Johannes Rainer

Johannes Rainer
Eurac Research · Institute for Biomedicine

Ph.D.

About

97
Publications
14,512
Reads
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2,434
Citations
Additional affiliations
January 2015 - present
Eurac Research
Position
  • Senior Researcher
February 2009 - February 2015
Medizinische Universität Innsbruck
Position
  • Junior Group Leader
January 2008 - July 2014
Medizinische Universität Innsbruck
Position
  • Genomics: Bioinformatics
Education
November 2003 - October 2007
Graz University of Technology
Field of study
  • Bioinformatics
October 1996 - October 2003
Graz University of Technology
Field of study
  • Biomedical Engineering

Publications

Publications (97)
Article
We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides infrastructure for the manipulation, processing and visualisation of mass spectrometry data. We focus on the new on-disk infrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for ele...
Article
Full-text available
Bioinformatics research frequently involves handling gene-centric data such as exons, transcripts, proteins and their positions relative to a reference coordinate system. The ensembldb Bioconductor package retrieves and stores Ensembl-based genetic annotations and positional information, and furthermore offers identifier conversion and coordinates...
Article
Full-text available
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and...
Article
Full-text available
Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment t...
Article
Full-text available
Metabolomics in human serum samples provide a snapshot of the current metabolic state of an individuum. Metabolite concentrations are influenced by both genetic and environmental factors. Concentrations of certain metabolites can further depend on age, sex, menopause, and diet of study participants. A better understanding of these relationships is...
Article
Arrhythmogenic cardiomyopathy (ACM) is a genetic disease associated with sudden cardiac death and cardiac fibro‐fatty replacement. Over the last years, several works have demonstrated that different epigenetic enzymes can affect not only gene expression changes in cardiac diseases but also cellular metabolism. Specifically, the histone acetyltransf...
Article
Full-text available
Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resul...
Article
Full-text available
LC–MS-based untargeted metabolomics is heavily dependent on algorithms for automated peak detection and data preprocessing due to the complexity and size of the raw data generated. These algorithms are generally designed to be as inclusive as possible in order to minimize the number of missed peaks. This is known to result in an abundance of false...
Article
Full-text available
Atrial fibrillation (AF) is a supraventricular arrhythmia deriving from uncoordinated electrical activation with considerable associated morbidity and mortality. To expand the limited understanding of AF biological mechanisms, we performed two screenings, investigating the genetic and metabolic determinants of AF in the Cooperative Health Research...
Poster
Serum samples collected from 5000 subjects were analyzed using Absolute IDQ p180 Kit from Biocrates, allowing the quantification of 186 metabolites by combining flow injection analysis and liquid chromatography assays and covering acylcarnitines (40), amino acids (21), biogenic amines (19), phosphatidylcholines (76), lyso-phosphatidylcholines (14),...
Poster
Using the large data set available from CHRIS (Cooperative Health Research in South Tyrol) study we here describe serum metabolites from 6872 participants which were found to be associated with sex, age and body mass index.
Article
Full-text available
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecu...
Article
Full-text available
Background Adipose-derived stem cells (ASC) and adipocytes are involved in numerous physiological and pathophysiological conditions, which have been extensively described in subcutaneous and visceral fat depots over the past two decades. However, much less is known about ASC and adipocytes outside classical fat tissue depots and their necessity in...
Article
Full-text available
Arrhythmogenic cardiomyopathy (ACM) is a genetic-based cardiac disease accompanied by severe ventricular arrhythmias and a progressive substitution of the myocardium with fibro-fatty tissue. ACM is often associated with sudden cardiac death. Due to the reduced penetrance and variable expressivity, the presence of a genetic defect is not conclusive,...
Preprint
Full-text available
Glucocorticoids (GCs) are an essential component of acute lymphoblastic leukemia (ALL) therapy. To identify genes mediating the anti-leukemic GC effects in vivo, we performed gene expression profiling of lymphoblasts from 46 children during the first 6-24h of systemic GC mono-therapy. Differential gene expression analysis across all patients reveal...
Preprint
Full-text available
Molecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships i...
Preprint
Full-text available
