Frank Edenhofer

• PhD. Prof. - Deputy Head
• Head Genomics, Stem Cells & Regenerative Medicine at University of Innsbruck

Generation of induced pluripotent stem cell (iPSCs) from adult skin fibroblasts and subsequent differentiation into somatic cells provides fascinating prospects for the derivation of autologous transplants that circumvent histocompatibility barriers. However, progression through a pluripotent state and subsequent complete differentiation into desir...

Parkinson’s disease, an aging-associated neurodegenerative disorder, is characterised by nigrostriatal pathway dysfunction caused by the gradual loss of dopaminergic neurons in the substantia nigra pars compacta of the midbrain. Human in vitro models are enabling the study of the dopaminergic neurons’ loss, but not the dysregulation within the dopa...

In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods used precomputed expression signatures covering limited cell types and tissues, second-generation tools use single-cell RNA sequencing data to build custom signatu...

The neurodevelopmental disorders Prader-Willi syndrome (PWS) and Schaaf-Yang syndrome (SYS) both arise from genomic alterations within human chromosome 15q11–q13. A deletion of the SNORD116 cluster, encoding small nucleolar RNAs, or frameshift mutations within MAGEL2 result in closely related phenotypes in individuals with PWS or SYS, respectively....

Schizophrenia (SCZ) is a neuropsychiatric disorder, caused by a combination of genetic and environmental factors. The etiology behind the disorder remains elusive although it is hypothesized to be associated with the aberrant response to neurotransmitters, such as dopamine and glutamate. Therefore, investigating the link between dysregulated metabo...

Acral burning pain triggered by fever, thermal hyposensitivity and skin denervation are hallmarks of small fibre neuropathy in Fabry disease, a life-threatening X-linked lysosomal storage disorder. Variants in the gene encoding alpha-galactosidase A may lead to impaired enzyme activity with cellular accumulation of globotriaosylceramide. To study t...

Background Similar to induced pluripotent cells (iPSCs), induced neural stem cells (iNSCs) can be directly converted from human somatic cells such as dermal fibroblasts and peripheral blood monocytes. While previous studies have demonstrated the resemblance of iNSCs to neural stem cells derived from primary sources and embryonic stem cells, respect...

Ehlers-Danlos syndrome (EDS) belongs to a spectrum of rare heritable connective tissue disorders and is characterised by hyperextensibility, joint hypermobility and tissue fragility. Peripheral blood mononuclear cells (PBMCs) from a vascular EDS (vEDS) patient, known as the rarest EDS subtype, carrying a heterozygous nonsense mutation c.430C > T (p...

Progressive multiple sclerosis (PMS) is characterized by a primary smoldering pathological disease process associated with a superimposed inflammatory activity. Cellular and molecular processes sustaining the pathobiology of PMS remain to be identified. We previously discovered senescence signatures in neural stem/progenitor cells (NSCs) from peopl...

Senescent neural progenitor cells have been identified in brain lesions of people with progressive multiple sclerosis (PMS). However, their role in disease pathobiology and contribution to the lesion environment remains unclear. By establishing directly induced neural stem/progenitor cell (iNSC) lines from PMS patient fibroblasts, we studied their...

Parkinsons disease (PD), one of the most common aging-associated neurodegenerative disorders, is characterised by nigrostriatal pathway dysfunction, caused by the gradual loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) of the midbrain and the dopamine depletion in the striatum. State of the art, human in vitro models are e...

Acral burning pain triggered by fever, thermal hyposensitivity, and skin denervation are hallmarks of small fibre neuropathy in Fabry disease, a life-threatening X-linked lysosomal storage disorder. Variants in the gene encoding alpha-galactosidase A may lead to impaired enzyme activity with cellular accumulation of globotriaosylceramide (Gb3). To...

