Biomarker discovery and drug testing in Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a devastating and lethal disease, with a median survival of 2-3 years after diagnosis. It is chronic, progressive and occurs predominantly in middle-age and older adults. Multiple working hypotheses speak of possible triggers of IPF development, e.g. multiple microinjuries of the alveolar epithelium, aberrant fibroblast activation, and immune deregulation. Currently, there are two drugs approved for the treatment of mild-to-moderate IPF worldwide, neither Pirfenidone or Nintedanib provide a definitive cure for disease, but slow in disease progression. Thus, animal models of pulmonary fibrosis are a critical tool for disease understanding, drug development and pre-clinical intervention. In chapter 2.1, the first study included in this thesis (Fernandez et al., 2016a), we comprehensively analyzed IPF-relevant peripheral biomarkers, histological compromise along with physiological parameters, to determine disease onset, progression and resolution in preclinical models of fibrosis. We observed and validated that the bleomycin-induced pulmonary fibrosis model reached its peak of fibrosis 14 days after treatment and from there on, resolution started. Furthermore, we created a semi-automatized histologic scoring system to quantify the degree of fibrosis, and correlated histology score with lung function decline during the initiation, peak and resolution phase of the model. Interestingly, we observed that at day 28 and 56 although histological compromise was still present, lung function was close to normal. Furthermore, we determine that plasma levels of ICAM-1 strongly correlate with the extent of fibrosis. We complemented and extended our characterization of the model further. In a following study, we performed multi-compartmental deep proteomics in lung tissue and bronchoalveolar lavage (Schiller, Fernandez et al., 2015), with emphasis on characterizing the matrisome, from the initiation to the resolution of bleomycin-induced fibrosis, in where we could determine the initial signatures of injury, as well as the ones that drive lung repair. In chapter 2.2, we highlighted the second study of this thesis (Sun et al., 2015), that goes along with a complementary publication of our authorship. We use the ability of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to simultaneously record the distribution of hundreds of molecules, in a highly multiplexed and unbiased manner. After oral administration of pirfenidone, we could detect, visualize, and quantify the pharmacokinetics and in-situ distribution of pirfenidone in lung, liver and kidney from unchallenged mice. Furthermore, we performed analysis in fibrotic mice and IPF patients, untreated and under pirfenidone therapy (Sun*, Fernandez* et al. 2018). As expected, we detected mouse and human specific and shared responses; specific alterations of metabolite pathways in fibrosis, and most importantly, metabolic recalibration following pirfenidone treatment. Taking together, bleomycin-induced pulmonary fibrosis is an extremely valuable tool for preclinical drugs evaluation, as well as for target validation and modulation of Idiopathic Pulmonary Fibrosis.Die idiopathische pulmonale Fibrose ist eine schwerwiegende und tödlich verlaufende Erkrankung mit einer durchschnittlichen Lebenserwartung von zwei bis drei Jahren nach Diagnosestellung. Die chronisch progressive Erkrankung tritt vorwiegend im mittleren Lebensalter sowie bei älteren Erwachsenen auf. Zahlreiche Arbeitshypothesen zeigten mögliche Auslöser der IPF auf, wie beispielsweise Mikroverletzungen des Alveolarepithels, eine gestörte Fibroblastenaktivierung sowie eine Fehlregulation des Immunsystems. Derzeit sind weltweit zwei Medikamente zur Behandlung von leichter bis mittelschwerer IPF zugelassen, Pirfenidon und Nintedanib. Beide Medikamente verlangsamen den Verlauf der Erkrankung führen jedoch zu keiner Heilung. Somit sind Tiermodelle der Lungenfibrose ein wichtiges Werkzeug für das Verständnis von Krankheiten, die Arzneimittelentwicklung und präklinische Intervention. Kapitel 2.1 fasst die erste Publikation dieser Arbeit zusammen. In Fernandez et al. 2016 analysierten wir IPF-relevante periphere Biomarker und führten einen histologischen Vergleich mit physiologischen Parametern durch, um die Entstehung der Erkrankung, den Verlauf und die Resolution in präklinischen Modellen der Fibrose zu bestimmen. Unsere Ergebnisse zeigten, dass die Fibrose im bleomycininduzierten Modell der Fibrose ihren Höhepunkt an Tag 14 nach Belomycinbehandlung erreichte und danach die Phase der Resolution begann. Wir generierten ein semi-automatisiertes histologisches Bewertungssystem um den Grad der Fibrose zu quantifizieren und korrelierten diesen Wert mit der Abnahme der Lungenfunktion während der Initiierungsphase, der maximalen Fibrose und der Resolutionsphase des Models. Interessanterweise beobachteten wir an Tag 28 und 56 eine nahezu normale Lungenfunktion, obwohl histologische Auffälligkeiten noch immer vorhanden waren. Wir entdeckten, dass die Plasmaspiegel von ICAM-1 stark mit dem Fibrosegrad korrelierten. Wir erweiterten die Charakterisierung des Fibrosemodells und schlossen eine weitere Studie an, in der wir eine multi-kompartmentelle tiefgehende Proteomanalyse von Lungengewebe und bronchoalveolären Lavagen durchführten. Der Fokus lag dabei auf der Charakterisierung des Matrisoms von der Initiierungs- bis zur Resolutionsphase der bleomycininduzierten Fibrose. Wir konnten die anfänglichen Signaturen der Verletzung bestimmen, sowie diejenigen, die die Lungenreparatur antreiben Kapitel 2.2 hebt die zweite Publikation der vorliegenden Arbeit hervor, Sun et al., 2015, der eine Koautorenschaft zugrunde liegt. Hierbei nutzten wir die Methode der Matrix–Assistierten Laser–Desorptions/Ionisierungs Massenspektrometrie Bildgebung (Imaging) (MALDI-MSI), welche es ermöglicht in einem multiplexen und ungezielten Ansatz simultan die Verteilung hunderter Moleküle zu messen. Nach oraler Gabe von Pirfenidon, visualisierten und quantifizierten wir die gemessene Pharmakokinetik und in situ Verteilung von Pirfenidon in Lunge, Leber und Niere von gesunden Mäusen. Zusätzlich analysierten wir fibrotische Mäuse und IPF-Patienten, unbehandelt als auch unter Pirfenidontherapie (Sun*, Fernandez* et al. 2018). Wie erwartet entdeckten wir sowohl maus- und menschspezifische als auch gemeinsame Reaktionen, bezüglich spezifischer Änderungen metabolischer Prozesse in Fibrose und, von besonderer Bedeutung, der metabolischen Neukalibrierung nach Pirfenidonbehandlung. Zusammengefasst ist das Tiermodell der bleomycininduzierten pulmonalen Fibrose ein wichtiges Werkzeug für die präklinische Arzneimittelbewertung, sowie für die Validierung potentieller Zielmoleküle und einer Modulation der idiopathischen pulmonalen Fibrose

