Biology subjects

Koch, S.

Publications and source records attributed to Koch, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Gene Supplementation of MYO7A or activation of Myo7b for treatment of Usher syndrome 1B

Mutations in MYO7A result in the most severe subtype of Usher syndrome, the leading genetic cause of deafblindness. The large size of MYO7A requires dual adeno-associated virus (AAV) vectors for gene transfer or alternative methods to treat retinal defects. Here, we evaluated two treatment approaches: i) Supplementation of the human MYO7A gene via dual mRNA trans-splicing AAVs, and ii) CRISPR/Cas-mediated activation of the related murine Myo7b gene. Upon MYO7A supplementation, the transgenic MYO7A transcript and protein were expressed and correctly localized in retinal pigment epithelial (RPE) and photoreceptors of mice, pigs, and human retinal organoids. In RPE-and photoreceptor-specific Myo7a knockout mice, we could restore MYO7A expression and localization of melanosomes in RPE cells to wild-type levels. Myo7b activation led to partial restoration of melanosome localization, and the localization of MYO7B protein was largely comparable to MYO7A. These findings indicate that both approaches are in principle suitable for the therapy of Usher syndrome.

molecular biology↗

bioRxiv2026

GATA transcription factors act as gatekeepers between the Wnt/β-catenin-mediated proliferation and differentiation in the intestinal epithelium

Wnt/{beta}-catenin signalling drives gene expression in a plethora of processes during development and tissue homeostasis. Yet, little is known about how {beta}-catenin, the transducer of the pathway, gives rise to context-specific transcriptional outcomes. For example, in the intestinal epithelium, stem cells and secretory cells lie adjacent to each other, are both exposed to and dependent on Wnt signals, but display divergent identities. We find that, in this tissue, GATA transcription factors functionally interact with Wnt/{beta}-catenin signaling to drive differential cell identity. This occurs because GATA selectively repress Wnt target secretory-lineage genes in stem cells. Mechanistically, we found that GATA factors physically engage with the {beta}-catenin transcriptional complex, and that this association is mediated by the bridge protein BCL9/9L. Our work implicates GATA factors as context dependent modulators of the Wnt/{beta}-catenin transcription, shows that the GATA/BCL9 module acts as a switch at the crossroads of cell identity decision, and uncovers how this epithelium maintains the fine balance between self-renewal and differentiation.

developmental biology↗

bioRxiv2025

Temporal dynamics of neuroplasticity and neurodegeneration in the central auditory system following noise-induced hearing loss: A multimodal imaging and histological study

Noise-induced hearing loss (NIHL) is a sensorineural disorder that triggers profound neuroplastic and neurodegenerative consequences in the central auditory nervous system (CNS). This study examined how neuronal density, axonal integrity and glutamatergic and GABAergic neurotransmission are affected after acute overstimulation in the central inferior colliculus (CIC) and the ventral medial geniculate body of the thalamus (MGV). To achieve this, a correlative multimodal approach combining audiometric, magnetic resonance imaging (MRI) and histological biomarkers was performed. Adult mice were noise-exposed to broadband white noise (5-20 kHz) for 3 hours at either high (115 dB SPL) or moderate (90 dB SPL) intensity, while unexposed mice were used as controls. Separate cohorts of mice were investigated 1-, 7-, 56- and 84-days post-exposure using in vivo magnetic resonance imaging (MRI) techniques: Voxel-based morphometry (VBM) of gray matter density (GMD), diffusion MRI (dMRI) of microstructure and connectivity, and single-voxel proton magnetic resonance spectroscopy (1H-MRS) for glutamate and GABA quantification. Frequency-specific auditory brainstem responses (ABR) were recorded at 4, 8, 16 and 32 kHz before and after exposure to examine hearing threshold (HT) shifts. Following imaging, brains were processed for fluorescence immunohistochemistry (FIHC) targeting Neuronal Nuclear Protein (NeuN), 4,6-diamidino-2-fenilindo (DAPI), Neurofilament (SMI312), vesicular GABA transporter (VGAT), and vesicular glutamate transporters 1 (VGLUT1) and 2 (VGLUT2). HTs were significantly elevated 7d, 56d and 84d after 115 dB noise exposure, suggesting a NIHL phenotype. Neurofilament density significantly increased in the CIC and MGV 1d after 115 dB noise exposure, and returned to baseline at later time points. dMRI transient microstructural alterations were observed 7d after 90 dB noise exposure. Glutamate and GABA decreases 84d after 90 dB exposure were also detected. Moreover, correlation analysis between audiometric, histological and MRI datasets revealed scarce relationships between the investigated parameters. These findings advance our understanding of the CNS adaptations of NIHL and emphasizes the need for more sensitive and integrative approaches to identify robust biomarkers of central auditory dysfunction.

