KFO309 - The clinical research unit Virus Induced Lung injury

Principal Investigators

Torsten Hain

PD Dr. rer. nat. Torsten Hain

Justus Liebig University Giessen
Institute of Medical Microbiology 
Schubertstraße 81; 35392 Giessen

+49-641-99-39860
Alexander Goesmann

Prof. Dr. Alexander Goesmann

Systems Biology
Heinrich-Buff-Ring 58; 35392 Giessen

+49 641 99-35800
Jochen Wilhelm

Dr. rer. nat. Jochen Wilhelm

Justus Liebig University Giessen
Department of Medicine II
Gaffkystr. 11; 35392 Giessen

+49-641-99-42545
Mario Looso

Dr. Mario Looso

Head of Bioinformatics Service Facility

Max Planck Institute for Heart and Lung Research

Ludwigstrasse 43

61231 Bad Nauheim

Loosolab.mpi-bn.mpg.de

+49-6032-705-1763

Core unit “Genome signatures and integrated systems biology of pathogen-host interaction and cellular networks in the infected and injured lung”

Summary

Understanding cell-specific gene regulatory events and their impact on cellular networks in infected lungs requires an integrative CRU platform which delivers high-throughput transcriptomics, genomics and epigenetics analyses from primary lung cells/organoids/tissues including highly purified cell populations even of rare subsets, as well as advanced tools for data exploitation. The core unit (Z1) provides methods and tools for processing of murine and human lung specimens including patient samples to all CRU projects, with a focus on cell specificity and after prior processing/enrichment of rare cell populations by Auto-MACS and FACS. Furthermore, automated sample/library preparation, whole-transcriptome analyses by microarrays and next-generation sequencing (NGS) including single cell RNA sequencing (scRNA-Seq) and droplet-based approaches (Drop-Seq) for transcriptomics and epigenomics, as well as microbiome/metagenome analysis are cutting edge techniques provided by Z1. A comprehensive portfolio of bioinformatics software solutions is offered to all CRU members to process and analyze the above-mentioned data sets in a standardized and highly automated fashion.

Z1 bersicht

 

Hompage MPI Bioinformatic

Homepage Goesmann lab

Single Cell RNAseq analysis software

Publications



The Role of the Redox Enzyme p66Shc in Biological Aging of the Lung

Aging Dis 2023 Jul 27. doi: 10.14336/AD.2023.0715


Prognostic Impact of the Immune-Cell Infiltrate in N1-Positive Non-Small-Cell Lung Cancer

Clin Lung Cancer 2023 Jun 28:S1525-7304(23)00139-0. doi: 10.1016/j.cllc.2023.06.013

The Viscum album Gene Space database

Front Plant Sci 2023 Jun 26;14:1193122. doi: 10.3389/fpls.2023.1193122

CEACAM6 as a Novel Therapeutic Target to Boost HO-1-mediated Antioxidant Defense in COPD

Am J Respir Crit Care Med 2023 Jun 15;207(12):1576-1590. doi: 10.1164/rccm.202208-1603OC

Nicotine promotes e-cigarette vapour-induced lung inflammation and structural alterations

Eur Respir J 2023 Apr 27:2200951. doi: 10.1183/13993003.00951-2022

Targeting Wnt-ß-Catenin-FOSL Signaling Ameliorates Right Ventricular Remodeling

Circ Res 2023 Apr 12. doi: 10.1161/CIRCRESAHA.122.321725

Draft Genome Sequence of Sinomicrobium sp. Strain PAP.21, Isolated from a Coast Sample of Papua, Indonesia

Microbiol Resour Announc 2023 Mar 21:e0126822. doi: 10.1128/mra.01268-22




Loss of SUV420H2-Dependent Chromatin Compaction Drives Right-Sided Colon Cancer Progression

Gastroenterology 2023 Feb;164(2):214-227. doi: 10.1053/j.gastro.2022.10.036

Notch1 Induces Defective Epithelial Surfactant Processing and Pulmonary Fibrosis

Am J Respir Crit Care Med 2023 Feb 1;207(3):283-299. doi: 10.1164/rccm.202105-1284OC


Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics

Antibiotics (Basel) 2022 Nov 12;11(11):1611. doi: 10.3390/antibiotics11111611


HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

Nat Commun 2022 Nov 2;13(1):6563. doi: 10.1038/s41467-022-34252-2


Unravelling the impact of aging on the human endothelial lncRNA transcriptome

Front Genet 2022 Oct 21;13:1035380. doi: 10.3389/fgene.2022.1035380


CXCL13 is expressed in a subpopulation of neuroendocrine cells in the murine trachea and lung

Cell Tissue Res 2022 Oct;390(1):35-49. doi: 10.1007/s00441-021-03552-2

Selected commensals educate the intestinal vascular and immune system for immunocompetence

Microbiome 2022 Sep 28;10(1):158. doi: 10.1186/s40168-022-01353-5

Targeting peptidyl-prolyl isomerase 1 in experimental pulmonary arterial hypertension

Eur Respir J 2022 Aug 25;60(2):2101698. doi: 10.1183/13993003.01698-2021.


TF-COMB - Discovering grammar of transcription factor binding sites

Comput Struct Biotechnol J 2022 Jul 21;20:4040-4051. doi: 10.1016/j.csbj.2022.07.025





i2dash: Creation of Flexible, Interactive, and Web-based Dashboards for Visualization of Omics Data

Genomics Proteomics Bioinformatics 2022 Jun;20(3):568-577. doi: 10.1016/j.gpb.2021.01.007





SPARC, a Novel Regulator of Vascular Cell Function in Pulmonary Hypertension

Circulation 2022 Mar 22;145(12):916-933. doi: 10.1161/CIRCULATIONAHA.121.057001


Multi-label classification for multi-drug resistance prediction of Escherichia coli

Comput Struct Biotechnol J 2022 Mar 10;20:1264-1270. doi: 10.1016/j.csbj.2022.03.007




Genetic deletion of p66shc and/or cyclophilin D results in decreased pulmonary vascular tone

Cardiovasc Res 2022 Jan 7;118(1):305-315. doi: 10.1093/cvr/cvaa310

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning

Bioinformatics 2022 Jan 3;38(2):325-334. doi: 10.1093/bioinformatics/btab681


Flower lose, a cell fitness marker, predicts COVID-19 prognosis

EMBO Mol Med 2021 Nov 8;13(11):e13714. doi: 10.15252/emmm.202013714






Sex-specific differences in plasma levels of FXII, HK, and FXIIa-C1-esterase inhibitor complexes in community-acquired pneumonia

Am J Physiol Lung Cell Mol Physiol 2021 Oct 1;321(4):L764-L774. doi: 10.1152/ajplung.00162.2021


Multi-level inhibition of coronavirus replication by chemical ER stress

Nat Commun 2021; 12: 5536, doi: 10.1038/s41467-021-25551-1

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Biology (Basel) 2021 Sep 15;10(9):916. doi: 10.3390/biology10090916






mRNA Inventory of Extracellular Vesicles from Ustilago maydis

J Fungi (Basel) 2021 Jul 14;7(7):562. doi: 10.3390/jof7070562

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure

Nucleic Acids Res 2021 Jul 2;49(W1):W185-W192. doi: 10.1093/nar/gkab341


Protocol for the generation of murine bronchiolospheres

STAR Protoc 2021 Jun 11;2(2):100594. doi: 10.1016/j.xpro.2021.100594

Microbiome of Odontogenic Abscesses

Microorganisms 2021 Jun 16;9(6):1307. doi: 10.3390/microorganisms9061307


Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef

Int J Syst Evol Microbiol 2021 Jun;71(6). doi: 10.1099/ijsem.0.004822


WASP: a versatile, web-accessible single cell RNA-Seq processing platform

BMC Genomics 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6

How animals distribute themselves in space: energy landscapes of Antarctic avian predators

Mov Ecol 2021 May 17;9(1):24. doi: 10.1186/s40462-021-00255-9

Noninvasive Surrogate Markers of Pulmonary Hypertension Are Associated with Poor Survival in Patients with Lung Cancer

Am J Respir Crit Care Med 2021 May 15;203(10):1316-1319. doi: 10.1164/rccm.202005-2023LE