Safety and Immunogenicity of a Human Papillomavirus Peptide Vaccine (CIGB-228) in Women with High-Grade Cervical Intraepithelial Neoplasia: First-in-Human, Proof-of-Concept Trial

Objective. CIGB-228 is a novel therapeutic vaccine consisting of HLA-restricted HPV16 E7 epitope adjuvated with VSSP. This trial was designed to evaluate the toxicity, safety, immunogenicity, HPV clearance, and lesion regression. Methods. Seven women were entered. All were HLA-A2 positive, had biopsy-proven high-grade CIN, histologically positive for HPV16, and beared persistent postbiopsy lesions visible by digital colposcopy. HLA-A2 women with biopsy-proven high-grade CIN, HPV16-positive, and beared persistent postbiopsy lesions visible by digital colposcopy were vaccinated. One weekly injections of CIGB-228 vaccine was given for four weeks. Then, loop electrosurgical excision procedure (LEEP) of the transformation zone was performed. Study subjects were followed for 1 year after LEEP. Results. No toxicity beyond grade 1 was observed during and after the four vaccinations. Five of seven women had complete and partial regression. Cellular immune response was seen in all patients. HPV was cleared in three of the patients with complete response. Conclusion. CIGB-228 vaccination was well tolerated and capable to induce IFNγ-associated T-cell response in women with high-grade CIN. In several patients, lesion regression and HPV clearance were observed