neuroscience↗

bioRxiv2025

Modulating Cardiac-Gut Microbiome Interaction Post-Myocardial Infarction with Engineered Bacteria

The gut microbiome plays a critical role in the pathophysiology of acute myocardial infarction (MI). MI events significantly impact intestinal integrity which results in leakage of bacterial products into the systemic circulation. We demonstrate that MI not only compromises intestinal integrity, leading to systemic leakage of bacterial products like LPS, but also results in the translocation and colonization of live, intact gut bacteria in the MI heart - a novel aspect of the heart-gut axis. Our initial findings with natural murine gut microbiome were substantiated using orally administered E. coli Nissle 1917 (EcN), as a tracer bacterium. Furthermore, we engineered EcN to express the microbial anti-inflammatory molecule (MAM) derived from the probiotic Faecalibacterium prausnitzii. Treatment with this engineered strain, EcN-MAM, led to significantly improved survival and cardiac function in MI mice. This was attributed to enhanced gut barrier integrity, resulting in reduced systemic bacterial permeation and subsequent inflammation. These findings shed light on a previously unrecognized dimension of the heart-gut axis and highlight the potential of microbiome-based interventions in MI management.

synthetic biology↗

bioRxiv2025

Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis

The increasing scale and complexity of neuroimaging datasets aggregated from multiple study sites present substantial analytic challenges, as existing statistical analysis tools struggle to handle missing voxel-data, suffer from limited computational speed and inefficient memory allocation, and are restricted in the types of statistical designs they are able to model. We introduce Image-Based Meta- & Mega-Analysis (IBMMA), a novel software package implemented in R and Python that provides a unified framework for analyzing diverse neuroimaging features, efficiently handles large-scale datasets through parallel processing, offers flexible statistical modeling options, and properly manages missing voxel-data commonly encountered in multi-site studies. IBMMA produced stronger effect sizes and revealed findings in brain regions that traditional software overlooked due to missing voxel-data resulting in gaps in brain coverage. IBMMA has the potential to accelerate discoveries in neuroscience and enhance the clinical utility of neuroimaging findings.

neuroscience↗

bioRxiv2025

Maternal obesity programs cardiac remodeling in offspring via epigenetic, metabolic, and immune dysregulations.

Maternal obesity during pregnancy predisposes the offspring to a high risk of developing cardiovascular and metabolic diseases later in life. This study investigated cardiac perturbations caused by maternal obesity by utilizing a mouse model of maternal high-fat diet (HFD)-induced obesity that recapitulates metabolic abnormalities observed in humans. Our study revealed that offspring of HFD-fed mothers (Off-HFD) exhibit a progression of obesity, dyslipidemia, and metabolic inflexibility when compared with offspring of regular diet-fed mothers (Off-RD). Deeper investigation of cardiac function revealed profound functional, metabolic, vascular, and immune perturbations in adult Off-HFD mice, with marked sex-specific differences. Although both male and female Off-HFD mice developed progressive cardiac hypertrophy, male offspring exhibited a more severe phenotype characterized by hypertension, increased vascular stiffness, impaired cardiac function, and myocardial fibrosis. To identify potential mechanisms underlying these changes, we performed DNA methylation analysis in collected hearts of newly weaned and adult offspring. This analysis revealed extensive, sex-dependent alterations in DNA methylation within or nearby genes involved in cardiac development, lipid metabolism, hypertrophic growth, and inflammatory signaling. Importantly, many of these epigenetic alterations persisted into adulthood, suggesting that maternal obesity establishes a durable molecular memory in the offspring heart. Consistent with these findings, transcriptome analysis of adult hearts revealed activation of gene programs associated with heart failure and pathological cardiac remodeling in male Off-HFD mice, whereas female Off-HFD mice showed activation of pathways consistent with adaptive or cardioprotective responses. Together, these findings demonstrate that maternal high fat diet induces early-life epigenetic remodeling in the offspring heart that persists into adulthood and is associated with sex-specific metabolic, functional, vascular, and immune dysregulations. By linking early epigenomic changes to adult cardiac disease susceptibility, this study identifies potential developmental windows for preventive and early therapeutic interventions aimed at reducing cardiovascular risk in offspring exposed to maternal obesity in utero.