Analysis of glycerol and dihydroxyacetone metabolism in Enterococcus faecium

FEMS Microbiol Lett 2021 May 6;368(8):fnab043. doi: 10.1093/femsle/fnab043



Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont

Proc Natl Acad Sci U S A 2021 Apr 27;118(17):e2023047118. doi: 10.1073/pnas.2023047118

Immunoglobulin deficiency as an indicator of disease severity in patients with COVID-19

Am J Physiol Lung Cell Mol Physiol 2021 Apr 1;320(4):L590-L599. doi: 10.1152/ajplung.00359.2020


WASP: a versatile, web-accessible single cell RNA-Seq processing platform

BMC Genomics 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6




Pseudomonas paracarnis sp. nov., isolated from refrigerated beef

Int J Syst Evol Microbiol 2021 Feb;71(2). doi: 10.1099/ijsem.0.004652


Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

Nucleic Acids Res 2021 Jan 25;49(2):986-1005. doi: 10.1093/nar/gkaa1229





iCLIP analysis of RNA substrates of the archaeal exosome

BMC Genomics 2020 Nov 16;21(1):797. doi: 10.1186/s12864-020-07200-x



Complete Genome Sequence of Staphylococcus aureus EDCC 5398, a Clinical Isolate from Implant-Associated Bone Infection

Microbiol Resour Announc 2020 Oct 22;9(43):e01136-20. doi: 10.1128/MRA.01136-20


Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants

FEMS Microbiol Ecol 2020 Oct 1;96(10):fiaa176. doi: 10.1093/femsec/fiaa176



Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Cell 2020 Sep 17;182(6):1419-1440.e23. doi: 10.1016/j.cell.2020.08.001

multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets

Life Sci Alliance 2020 Sep 9;3(11):e202000757. doi: 10.26508/lsa.202000757


The status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992)

Int J Syst Evol Microbiol 2020 Sep;70(9):5165-5171. doi: 10.1099/ijsem.0.004404

Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System

Mol Cell Proteomics 2020 Sep;19(9):1523-1532. doi: 10.1074/mcp.RA120.001947


IL-13 as Target to Reduce Cholestasis and Dysbiosis in Abcb4 Knockout Mice

Cells 2020 Aug 24;9(9):1949. doi: 10.3390/cells9091949


Acute kidney injury and urinary biomarkers in hospitalized patients with coronavirus disease-2019

Nephrol Dial Transplant 2020 Jul 1;35(7):1271-1274. doi: 10.1093/ndt/gfaa162






NADPH oxidase subunit NOXO1 is a target for emphysema treatment in COPD

Nat Metab 2020 Jun;2(6):532-546. doi: 10.1038/s42255-020-0215-8

Tigecycline efflux in Acinetobacter baumannii is mediated by TetA in synergy with RND-type efflux transporters

J Antimicrob Chemother 2020 May 1;75(5):1135-1139. doi: 10.1093/jac/dkaa015




Pseudomonas carnis sp. nov., isolated from meat

Int J Syst Evol Microbiol 2020 Mar;70(3):1528-1540. doi: 10.1099/ijsem.0.003928

Identification of the general stress stimulon related to colonization in Enterococcus faecalis

Arch Microbiol 2020 Mar;202(2):233-246. doi: 10.1007/s00203-019-01735-8




Pseudomonas bubulae sp. nov., isolated from beef

Int J Syst Evol Microbiol 2020 Jan;70(1):292-301. doi: 10.1099/ijsem.0.003751

Doppler-Derived Renal Venous Stasis Index in the Prognosis of Right Heart Failure

J Am Heart Assoc 2019 Nov 5;8(21):e013584. doi: 10.1161/JAHA.119.013584






Pleiotropic effects of laminar flow and statins depend on the Krüppel-like factor-induced lncRNA MANTIS

Eur Heart J 2019 Aug 7;40(30):2523-2533. doi: 10.1093/eurheartj/ehz393

MARMoSET - Extracting Publication-ready Mass Spectrometry Metadata from RAW Files

Mol Cell Proteomics 2019 Aug;18(8):1700-1702. doi: 10.1074/mcp.TIR119.001505


Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany

Microbiol Resour Announc 2019 Jul 18;8(29):e00465-19. doi: 10.1128/MRA.00465-19


Regulation and role of the ER stress transcription factor CHOP in alveolar epithelial type-II cells

