational education more often received premature pension than those without formal training. A cardiac load test showed that cardiac efficiency does not correlate with the return-to-work/pensioning rate. Age seems to play an important additional role in this respect, as older beneficiaries were pensioned more often than younger ones, with the same cardiac fitness found for both groups in cardiac load testing.

Results of statutory rehabilitation measures in Germany

The success of medical rehabilitation measures taken by the LVA Oberfranken and Mittelfranken in 1984 was scrutinized for 12,291 insured people. The criteria for evaluating success were the state of health of the insured persons before rehabilitation and at one month and one year afterwards. Two thirds of the insured persons were at work again one month after discharge from rehabilitation. One year after rehabilitation 14 per cent received a disablement pension. Only every second person insured who was ill before rehabilitation took up work again afterwards. Most of the insured people who were already receiving a pension before rehabilitation continued to receive their pension afterwards (86 per cent). The highest rate of inability to work and also the highest pension rate is found with insured persons suffering from an ischaemic cardiac disease. Only 33 per cent of these persons resume work after rehabilitation.

[Intestinal abnormalities as a cause of ileus in the newborn infant]

Between 1971 and 1984 58 neonates were operated on because of bowel obstructing intestinal malformations. The most significant postoperative complications were cardiac insufficiency (7), mechanical bowel obstruction (5), sepsis (4), short bowel syndrome (3), respiratory insufficiency or pneumonia (3), anastomotic leak (2) or stenosis (1), bleeding (2), bowel infarction (1). Overall mortality: 15/58 (26%).

[Surgery of Crohn's disease: a study of 155 patients after intestinal resection (author's transl)]

Operative mortality after intestinal resection in 155 patients with Crohn's disease was 8.4%. In 12 of 13 the cause of death was septic complications, most of them related to prolonged pre-operative cortisone medication. Follow-up examination was possible in 90% of all discharges. Five-year recurrence rate was 37.6%. Recurrence was not prevented by long-term drug treatment. Purely macroscopic assessment of the resection margins would have led to excision within diseased gut: for this reason frozen sections are recommended before the anastomosis is made. Primary death-rate in 30 cases of colectomy with primary ileorectostomy was 3%. In three patients the rectum had to be excised, while in one the anastomosis had to be taken down because of recurrence. The failure rate was thus only 11%. If rectoscopy, stepwise biopsy and intra-operative frozen section indicate a normal rectum it is recommended that ileorectostomy be done rather than diversion ileostomy with occlusion of the rectum or even proctocolectomy.

Surgical treatment of metastases to the lung and liver

We resected 120 pulmonary metastases in 67 patients and 49 hepatic metastases in 38 patients. After surgical removal of pulmonary metastases, 14 patients survived five years; without surgical therapy, only one patient survived. As for the prognosis, as many as four resected pulmonary metastases are unimportant. In instances of several metastases, resections should be performed carefully and as rarely as possible. After lobectomy, nine patients have survived for five years; after wedge excisions, four patients have survived for five years, and after bilobectomies or pneumonectomy, one patient has survived for five years. If the lungs are the first filter of hematogen metastases, more patients survive for five years than if the liver is the first filter. With a prolonged free interval period, the prognosis is better. The tumor-doubling time must not influence indication. After resection of hepatic metastases, four patients survived for five years. The prognosis is more favorable for patients with solitary metastasis and if local resection will be sufficient. When the primary tumor and hepatic metastases are removed at the same operation, the prognosis is better than in an instance of delayed diagnosis and removal. If the liver is the first hematogen filter for cleaned off cells of the primary tumor, the survival rates are higher than when the lungs are the first filter.

Are growth rates of tumors of any clinical importance?

The tumor doubling times were determined in 142 rounded pulmonary lesions of 78 patients (13 bronchial carcinomas, 7 benign pulmonary tumors, and 122 pulmonary metastases). They varied between +12 and +8863 days of tumor growth and of -1810 days of decrease in tumor mass. Forty-four percent of all pulmonary metastases doubled their volume within 60 to 250 days. The growth rates during the period of observation varied greatly in several pulmonary metastases of the same patient, even for the same solitary circular lung focus of the same person. There is no relationship between tumor doubling time and histological type of the tumor, nor between the interval between operative removal of the primary tumor and the occurrence of pulmonary metastases. In patients between the ages of 10 and 30 years only rapidly growing pulmonary metastases with a tumor doubling time of less than 60 days could be found; even though there is no proved relationship between growth rate and age. The tumor doubling time gives no useful information on the nature of a circular lung focus, and there are no clinical consequences for diagnosis.

[Has the calculation of the rate of tumor growth clinical significance?]

In 142 circular lung foci of 78 patients we determined the tumor doubling times (13 bronchial carcinomas, 7 benign pulmonary tumors, and 122 pulmonary metastases). They fluctuated between + 12 and + 8,863 days of tumor growth and a diminuation of -1,810 days of half-life. 44% of all pulmonary metastases doubled their volumes within 60 to 250 days. During the observation period the times of tumor growth varied not only in different pulmonary metastases of the same patient, but also in solitary circular lung foci of the same person considerably. There is no connexion between tumor doubling time and histological tumor type as well as the interval between surgery of the primary tumor and occurrence of pulmonary metastases. Though we found in patients of 10 to 30 years of age only quickly growing pulmonary metastases with a tumor doubling time of less than 60 days a corrlation between time of tumor growth and age could not be proved. By the determination of the tumor doubling time neither binding statements on the nature of a circular lung focus can be made nor clinical consequences for diagnostics or therapy be drawn.

[Surgical treatment of pulmonary metastases (author's transl)]

120 pulmonary metastases were resected in 67 patients. The five year survival rate is 42.3% after surgical removal and only 2.6% without surgery. Up to 4 resected pulmonary metastases have no influence on the prognosis. In cases with several metastases resection should be strictly limited. Lobectomy had the best five year survival rate (58%); wedge excision and pneumonectomy fared clearly worse (25% each). When the lung is the first filtre of haematogenous metastases the five year survival rate is better (48%) than when the liver filters first (18.5%). A prolonged interval before recurrence improves prognosis. Intervals of less than a year lead to survival after 4 years in only 14.5%, intervals of more than two years are accompanied by survival of 65%.