molecular biology↗

bioRxiv2024

Fast skeletal myosin binding protein-C expression exacerbates dysfunction in heart failure

During heart failure, gene and protein expression profiles undergo extensive compensatory and pathological remodeling. We previously observed that fast skeletal myosin binding protein-C (fMyBP-C) is upregulated in diseased mouse hearts. While fMyBP-C shares significant homology with its cardiac paralog, cardiac myosin binding protein-C (cMyBP-C), there are key differences that may affect cardiac function. However, it is unknown if the expression of fMyBP-C expression in the heart is a pathological or compensatory response. We aim to elucidate the cardiac consequence of either increased or knockout of fMyBP-C expression. To determine the sufficiency of fMyBP-C to cause cardiac dysfunction, we generated cardiac-specific fMyBP-C over-expression mice. These mice were further crossed into a cMyBP-C null model to assess the effect of fMyBP-C in the heart in the complete absence of cMyBP-C. Finally, fMyBP-C null mice underwent transverse aortic constriction (TAC) to define the requirement of fMyBP-C during heart failure development. We confirmed the upregulation of fMyBP-C in several models of cardiac disease, including the use of lineage tracing. Low levels of fMyBP-C caused mild cardiac remodeling and sarcomere dysfunction. Exclusive expression of fMyBP-C in a heart failure model further exacerbated cardiac pathology. Following 8 weeks of TAC, fMyBP-C null mice demonstrated greater protection against heart failure development. Mechanistically, this may be due to the differential regulation of the myosin super-relaxed state. These findings suggest that the elevated expression of fMyBP-C in diseased hearts is a pathological response. Targeted therapies to prevent upregulation of fMyBP-C may prove beneficial in the treatment of heart failure. Significance StatementRecently, the sarcomere - the machinery that controls heart and muscle contraction - has emerged as a central target for development of cardiac therapeutics. However, there remains much to understand about how the sarcomere is modified in response to disease. We recently discovered that a protein normally expressed in skeletal muscle, is present in the heart in certain settings of heart disease. How this skeletal muscle protein affects the function of the heart remained unknown. Using genetically engineered mouse models to modulate expression of this skeletal muscle protein, we determined that expression of this skeletal muscle protein in the heart negatively affects cardiac performance. Importantly, deletion of this protein from the heart could improve heart function suggesting a possible therapeutic avenue.

physiology↗

bioRxiv2023

The Developmental Transcription Factor TBX3 Physically Engages with the Wnt/β-catenin Transcriptional Complex in Human Colorectal Cancer Cells to Regulate Metastasis Genes

Wnt signaling orchestrates gene expression in a plethora of processes during development and adult cell homeostasis via the action of nuclear {beta}-catenin. Furthermore, neoplasia of the colorectal epithelium begins with aberrant Wnt/{beta}-catenin signaling. Yet, little is known about how {beta}-catenin generates context-specific transcriptional outcomes. We have previously identified the developmental transcription factor TBX3 as a tissue-specific component of the Wnt/{beta}-catenin nuclear complex during mouse forelimb development. In this study, we show that TBX3 is present and functionally active in human colorectal cancers. TBX3s genomic binding pattern suggests a regulatory role that broadly coincides with that of Wnt/{beta}-catenin. Moreover, proteomics proximity labelling indicated that, during Wnt pathway activation, TBX3 is vicinal to several protein partners, including the transcription factors TCF/LEF and chromatin remodeling complexes which are usually found at Wnt responsive elements. Sequence and structure analysis revealed that TBX3 possesses an exposed Asp-Pro-Phe (NPF) motif predicted by AlphaFold2 Multimer to mediate direct interactions with several Wnt-activated TBX3 partners. Deletion of NPF abrogates TBX3 proximity to these partners and its ability to modulate Wnt-dependent transcription. TBX3 emerges as a key modulator of the oncogenic activity of Wnt/{beta}-catenin in colorectal cancer, and its mechanism of action exposes a novel druggable protein-interaction surface.