J Mol Med (Berl) 2019 Jul;97(7):973-990. doi: 10.1007/s00109-019-01787-9

Riociguat for treatment of pulmonary hypertension in COPD: a translational study

Eur Respir J 2019 Jun 27;53(6):1802445. doi: 10.1183/13993003.02445-2018

Lnc-ITM2C-1 and GPR55 Are Proviral Host Factors for Hepatitis C Virus

Viruses 2019 Jun 13;11(6):549. doi: 10.3390/v11060549

Streptomyces dysideae sp. nov., isolated from a marine Mediterranean sponge Dysidea tupha

Int J Syst Evol Microbiol 2019 Jun;71(3). doi: 10.1099/ijsem.0.004672

Fabry disease: Detection of Alu-mediated exon duplication by NGS

Mol Cell Probes 2019 Jun;45:79-83. doi: 10.1016/j.mcp.2019.03.008

Regulation and role of the ER stress transcription factor Chop in alveolar epithelial type-II cells

J Mol Med (Berl) 2019 Jul;97(7):973-990. doi:10.1007/s00109-019-01787-9


Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035

Microbiol Resour Announc 2019 Apr 25;8(17):e00050-19. doi: 10.1128/MRA.00050-19




WIlsON: Web-based Interactive Omics VisualizatioN

Bioinformatics 2019 Mar 15;35(6):1055-1057. doi: 10.1093/bioinformatics/bty711



ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function

J Immunol 2019 Feb 15;202(4):1099-1111. doi: 10.4049/jimmunol.180026

Connect-four: genomic analyses of regenerating stem cells identifies zygotic Dux factors as tumor initiators

Mol Cell Oncol 2019 Feb 8;6(2):1565469. doi: 10.1080/23723556.2019.1565469




Reserve of Right Ventricular-Arterial Coupling in the Setting of Chronic Overload

Circ Heart Fail 2019 Jan;12(1):e005512. doi: 10.1161/CIRCHEARTFAILURE.118.005512


aPKC controls endothelial growth by modulating c-Myc via FoxO1 DNA-binding ability

Nat Commun 2018 Dec 17;9(1):5357. doi: 10.1038/s41467-018-07739-0



Redox status of patients before cardiac surgery

Redox Rep 2018 Dec;23(1):83-93. doi: 10.1080/13510002.2017.1418620

Evaluating Systolic and Diastolic Cardiac Function in Rodents Using Microscopic Computed Tomography

Circ Cardiovasc Imaging 2018 Dec;11(12):e007653. doi: 10.1161/CIRCIMAGING.118.007653

Transcriptome profiling reveals the complexity of pirfenidone effects in idiopathic pulmonary fibrosis

Eur Respir J 2018 Nov 22;52(5):1800564. doi: 10.1183/13993003.00564-2018


Myh10 deficiency leads to defective extracellular matrix remodeling and pulmonary disease

Nat Commun 2018 Nov 2;9(1):4600. doi: 10.1038/s41467-018-06833-7

Listeria goaensis sp. nov

Int J Syst Evol Microbiol 2018 Oct;68(10):3285-3291. doi: 10.1099/ijsem.0.002980




A reference genome of the Chinese hamster based on a hybrid assembly strategy

Biotechnol Bioeng 2018 Aug;115(8):2087-2100. doi: 10.1002/bit.26722







Flexible metagenome analysis using the MGX framework

Microbiome 2018 Apr 24;6(1):76. doi: 10.1186/s40168-018-0460-1



Exercise training reverses inflammation and muscle wasting after tobacco smoke exposure

Am J Physiol Regul Integr Comp Physiol 2018 Mar 1;314(3):R366-R376. doi: 10.1152/ajpregu.00316.2017

Long noncoding RNA LISPR1 is required for S1P signaling and endothelial cell function

