CardiOmics

The unit carries out research into infectious diseases relevant to cardiac surgery using state-of-the-art OMICS technology platforms. Infective endocarditis and the development of molecular biological diagnostic procedures are of particular scientific interest here, as is the translation of such procedures into routine clinical practice. Based on improved diagnostics, alternative treatment methods are evaluated and new interventional procedures taken to clinical maturity.

The unit will concentrate on the connection between infectious diseases and molecular regulatory mechanisms associated with haemostasis. In the interdisciplinary field of intervention strategies relating to cardiac surgery, the diagnosis and therapeutic intervention of the coagulation system play a vital role. The unit primarily develops diagnostic procedures to determine the effect of factor X inhibitors and / or coagulation diagnostics during the final stages of plasma coagulation.

Experimental surgical procedures

  • Development of a bioreactor to simulate heart valve infections
  • Development of alternative treatment options for local pockets of infection

Infection diagnostics relevant to cardiac surgery

Genome and transcriptome analyses of human and microbial analytes

  • Next-generation sequencing (Illumina sequencing systems; MiSeq; ultra-high-throughput sequencing system HiSeq 2500)
  • DNA capture sequencing and DNA amplicon sequencing

Structural and ultrastructural investigations of infected tissues

  • Immunohistological examinations (immunofluorescence, FACS analyses, FISH assays)
  • Electron-microscopical examinations (FIB-SEM, 3View), infection serology
  • Detection of antigens of particular pathogens and / or antibodies

Thrombin generation

  • The determination of thrombin generation using the Thrombodynamics assay (HemaCore SA, Route de l'Ile-au-Bois, 1870 Monthey, Switzerland) is based on traditional fluorimetry combined with time-resolved microscopy.

Verification of the virulence profil of organ-specific infection

In the past decade, infectious diseases in the cardiovascular sector have been increasingly emerging as a clinical challenge. This is not only to be attributed to an increasing pathogen-specific resistance to chemotherapy but also to an improved therapy landscape, such as implanting cardiac pacemakers, heart valve systems and artificial heart systems. Current research results show that a polymicrobial pathogen infiltration defines the disease status and course. Previous research efforts focused on identifying pathogen spectra by means of total genome investigations. Further, the goal of the research effort is to identify disease-causing pathomechanisms. To this end, it is necessary to ensure the identification agents up to the root level to allow conclusions on disease mechanisms. Initially, the microbial community of a patient sample was analyzed via a specifically defined PCR panel. The PCR allows a quick analysis of known pathogenic germs. As unknown bacteria, which may also be pathogenic, remained undetected, the T-RLFP analysis was also used to characterise the diversity of the samples. This non-targeted method is based on the amplification and restriction of 16S RDNA and then uncovers unknown germs via cloning and sequencing. However, the sensitivity of the method is limited by the number of clones analyzed, and in some cases it does not read a differentiation of the species of a genus. A more sensitive process is genome sequencing based on the 16S RDNA or the overall genome. It was possible analyse the microbial composition of a patient sample and also detect bacteria in low concentrations up to the species level. The main challenge in applying the new analysis methods lies at the level of bioinformatics diagnostic strategies. This ranges from the assignment of pathogen-specific DNA molecules to the identification of the pathogen stem to the classification of virulence factors. These virulence factors must be correlated with the patient outcome in prospective clinical trials and thus their clinical relevance will be developed. The aim of the working group is to develop this clinical molecular biological diagnostic path, to establish necessary bioinformatic tools and to incorporate the findings into the daily routine in clinics.

Infectious diseases relevant to cardiac surgery

The "Infectious diseases relevant to cardiac surgery" project aims to depict the pathogen spectrum of infectious diseases affecting the cardiovascular system. Special attention is given to infective endocarditis (IE), which is becoming more and more clinically relevant due to increasing heart valve interventions. In spite of the medical advancement seen over the past century, patients suffering from IE are faced with just as poor an outlook as in the past. The unit is developing a comprehensive approach which shall serve as a model and aim to improve clinical diagnosis based on next-generation sequencing (NGS), electron microscopy (EM) and a point-of-care (PoC) platform, thus facilitating more targeted treatment and prevention strategies. The knowledge gained from OMICS technnologies will be used to establish immunology-based assays, which will be developed to clinical market-maturity.

Diagnosis of primary and secondary haemostasis

The "Diagnosis of primary and secondary haemostasis" project focuses on establishing thrombin generation as a clinical monitoring tool for the sensitive determination of the entire plasma coagulation cascade. Determining the final stage of plasma coagulation is also suitable to sufficiently map the factor X inhibitors and their effect on the coagulation system. Based on experimental molecular biology experiments, a point-of-care assay will be developed and later validated during the course of routine clinical practice.