developmental biology↗

bioRxiv2023

The glucocorticoid receptor as a master regulator of Müller cell gliosis in the diabetic retina

Diabetic retinopathy (DR) is considered a primarily microvascular complication of diabetes. Muller glia cells are at the center of the retinal neurovascular unit and play a critical role in DR. We therefore investigated Muller cell-specific signaling pathways that are altered in DR to identify novel targets for gene therapy. Using a multi-omics approach on purified Muller cells from diabetic db/db mice, we found the mRNA and protein expression of the glucocorticoid receptor (GR) to be significantly decreased, while its target gene cluster was down-regulated. Further, oPOSSUM TF analysis and ATAC-sequencing identified the GR as a master regulator of Muller cell gliosis in DR. Cortisol not only increased GR phosphorylation. It also induced changes in the expression of known GR target genes in retinal explants. Finally, retinal functionality was improved by AAV-mediated overexpression of GR in Muller cells. Our study demonstrates an important role of the glial GR in DR and implies that therapeutic approaches targeting this signalling pathway should be aimed at increasing GR expression rather than the addition of more ligand. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/556478v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@c7869forg.highwire.dtl.DTLVardef@1574edforg.highwire.dtl.DTLVardef@fb1329org.highwire.dtl.DTLVardef@1a6ee60_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

FOX transcription factors are common regulators of Wnt/β-catenin signaling

The Wnt/{beta}-catenin signaling pathway is a critical regulator of development and stem cell maintenance. Mounting evidence suggests that the context-specific outcome of Wnt signaling is determined by the collaborative action of multiple transcription factors, including members of the highly conserved forkhead box (FOX) protein family. However, the contribution of FOX transcription factors to Wnt signaling has not been investigated in a systematic manner. Here, we performed uniform gain-of-function screens of all 44 human FOX transcription factors to identify and classify new regulators of the Wnt/{beta}-catenin pathway. By combining {beta}-catenin reporter assays with Wnt pathway-focused qPCR arrays and proximity proteomics of selected FOX family members, we determine that most FOX proteins are involved in the regulation of Wnt pathway activity and the expression of Wnt ligands and target genes. Moreover, as a proof of principle we characterize class D and I FOX transcription factors as physiologically relevant positive and negative regulators of Wnt/{beta}-catenin signaling, respectively. We conclude that FOX proteins are common regulators of the Wnt/{beta}-catenin pathway that may control the outcome of Wnt signaling in a tissue-specific manner.

cell biology↗

bioRxiv2022

The oncogene FOXQ1 is a selective activator of Wnt/β-catenin signalling

The forkhead box transcription factor FOXQ1 is aberrantly induced in various cancers, and contributes to tumour growth and metastasis. It has been suggested that FOXQ1 exacerbates cancer by activating the oncogenic Wnt/{beta}-catenin signalling pathway. However, the mode of action of FOXQ1 in the Wnt pathway remains to be resolved. Here, we report that FOXQ1 is a bimodal transcriptional activator of Wnt target gene expression in normal and cancer cells. Using co-immunoprecipitation, proximity proteomics, and reporter assays, we show that FOXQ1 engages the Wnt transcriptional complex to promote gene expression via TCF/LEF transcription factors. In parallel, FOXQ1 differentially regulates the expression of Wnt target genes independently of {beta}-catenin and TCF/LEFs, which is facilitated by spatially separated activator and repressor domains. Our results suggest that FOXQ1 is a novel component of the Wnt transcriptional complex that reinforces and specifies Wnt signalling in a context-dependent manner.

molecular biology↗

bioRxiv2021

A preclinical randomized multicenter trial of anti-IL-17A treatment for acute ischemic stroke

Multiple consensus statements have called for preclinical randomized controlled trials (pRCT) to improve translation in stroke research. Here, we investigated the efficacy of IL-17A neutralizing antibodies in a multicentric pRCT using a murine stroke model. C57/Bl.6 mice were subjected to transient middle cerebral artery occlusion (tMCAO). Mice were randomly allocated (1:1). Either anti-IL-17A (500 {micro}g) or isotype antibody (500 {micro}g) were administered 1 h after tMCAO. Primary analysis of infarct volumes was done by MRI after three days. Secondary analysis included mortality, neurological score, neutrophil infiltration and the impact of the gut microbiome on treatment effects. Out of 136 mice, 109 mice were included in the analysis. Mixed model analysis revealed that the IL-17A neutralization significantly reduced infarct sizes (anti IL-17A: 61.77 {+/-} 31.04 mm3; IgG control: 75.66 {+/-} 34.79 mm3; p=0.01). Secondary outcome measures showed a decrease in mortality (Hazard Ratio=3.43, 95% CI = 1.157 - 10.18; p=0.04) and neutrophil invasion into ischemic cortices. There was no difference in the neurological score. The analysis of the gut microbiome showed significant differences between centers. Taken together, this is the first positive pRCT in an ischemia reperfusion model. It suggests IL-17A neutralization as a potential target in stroke.