J Mol Cell Cardiol 2018 Mar;116:57-68. doi: 10.1016/j.yjmcc.2018.01.015

New Lineage of Lassa Virus, Togo, 2016

Emerg Infect Dis 2018 Mar;24(3):599-602. doi: 10.3201/eid2403.171905


Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment

Mol Cell Proteomics 2018 Feb;17(2):270-289. doi: 10.1074/mcp.RA117.000400





Bioinformatics for NGS-based metagenomics and the application to biogas research

J Biotechnol 2017 Nov 10;261:10-23. doi: 10.1016/j.jbiotec.2017.08.012

Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713

Genome Announc 2017 Nov 9;5(45):e01262-17. doi: 10.1128/genomeA.01262-17

Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71

Genome Announc 2017 Oct 26;5(43):e01227-17. doi: 10.1128/genomeA.01227-17

Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655

2017 Oct 26;5(43):e01196-17. doi: 10.1128/genomeA.01196-17



The Regulatory Small RNA MarS Supports Virulence of Streptococcus pyogenes

Sci Rep 2017 Sep 25;7(1):12241. doi: 10.1038/s41598-017-12507-z


Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism

J Biotechnol 2017 Sep 10;257:58-60. doi: 10.1016/j.jbiotec.2017.02.020

Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3

Arch Microbiol 2017 Sep;199(7):1065-1068. doi: 10.1007/s00203-017-1394-x


Single-cell profiling reveals GPCR heterogeneity and functional patterning during neuroinflammation

JCI Insight 2017 Aug 3;2(15):e95063. doi: 10.1172/jci.insight.95063



Long Noncoding RNA MANTIS Facilitates Endothelial Angiogenic Function

Circulation 2017 Jul 4;136(1):65-79. doi: 10.1161/CIRCULATIONAHA.116.026991




UROPA: a tool for Universal RObust Peak Annotation

Sci Rep 2017 Jun 1;7(1):2593. doi: 10.1038/s41598-017-02464-y



Pulmonary endothelial cell DNA methylation signature in pulmonary arterial hypertension

Oncotarget 2017 May 19;8(32):52995-53016. doi: 10.18632/oncotarget.18031


Microbial diversity in different compartments of an aquaponics system

Arch Microbiol 2017 May;199(4):613-620. doi: 10.1007/s00203-016-1334-1

Pirfenidone exerts antifibrotic effects through inhibition of GLI transcription factors

FASEB J 2017 May;31(5):1916-1928. doi: 10.1096/fj.201600892RR

Promoter hypermethylation as a mechanism for Lamin A/C silencing in a subset of neuroblastoma cells

PLoS One 2017 Apr 19;12(4):e0175953. doi: 10.1371/journal.pone.0175953

Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

BMC Genomics 2017 Apr 7;18(1):282. doi: 10.1186/s12864-017-3616-7




Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

PLoS Pathog 2017 Feb 3;13(2):e1006195. doi: 10.1371/journal.ppat.1006195



Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

BMC Genomics 2017 Jan 5;18(1):35. doi: 10.1186/s12864-016-3422-7


A reverse signaling pathway downstream of Sema4A controls cell migration via Scrib

J Cell Biol 2017 Jan 2;216(1):199-215. doi: 10.1083/jcb.201602002



Laser Capture Microdissection of Tissue Sections for High-Throughput RNA Analysis

Methods Mol Biol 2017;1627:325-340. doi: 10.1007/978-1-4939-7113-8_21

Principal Investigators

Torsten Hain

PD Dr. rer. nat. Torsten Hain

Justus Liebig University Giessen
Institute of Medical Microbiology 
Schubertstraße 81; 35392 Giessen

+49-641-99-39860
Alexander Goesmann

Prof. Dr. Alexander Goesmann

Systems Biology
Heinrich-Buff-Ring 58; 35392 Giessen

+49 641 99-35800
Jochen Wilhelm

Dr. rer. nat. Jochen Wilhelm

Justus Liebig University Giessen
Department of Medicine II
Gaffkystr. 11; 35392 Giessen

+49-641-99-42545
Mario Looso

Dr. Mario Looso

Head of Bioinformatics Service Facility

Max Planck Institute for Heart and Lung Research

Ludwigstrasse 43

61231 Bad Nauheim

Loosolab.mpi-bn.mpg.de

+49-6032-705-1763

Project group

  • Burkhard Linke

    Dr. Burkhard Linke

    Postdoc

  • Andreas Hoek

    Andreas Hoek

    Bioinformatician

  • Monika Heiner

    Dr. Monika Heiner

    Postdoc

  • Jan Philipp Mengel

    Jan Philipp Mengel

    PhD student

  • Sweta Taylan

    Sweta Taylan , Postdoc