Schizophrenia is a neuropsychiatric disorder, caused by a combination of genetic and environmental factors. Recently, metabolomic studies based on patients’ biofluids and post-mortem brain specimens have revealed altered levels of distinct metabolites between healthy individuals and patients with schizophrenia (SCZ). However, a putative link betwee...

Recent studies show an association of Parkin RBR E3 ubiquitin protein ligase (PARK2) copy number variations (CNVs) with attention deficit hyperactivity disorder (ADHD). The aim of our pilot study to investigate gene expression associated with PARK2 CNVs in human-derived cellular models. We investigated gene expression in fibroblasts, hiPSC and dopa...

Congenital hyperinsulinemic hypoglycemia (HH) is the most frequent cause of persistent and recurrent hypoglycemia. Peripheral mononuclear blood cells (PBMCs) from a patient diagnosed with HH, alongside autism-spectrum-disorder (ASD), carrying a heterozygous c.812T>A (L271H) mutation in the voltage-gated calcium channel subunit Cav1.3-encoding gene...

Parkinson's disease (PD) is a progressive, neurodegenerative disorder characterized by motor and non-motor symptoms. To date, no specific treatment to halt disease progression is available, only medication to alleviate symptoms can be prescribed. The main pathological hallmark of PD is the development of neuronal inclusions, positive for α-synuclei...

Alpha-synucleinopathies comprise progressive neurodegenerative diseases, including Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). They all exhibit the same pathological hallmark, which is the formation of α-synuclein positive deposits in neuronal or glial cells. The aggregation of α-synuclein in the ce...

Mitochondria play a key role in metabolic transitions involved in the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs), but the underlying molecular mechanisms remain largely unexplored. To obtain new insight into the mechanisms of cellular reprogramming, we studied the role of FAH domain-containing protein 1 (FAHD1) in th...

Sporadic Alzheimer’s disease (AD) exclusively affects elderly people. Using direct conversion of AD patient fibroblasts into induced neurons (iNs), we generated an age-equivalent neuronal model. AD patient-derived iNs exhibit strong neuronal transcriptome signatures characterized by downregulation of mature neuronal properties and upregulation of i...

Human induced pluripotent stem cells (hiPSCs) have revolutionized the generation of experimental disease models, but the development of protocols for the differentiation of functionally active neuronal subtypes with defined specification is still in its infancy. While dysfunction of the brain serotonin (5-HT) system has been implicated in the etiol...

Arrhythmogenic cardiomyopathy (ACM) is characterized by fibro-fatty replacement of the myocardium, heart failure and life-threatening ventricular arrhythmias. Causal mutations were identified in genes encoding for proteins of the desmosomes, predominantly plakophilin-2 (PKP2) and desmoglein-2 (DSG2). We generated gene-edited knock-out iPSC lines fo...

Fibroblasts isolated from a skin biopsy of a healthy 46-year-old female were infected with Sendai virus containing the Yamanaka factors to produce transgene-free human induced pluripotent stem cells (iPSCs). CRISPR/Cas9 was used to generate isogenic cell lines with a gene dose-dependent deficiency of CDH13, a risk gene associated with neurodevelopm...

The main goal of the present study was the identification of cellular phenotypes in attention-deficit-/hyperactivity disorder (ADHD) patient-derived cellular models from carriers of rare copy number variants (CNVs) in the PARK2 locus that have been previously associated with ADHD. Human-derived fibroblasts (HDF) were cultured and human-induced plur...

Treatment of terminal heart failure still poses a significant clinical problem. Cardiac tissue engineering could offer autologous solutions for the replacement of non-functional myocardial tissue. So far, soft matrix construction and missing large scale prevascularization prevented the application of sizeable cardiac repair patches. We developed a...

Spinal cord injury (SCI) is a debilitating neurological condition characterised by different cellular and molecular mechanisms that interplay in exacerbating the progression of the pathology. No fully restorative therapies are yet available, and it is thus becoming recognized that combinatorial approaches aimed at addressing different aspects of SC...