neuroscience↗

bioRxiv2021

Microglial refinement of spinal cord sensory circuitry regulates normal maturation of dynamic touch.

Sensory systems are shaped in postnatal life by the refinement of synaptic connections. In the dorsal horn of the spinal cord, sensory circuits undergo postnatal activity dependent reorganisation, including the retraction of primary afferent A-fibres from superficial to deeper laminae which is accompanied by decreases in cutaneous sensitivity. Here we show that microglia, the resident immune cells in the CNS, phagocytose A-fibre terminals in superficial laminae in the first weeks of life. Genetic perturbation of microglial engulfment at that time prevents the normal process of A-fibre retraction, resulting in increased sensitivity of dorsal horn cells to dynamic tactile cutaneous stimulation, and behavioural hypersensitivity to dynamic touch. Thus, functional microglia are necessary for normal postnatal development of dorsal horn sensory circuits. In the absence of microglial engulfment, superfluous A-fibre projections remain in the dorsal horn and the balance of sensory connectivity is disrupted, leading to lifelong hypersensitivity to dynamic touch. Impact statementMicroglia phagocytose superfluous A-fibres in the superficial spinal dorsal horn during normal development, the disruption of which leads to long term aberrant dynamic touch processing and behaviour.

neuroscience↗

bioRxiv2021

Structural Covariance Networks in Post-Traumatic Stress Disorder: A Multisite ENIGMA-PGC Study

IntroductionCortical thickness (CT) and surface area (SA) are established biomarkers of brain pathology in posttraumatic stress disorder (PTSD). Structural covariance networks (SCN) constructed from CT and SA may represent developmental associations, or unique interactions between brain regions, possibly influenced by a common causal antecedent. The ENIGMA-PGC PTSD Working Group aggregated PTSD and control subjects data from 29 cohorts in five countries (n=3439). MethodsUsing Destrieux Atlas, we built SCNs and compared centrality measures between PTSD subjects and controls. Centrality is a graph theory measure derived using SCN. ResultsNotable nodes with higher CT-based centrality in PTSD compared to controls were left fusiform gyrus, left superior temporal gyrus, and right inferior temporal gyrus. We found sex-based centrality differences in bilateral frontal lobe regions, left anterior cingulate, left superior occipital cortex and right ventromedial prefrontal cortex (vmPFC). Comorbid PTSD and MDD showed higher CT-based centrality in the right anterior cingulate gyrus, right parahippocampal gyrus and lower SA-based centrality in left insular gyrus. ConclusionUnlike previous studies with smaller sample sizes ([≤]318), our study found differences in centrality measures using a sample size of 3439 subjects. This is the first cross-sectional study to examine SCN interactions with age, sex, and comorbid MDD. Although limited to group level inferences, centrality measures offer insights into a nodes relationship to the entire functional connectome unlike approaches like seed-based connectivity or independent component analysis. Nodes having higher centrality have greater structural or functional connections, lending them invaluable for translational treatments like neuromodulation.

neuroscience↗

bioRxiv2021

Nano-CT characterization reveals coordinated growth of a rudimentary organ necessary for soldier development in the ant Pheidole hyatti