We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides infrastructure for the manipulation, processing and visualisation of mass spectrometry data. We focus on the new on-disk infrastructure, that allows the handling of large raw mass spectrometry experiment on commodity hardware and illustrate how the package is used for eleg...
Preprint
Full-text available
Molecular networking has become a key method used to visualize and annotate the chemical space in non-targeted mass spectrometry-based experiments. However, distinguishing isomeric compounds and quantitative interpretation are currently limited. Therefore, we created Feature-based Molecular Networking (FBMN) as a new analysis method in the Global N...
Article
Full-text available
Late endosomal/lysosomal adaptor and MAPK and mTOR activator (LAMTOR/Ragulator) is a scaffold protein complex that anchors and regulates multiprotein signaling units on late endosomes/lysosomes. To identify LAMTOR‐modulated endolysosomal proteins, primary macrophages were derived from bone marrow of conditional knockout mice carrying a specific del...
Preprint
Adipogenesis is a complex process governed by multiple signaling cascades operating through various regulatory factors and specific downstream genes. Here we identified TIS7 (IFRD1) and its orthologue SKMc15 (IFRD2) as new regulators of adipogenesis and fat metabolism. Mice deficient in both TIS7 and SKMc15 (dKO) had severely reduced adipose tissue...
Article
Background: Plasma and serum are the most widely used matrices in clinical studies. However, some variability in absolute concentrations of metabolites are likely to be observed in these collection tubes matrices. Methods: We analyzed 189 metabolites using the same protocol for quantitative targeted metabolomics (LC-MS/MS AbsoluteIDQ p180 Kit Bi...
Article
Full-text available
Motivation Familial aggregation analysis is an important early step for characterizing the genetic determinants of phenotypes in epidemiological studies. To facilitate this analysis, a collection of methods to detect familial aggregation in large pedigrees has been made available recently. However, efficacy of these methods in real world scenarios...
Article
Full-text available
Background: Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recently described, cardiac stroma...
Article
Full-text available
Human abdominal subcutaneous adipose tissue consists of two individual layers—the superficial adipose tissue (SAT) and deep adipose tissue (DAT)—separated by the Scarpa’s fascia. The present study focuses on the analysis of morphological and immunological differences of primary adipocytes, adipose-derived stem cells (ASC), and tissue-infiltrating i...
Article
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This work evaluated gene expression differences between a hanging-drop 3D NSCLC model and 2D cell cultures and their in-vivo relevance by comparison to patient-derived data from The Cancer Genome Atlas. Gene expression of 2D and 3D cultures for Colo699 and A549 were assessed using Affymetrix HuGene 1.0 ST gene chips. Biostatistical analyses tested...
Article
Full-text available
Volumetric absorptive microsampling (VAMS) is a novel approach that allows single-drop (10 μL) blood collection. Integration of VAMS with mass spectrometry (MS)-based untargeted metabolomics is an attractive solution for both human and animal studies. However, to boost the use of VAMS in metabolomics, key pre-analytical questions need to be address...
Article
Full-text available
Extinction-based exposure therapy is used to treat anxiety- and trauma-related disorders; however, there is the need to improve its limited efficacy in individuals with impaired fear extinction learning and to promote greater protection against return-of-fear phenomena. Here, using 129S1/SvImJ mice, which display impaired fear extinction acquisitio...
Raw Data
Introduction: Due to the increasing understanding of the mechanisms relevant to the genesis of cancer, we are experiencing a transition from disease to target-oriented therapy. One major hurdle for the development of these targeted therapeutic regimens, however, is the limited availability of predictive in vitro models. The critical challenge is to...
Article
Full-text available
Due to the urgent need for new prostate cancer (PCa) therapies, the role of androgen receptor (AR) interacting proteins should be investigated. In this study we aimed to address whether the AR coactivator nuclear receptor coactivator 1 (NCOA1) is involved in PCa progression. Therefore, we tested the effect of long-term NCOA1 knockdown on processes...
Data
Data S1. Methods and results. Figure S1. Venn diagram showing the number and overlap of the SAPs’ genes. Benign = unique number of genes of the benign SAPs; pathogenic = unique number of genes of the pathogenic SAPs. (A) training data set. (B) validation data set. Figure S2. Overlap of the training and validation datasets with ExoVar, HumVar, Swi...
Data
Table S5. “Difficult SAPs” (without SAPs from HGMD).
Article
Full-text available
Skeletal muscle excitation-contraction (EC) coupling is independent of calcium influx. In fact alternative splicing of the voltage-gated calcium channel CaV1.1 actively suppresses calcium currents in mature muscle. Whether this is necessary for normal development and function of muscle is not known. However, splicing defects causing aberrant expres...