Multiple Sclerosis (MS) causes neurologic disability due to inflammation, demyelination, and neurodegeneration. Immunosuppressive treatments can modify the disease course but do not effectively promote remyelination or prevent long term neurodegeneration. As a novel approach to mitigate chronic stage pathology, we tested transplantation of mouse in...

Dilated cardiomyopathy with ataxia (DCMA) is an autosomal recessive disorder arising from mutations in DNAJC19. Two patient-derived dermal fibroblast cell lines of siblings with the same homozygous splice acceptor site mutation in DNAJC19 (NM_145261.4):c.130-1G>C were reprogrammed into induced pluripotent stem cell (iPSC) lines (LIBUCi001-A and LIB...

Within just over a decade, human reprogramming‐based disease modeling has developed from a rather outlandish idea into an essential part of disease research. While iPSCs are a valuable tool for modeling developmental and monogenetic disorders, their rejuvenated identity poses limitations for modeling age‐associated diseases. Direct cell‐type conver...

Induced pluripotent stem cells (iPSC) were derived from human dermal fibroblasts (HDF) of two siblings with small fiber neuropathy (SFN) potentially based on the same variation in SCN10A but exhibiting diverse disease phenotypes. HDF were reprogrammed using a non-integrating mRNA approach and showed robust expression of pluripotency markers. iPSC d...

We report the direct reprogramming of both adult human fibroblasts and blood cells into induced neural plate border stem cells (iNBSCs) by ectopic expression of four neural transcription factors. Self-renewing, clonal iNBSCs can be robustly expanded in defined media while retaining multilineage differentiation potential. They generate functional ce...

Genetic integrity of induced pluripotent stem cells (iPSCs) is essential for their validity as disease models and for potential therapeutic use. We describe the comprehensive analysis in the ForIPS consortium: an iPSC collection from donors with neurological diseases and healthy controls. Characterization included pluripotency confirmation, fingerp...

Rationale: Regeneration of lost cardiomyocytes is a fundamental unresolved problem leading to heart failure. Despite several strategies developed from intensive studies performed in the past decades, endogenous regeneration of heart tissue is still limited and presents a big challenge that needs to be overcome to serve as a successful therapeutic...

Human dermal fibroblasts (HDF) were isolated from the skin punch biopsy of a 25-year-old woman with Fabry disease (FD), carrying a heterozygous c.708 G > C missense mutation in the alpha-galactosidase A gene. HDF were reprogrammed to induced pluripotent stem cells (iPSC) using synthetic mRNA, preventing the alteration of the genome and retaining th...

Genetic integrity of induced pluripotent stem cells (iPSCs) is essential for their validity as disease models and for potential therapeutic use. We describe the comprehensive analysis in the ForIPS consortium: an iPSC collection from donors with neurological diseases and healthy controls. Characterization included pluripotency confirmation, fingerp...

Background: Recent developments in cellular reprogramming technology enable the production of virtually unlimited numbers of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). Although hiPSC-CM share various characteristic hallmarks with endogenous cardiomyocytes, it remains a question as to what extent metabolic characteristic...

Mitochondria are a major target for aging and are instrumental in the age-dependent deterioration of the human brain, but studying mitochondria in aging human neurons has been challenging. Direct fibroblast-to-induced neuron (iN) conversion yields functional neurons that retain important signs of aging, in contrast to iPSC differentiation. Here, we...

Table S1. Unbiased LC-MS Analysis of Matched CSF and Plasma Metabolites from EAE Mice, Related to Figure 1 (A) Expression matrix of the metabolic changes in the CSF. (B) Expression matrix of the metabolic changes in the plasma. Colored rectangles indicate p ≤ 0.05 (red indicates that the mean values are significantly higher for that comparison; gr...