The growth of imaginal discs in holometabolous insects is coordinated with larval growth to ensure the symmetrical and proportional development of the adult appendages. In ants, the differential growth of these discs generates distinct castes - the winged male and queen castes and the wingless worker caste. In the hyperdiverse ant genus Pheidole, the worker caste is composed of two morphologically distinct subcastes: small minor workers and larger, big-headed soldiers. Although these worker subcastes are completely wingless, soldier larvae develop rudimentary forewing discs that are necessary for generating the disproportionate head-to-body scaling of the big-headed soldier subcaste. However, it remains unclear whether rudimentary forewing discs in soldier larvae are coordinated with other imaginal discs, and whether disc growth and coordination patterns vary between the minor worker and soldier subcastes. Here we show, using quantitative nano-CT three-dimensional analyses, that growth of the soldier rudimentary forewing discs is coordinated with the increase in volume of the leg and eye-antennal (head) discs as well as with larval size. We found that the growth rate of the rudimentary forewing discs differs from the leg discs but is similar to the growth of the head (eye-antennal) discs relative to larval size, suggesting that growth of each type of imaginal disc may be differentially regulated. In addition to their larger size, the soldier eye-antennal discs increase in width as they undergo morphogenesis to generate the characteristic shape of the large soldier head, suggesting that the rudimentary forewing discs may regulate their patterning in addition to their growth. Finally, we observe little growth of the leg and eye-antennal discs during the bipotential stage, while in minor worker development these discs grow at similar rates to one another in coordination with larval size to generate the smaller minor worker subcaste. Our results suggest that rudimentary organs with regulatory functions may participate in new patterns of inter-organ coordination and regulation to produce novel phenotypes and complex worker caste systems. We provide characterization of larval development and imaginal disc growth and morphogenesis with the aim of highlighting this as an emerging system for the study of rudimentary organs during development and evolution.

developmental biology↗

bioRxiv2020

Selective inhibition of histone deacetylase 1 and 3 improves motor phenotype and alleviates transcriptional dysregulation in Huntington's disease mice

Huntingtons disease (HD) is an autosomal dominant neurodegenerative disease characterized by a late clinical onset of psychiatric, cognitive, and motor symptoms. Transcriptional dysregulation is an early and central disease mechanism which is accompanied by epigenetic alterations in HD. Previous studies demonstrated that targeting transcriptional changes by inhibition of histone deacetylases (HDACs), especially the class I HDACs, provides therapeutic effects. Yet, their exact mechanisms of action and the features of HD pathology, on which these inhibitors act remain to be elucidated. Here, using transcriptional profiling, we found that selective inhibition of HDAC1 and HDAC3 by RGFP109 repaired the expression of a number of genes, including the transcription factor genes Neurod2 and Nr4a2, and 43% of the gene sets that were dysregulated by mutant Huntingtin expression in the striatum and improved motor skill learning deficit in the R6/1 mouse model of HD. RGFP109-treated R6/1 mice showed improved coordination on the RotaRod over four consecutive trials, while vehicle-treated R6/1 animals displayed no improvement in coordination skills and fell 50 seconds earlier off the rod in the fourth trial. We also found, by volumetric MRI, a widespread brain atrophy in the R6/1 mice at the symptomatic disease stage, on which RGFP109 showed a modest effect. Collectively, our combined work presents new evidence for specific HDAC1 and HDAC3 inhibition as a therapeutic strategy for alleviating the phenotypic and molecular features of HD.

neuroscience↗

bioRxiv2020

HLAssign 2.0: An advanced Graphical User Interface for the analysis of short and long read Human Leukocyte Antigen-typing data

Next Generation Sequencing (NGS) based Human Leukocyte Antigen (HLA) typing has been a challenge due to the polymorphism of the HLA region. Nevertheless, the methods accuracy has increased during the last years and it is now routinely used by many large centers including bone marrow registries. However, challenging HLA genotype compositions exist, which hinder a fully automated analysis. Therefore, HLA typing results are still visually inspected in diagnostics, i.e. the underlying read mappings and phasing information is controlled. Here, we present HLAssign 2.0 that now includes a strict workflow, improved tools for visual inspection and read phasing analysis in the automatic caller. In collaboration with interface design researchers, biologists and informaticians we developed an elaborate graphical user interface for visual evaluation of automated HLA calls for Illumina NGS reads. We also provide tools to preprocess 10x Genomics and PacBio sequencing reads for HLAssign analysis. We benchmarked our automatic caller against STC-seq and xHLA, showing comparable automatic call rates. Additional manual inspection of the automatic results in our GUI assists the user to assign the correct HLA calls and to achieve diagnostic accuracy. HLAssign 2.0 is free for research and commercial use and is available for Windows and MacOS.

bioinformatics↗

bioRxiv2019

MaxQuant software for ion mobility enhanced shotgun proteomics

Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides, proteins and posttranslational modification sites in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.

bioinformatics↗