Association Between Interstitial Lung Abnormalities and All-Cause Mortality.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Interstitial lung abnormalities have been associated with lower 6-minute walk distance, diffusion capacity for carbon monoxide, and total lung capacity. However, to our knowledge, an association with mortality has not been previously investigated.To investigate whether interstitial lung abnormalities are associated with increased mortality.Prospective cohort studies of 2633 participants from the FHS (Framingham Heart Study; computed tomographic [CT] scans obtained September 2008-March 2011), 5320 from the AGES-Reykjavik Study (Age Gene/Environment Susceptibility; recruited January 2002-February 2006), 2068 from the COPDGene Study (Chronic Obstructive Pulmonary Disease; recruited November 2007-April 2010), and 1670 from ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints; between December 2005-December 2006).Interstitial lung abnormality status as determined by chest CT evaluation.All-cause mortality over an approximate 3- to 9-year median follow-up time. Cause-of-death information was also examined in the AGES-Reykjavik cohort.Interstitial lung abnormalities were present in 177 (7%) of the 2633 participants from FHS, 378 (7%) of 5320 from AGES-Reykjavik, 156 (8%) of 2068 from COPDGene, and in 157 (9%) of 1670 from ECLIPSE. Over median follow-up times of approximately 3 to 9 years, there were more deaths (and a greater absolute rate of mortality) among participants with interstitial lung abnormalities when compared with those who did not have interstitial lung abnormalities in the following cohorts: 7% vs 1% in FHS (6% difference [95% CI, 2% to 10%]), 56% vs 33% in AGES-Reykjavik (23% difference [95% CI, 18% to 28%]), and 11% vs 5% in ECLIPSE (6% difference [95% CI, 1% to 11%]). After adjustment for covariates, interstitial lung abnormalities were associated with a higher risk of death in the FHS (hazard ratio [HR], 2.7 [95% CI, 1.1 to 6.5]; P = .03), AGES-Reykjavik (HR, 1.3 [95% CI, 1.2 to 1.4]; P < .001), COPDGene (HR, 1.8 [95% CI, 1.1 to 2.8]; P = .01), and ECLIPSE (HR, 1.4 [95% CI, 1.1 to 2.0]; P = .02) cohorts. In the AGES-Reykjavik cohort, the higher rate of mortality could be explained by a higher rate of death due to respiratory disease, specifically pulmonary fibrosis.In 4 separate research cohorts, interstitial lung abnormalities were associated with a greater risk of all-cause mortality. The clinical implications of this association require further investigation.National Institutes of Health (NIH) T32 HL007633 Icelandic Research Fund 141513-051 Landspitali Scientific Fund A-2015-030 National Cancer Institute grant 1K23CA157631 NIH K08 HL097029 R01 HL113264 R21 HL119902 K25 HL104085 R01 HL116931 R01 HL116473 K01 HL118714 R01 HL089897 R01 HL089856 N01-AG-1-2100 HHSN27120120022C P01 HL105339 P01 HL114501 R01 HL107246 R01 HL122464 R01 HL111024 National Heart, Lung, and Blood Institute's Framingham Heart Study contract N01-HC-2519.5 GlaxoSmithKline NCT00292552 5C0104960 National Institute on Aging (NIA) grant 27120120022C NIA Intramural Research Program, Hjartavernd (the Icelandic Heart Association) Althingi (the Icelandic Parliament) NIA 27120120022

Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

Abstract The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for ‘reverse phenotyping’. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis

Search for heavy resonances decaying to two Higgs bosons in final states containing four b quarks

A search is presented for narrow heavy resonances X decaying into pairs of Higgs bosons (H) in proton-proton collisions collected by the CMS experiment at the LHC at root s = 8 TeV. The data correspond to an integrated luminosity of 19.7 fb(-1). The search considers HH resonances with masses between 1 and 3 TeV, having final states of two b quark pairs. Each Higgs boson is produced with large momentum, and the hadronization products of the pair of b quarks can usually be reconstructed as single large jets. The background from multijet and t (t) over bar events is significantly reduced by applying requirements related to the flavor of the jet, its mass, and its substructure. The signal would be identified as a peak on top of the dijet invariant mass spectrum of the remaining background events. No evidence is observed for such a signal. Upper limits obtained at 95 confidence level for the product of the production cross section and branching fraction sigma(gg -> X) B(X -> HH -> b (b) over barb (b) over bar) range from 10 to 1.5 fb for the mass of X from 1.15 to 2.0 TeV, significantly extending previous searches. For a warped extra dimension theory with amass scale Lambda(R) = 1 TeV, the data exclude radion scalar masses between 1.15 and 1.55 TeV

Search for supersymmetry in events with one lepton and multiple jets in proton-proton collisions at root s=13 TeV

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Measurement of the top quark mass using charged particles in pp collisions at root s=8 TeV

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