Table S3. Unbiased LC-MS Analysis of the Extracellular and Intracellular Metabolic Content of Type 1 Inflammatory Mφs In Vitro, Related to Figure 2 (A) Expression matrix of the intracellular metabolic changes (INTRA_Metab) in MφLPS. (B) Expression matrix of the extracellular metabolic changes (EXTRA_Metab) in MφLPS. (C) Expression matrix of the in...

Table S2. Gene Expression Microarrays of Type 1 Inflammatory Mφs In Vitro, Related to Figure 2 (A) Expression matrix of the microarray intensities for Mφ, MφLPS, MφLPS-iNSCs or MφLPS-NSCs. (B) Results of differential expression analysis for MφLPS versus Mφ. (C and D) Results of differential expression analysis for MφLPS-iNSCs (C) or MφLPS-NSCs ver...

Table S4. Gene Expression Microarrays of NSCs and Sucnr1−/− NSCs after Succinate Treatment, Related to Figure 4 (A) Expression matrix of the microarray intensities for NSCs and Sucnr1−/− NSCs either untreated (UT) or stimulated with Succinate (Succ). (B–D) Results of differential expression analysis of Sucnr1−/− NSC_UT versus NSC_UT (B), NSCsSucc...

Neural stem cell (NSC) transplantation can influence immune responses and suppress inflammation in the CNS. Metabolites, such as succinate, modulate the phenotype and function of immune cells, but whether and how NSCs are also activated by such immunometabolites to control immunoreactivity and inflammatory responses is unclear. Here, we show that t...

Neural stem cell (NSC) transplantation can influence immune responses and suppress inflammation in the central nervous system (CNS). Metabolites such as succinate modulate the phenotype and function of immune cells, but whether and how NSCs are also activated by such immunometabolites to control immunoreactivity and inflammatory responses is unclea...

This image shows a dopaminergic neuron immunostained for cytosolic tyrosine hydroxylase (red), plasma-membrane-bound dopamine transporter (green), and nuclear DAPI staining (blue). The neuron was generated from BMP5/7-treated human induced pluripotent stem cells. The BMP/SMAD pathway has a critical role in the formation of dopaminergic neurons in v...

Fibroblasts were isolated from a skin biopsy of a clinically diagnosed 51-year-old female attention-deficit/hyperactivity disorder (ADHD) patient carrying a duplication of SLC2A3, a gene encoding neuronal glucose transporter-3 (GLUT3). Patient fibroblasts were infected with Sendai virus, a single-stranded RNA virus, to generate transgene-free human...

The embryonic formation of midbrain dopaminergic (mDA) neurons in vivo provides critical guidelines for the in vitro differentiation of mDA neurons from stem cells, which are currently being developed for Parkinson’s disease cell replacement therapy. Bone morphogenetic protein (BMP)/SMAD inhibition is routinely used during early steps of stem cell...

Medullary thymic epithelial cell (mTEC)-restricted expression of autoimmune regulator (Aire) is essential for establishment of immune tolerance. Recently, Aire was also shown to be expressed in cells of hematopietic and reproductive lineages. Thus, the generation of Airefl/fl mouse strain enables the investigation of the cell-specific function of A...

3D reconstruction of triple IF of 5-HT, RC2, and Cdh13. Movies illustrating 3D reconstruction using Imaris. 5-HT-positive neurons are labeled in blue, RC2-fibers are labeled in red and Cdh13 immunofluorescence is represented in green.

Counting of 5-HTT-ir fibers in the prefrontal cortex. (A) Illustrations of selected areas used for the counting of 5-HTT-ir fibers in the infralimbic (IL) and cingulate (CG) cortices. A grid of 70*70 μm (red) containing three yellow lines with intervals of 17.5 μm was placed over the binary image. (B) Example of the intensity profile of the measure...

Background: During early prenatal stages of brain development, serotonin (5-HT)-specific neurons migrate through somal translocation to form the raphe nuclei and subsequently begin to project to their target regions. The rostral cluster of cells, comprising the median and dorsal raphe (DR), innervates anterior regions of the brain, including the pr...