Article
Full-text available
Background: Although several methods have been proposed for predicting the effects of genetic variants and their role in disease, it is still a challenge to identify and prioritize pathogenic variants within sequencing studies. Methods: Here, we compare different variant and gene-specific features as well as existing methods and investigate thei...
Article
Full-text available
Familial aggregation analysis is the first fundamental step to perform when assessing the extent of genetic background of a disease. However, there is a lack of software to analyze the familial clustering of complex phenotypes in very large pedigrees. Such pedigrees can be utilized to calculate measures that express trait aggregation on both the fa...
Data
Figure S1. Representative tandem mass spectrum for PAX‐5 protein (peptide sequence:ANLASPTPADIGSSVPGPQSYPIVTGR). 932.8, triply charged ion. The inset shows the peak area at the low mass/charge (m/z) region with the iTRAQ reporter ions. Figure S2. Differential induction of IRF4 protein in PreB 697 compared to R3F9 cell lines in response to dexameth...
Article
Full-text available
Genome-wide association studies have identified genomic loci, whose single nucleotide polymorphisms (SNPs) predispose to prostate cancer (PCa). However, the mechanisms of most of these variants are largely unknown. We integrated chromatin-IP coupled sequencing and microarray expression profiling in TMPRSS2-ERG gene rearrangement positive DUCaP cell...
Article
Full-text available
Glucocorticoid (GC) resistance is a continuing clinical problem in childhood acute lymphoblastic leukaemia (ALL) but the underlying mechanisms remain unclear. A proteomic approach was used to compare profiles of the B-lineage ALL GC-sensitive cell line, PreB 697, and its GC-resistant sub-line, R3F9, pre- and post-dexamethasone exposure. PAX5, a tra...
Article
This is a correspondence about “Beclin‐1 is required for chromosome congression and proper outer kinetochore assembly”.
Poster
Introduction: Increasing efforts to integrate tumour-stroma interaction and 3-dimensional structures in innovative in-vitro models were made within the last years. We established a 3D co-culture system in non-small-cell lung cancer applicable for drug testing. In this work, we present data on the differences in RNA expression and drug sensitivity i...
Article
The normal prostate as well as early-stages and advanced prostate cancer (PCa) require a functional androgen receptor (AR) for growth and survival. The recent discovery of microRNAs (miRNAs) as novel effector molecules of AR disclosed the existence of an intricate network between AR, miRNAs and down-stream target genes. In this study DUCaP cells, c...
Article
Full-text available
FOXO transcription factors control cellular levels of reactive oxygen species (ROS) which critically contribute to cell survival and cell death in neuroblastoma. In the present study we investigated the regulation of C10orf10/DEPP by the transcription factor FOXO3. As a physiological function of C10orf10/DEPP has not been described so far we analyz...
Article
Full-text available
Glucocorticoids (GCs) cause apoptosis in malignant cells of lymphoid lineage by transcriptionally regulating a plethora of genes. As a result, GCs are included in almost all treatment protocols for lymphoid malignancies, particularly childhood acute lymphoblastic leukemia (chALL). The most commonly used synthetic GCs in the clinical setting are pre...
Article
Purpose: The eukaryotic translation initiation factor (eIF) 3a, the largest subunit of the eIF3 complex, is a key functional entity in ribosome establishment and translation initiation. In the past, aberrant eIF3a expression has been linked to the pathology of various cancer types but, so far, its expression has not been investigated in transition...
Article
Full-text available
Glucocorticoids (GCs) are natural stress induced steroid hormones causing cell cycle arrest and cell death in lymphoid tissues. Therefore they are the central component in the treatment of lymphoid malignancies, in particular childhood acute lymphoblastic leukemia (chALL). GCs act mainly via regulating gene transcription, which has been intensively...
Article
Full-text available
Deregulation of cytokine- and growth factor signaling due to altered expression of endogenous regulators is well recognized in prostate and other cancers. Suppressor of cytokine signaling 2 (SOCS2) is a key regulator of growth hormone, insulin-like growth factor and prolactin signaling pathways that have been implicated in carcinogenesis. In this s...
Article
Full-text available
The Epithelial Cell Adhesion Molecule (EpCAM) has been shown to be strongly expressed in human breast cancer and cancer stem cells and its overexpression has been supposed to support tumor progression and metastasis. However, effects of EpCAM overexpression on normal breast epithelial cells have never been studied before. Therefore, we analyzed eff...