  • Illumina sequencing platform Hiseq 2500 (Ultra-High-Throughput Sequencing System)
  • Illumina sequencing platform Miseq
  • Microlab STARlet (Hamilton, automatically prepares samples for sequencing)
  • Qiacube (semi-automated extraction and purification of nucleic acids)
  • Microarray scanner (Agilent, Affymetrix)
  • Perkin Elmer Labchip GX (to determine the quality of nucleic acids, can be integrated into automation)
  • Perkin Elmer Labchip DS (to quantify nucleic acids, can be integrated into automation)
  • Agilent Bioanalyzer (to determine the quality of nucleic acids and proteins)
  • Nanodrop (to quantify nucleic acids)
  • Qubit 2.0 (extremely sensitive fluorometric quantification of specific nucleic acids)
  • Covaris M220 Focused-ultrasonicator™ (nucleic acid shearing, active paraffin removal from FFPE tissues)
  • Cell sorter / FACS
  • Confocal Laser Scanning Microscopy (Zeiss LSM 710)
  • Focused Ion Beam Scanning Electron Microscopes (Crossbeam 540)
  • Xradia 810 Ultra

  • Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N. Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins. Clin Chim Acta. 2016 Jan 30;453:114-22. DOI dx.doi.org/10.1016/j.cca.2015.12.005.
  • Lehmann S, Merk DR, Etz CD, Oberbach A, Uhlemann M, Emrich F, Funkat AK, Meyer A, Garbade J, Bakhtiary F, Misfeld M, Mohr FW. Porcine xenograft for aortic, mitral and double valve replacement: long-term results of 2544 consecutive patients. Eur J Cardiothorac Surg. 2015 Oct 30. pii: ezv383.
  • Kumbhari V, Oberbach A, Nimgaonkar A. Primary endoscopic therapies for obesity and metabolic diseases. Curr Opin Gastroenterol. 2015 Sep;31(5):351-8.
  • Kumbhari V, Heinrich M, Khashab MA, Kalloo AN, Oberbach A. Gastric restriction and delayed gastric emptying may not be the keys to an effective endoscopic metabolic therapy. Gastrointest Endosc. 2015 Jul;82(1):185-6.
  • Leontyev S, Davierwala PM, Krögh G, Feder S, Oberbach A, Bakhtiary F, Misfeld M, Borger MA, Mohr FW. Early and late outcomes of complex aortic root surgery in patients with aortic root abscesses†. Eur J Cardiothorac Surg. 2016 Feb;49(2):447-55.
  • Kumbhari V, Oberbach A. Is excision of the gastric mucosa responsible for the superior outcomes of sleeve gastrectomy compared with gastric plication? Surg Obes Relat Dis. 2015 May-Jun;11(3):732.
  • Lehmann S, Merk DR, Etz CD, Seeburger J, Schroeter T, Oberbach A, Uhlemann M, Hoellriegel R, Haensig M, Leontyev S, Garbade J, Misfeld M, Mohr FW. Minimally invasive aortic valve replacement: the Leipzig experience. Ann Cardiothorac Surg. 2015 Jan;4(1):49-56.
  • Bowen TS, Mangner N, Werner S, Glaser S, Kullnick Y, Schrepper A, Doenst T, Oberbach A, Linke A, Steil L, Schuler G, Adams V. Diaphragm muscle weakness in mice is early-onset post-myocardial infarction and associated with elevated protein oxidation. J Appl Physiol (1985). 2015 Jan 1;118(1):11-9.
  • Oberbach A, Schlichting N, Neuhaus J, Kullnick Y, Lehmann S, Heinrich M, Dietrich A, Mohr FW, von Bergen M, Baumann S. Establishing a reliable multiple reaction monitoring-based method for the quantification of obesity-associated comorbidities in serum and adipose tissue requires intensive clinical validation. J Proteome Res. 2014 Dec 5;13(12):5784-800.
  • Matsuo Y, Oberbach A, Till H, Inge TH, Wabitsch M, Moss A, Jehmlich N, Völker U, Müller U, Siegfried W, Kanesawa N, Kurabayashi M, Schuler G, Linke A, Adams V. Impaired HDL function in obese adolescents: impact of lifestyle intervention and bariatric surgery. Obesity (Silver Spring). 2013 Dec;21(12):E687-95.
  • Haange SB, Oberbach A, Schlichting N, Hugenholtz F, Smidt H, von Bergen M, Till H, Seifert J. Metaproteome analysis and molecular genetics of rat intestinal microbiota reveals section and localization resolved species distribution and enzymatic functionalities. J Proteome Res. 2012 Nov 2;11(11):5406-17.
  • Ferrer M, Ruiz A, Lanza F, Haange SB, Oberbach A, Till H, Bargiela R, Campoy C, Segura MT, Richter M, von Bergen M, Seifert J, Suarez A. Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure. Environ Microbiol. 2013 Jan;15(1):211-26.