The production of human induced pluripotent stem cells (hiPSCs) in quantities that are relevant for cell-based therapies and cell-loaded implants through standard adherent culture is hardly achievable and lacks process scalability. A promising approach to overcoming these hurdles is the culture of hiPSCs in suspension. In this study, stirred suspen...

Document S1. Supplemental Experimental Procedures, Figures S1 and S2, and Tables S1–S5

In vitro models of the human blood-brain barrier (BBB) are highly desirable for drug development. This study aims to analyze a set of ten different BBB culture models based on primary cells, human induced pluripotent stem cells (hiPSCs), and multipotent fetal neural stem cells (fNSCs). We systematically investigated the impact of astrocytes, pericy...

Although there are improvements in acute care, ischemic heart disease is the major cause of death worldwide. As a treatment for heart failure or heart infarction, stem cell therapies emerged as a potential therapeutic option. First results have shown moderate improvements and have revealed several limitations, such as an insufficient retention, hom...

Gap junctional intercellular communication (GJIC) has been suggested to be involved in early embryonic development but the actual functional role remained elusive. Connexin (Cx) 43 and Cx45 are co-expressed in embryonic stem (ES) cells, form gap junctions and are considered to exhibit adhesive function and/or to contribute to the establishment of d...

Until a decade ago it was believed that the wall of adult blood vessels exclusively contains terminally differentiated cell types. A paradigm shift was unavoidable since studies from different groups convincingly showed the presence of vascular wall-resident stem and progenitor cells (VW-SCs) which were identified to particularly reside in the sub-...

In this poster recent findings on the characterization of novel human neural precursor cells derived from embryonic brain tissue were presented and discussed.

Objective: The induction of neural stem cells (NSCs) from human induced pluripotent stem cells (hiPSCs) developed into an important strategy to derive patient-specific neuronal and glial cells. Several neural differentiation protocols have been developed mainly involving laborious experimentation such as embryoid body (EB) formation or manual neura...

The LDL family of receptors and its member low-density lipoprotein receptor-related protein 1 (LRP1) have classically been associated with a modulation of lipoprotein metabolism. Current studies, however, indicate diverse functions for this receptor in various aspects of cellular activities, including cell proliferation, migration, differentiation,...

Mouse embryonic stem cells (ESCs) are maintained in a naive ground state of pluripotency in the presence of MEK and GSK3 inhibitors. Here, we show that ground-state ESCs express low Myc levels. Deletion of both c-myc and N-myc (dKO) or pharmacological inhibition of Myc activity strongly decreases transcription, splicing, and protein synthesis, lead...

Table S1. Number of cDNA Sequenced Fragments per Sample per Gene, Related to Figure 2 Each column of the matrix represents a sample and each row represents one gene. The matrix is filled with the number of reads that were tabulated to each gene based on the genomic coordinates of both the read alignments to the reference genome and the annotation...

Data S1. Workflow for RNA-Seq Analysis, Related to Figure 2 and Supplemental Experimental Procedures

Mouse embryonic stem cells (ESCs) are maintained in a naive ground state of pluripotency in the presence of MEK and GSK3 inhibitors. Here, we show that ground-state ESCs express low Myc levels. Deletion of both c-myc and N-myc (dKO) or pharmacological inhibition of Myc activity strongly decreases transcription, splicing, and protein synthesis, lead...

A comprehensive analysis of the molecular network of cellular factors establishing and maintaining pluripotency as well as self renewal of pluripotent stem cells is key for further progress in understanding basic stem cell biology. Nanog is necessary for the natural induction of pluripotency in early mammalian development but dispensable for both,...

A comprehensive analysis of the molecular network of cellular factors establishing and maintaining pluripotency as well as self renewal of pluripotent stem cells is key for further progress in understanding basic stem cell biology. Nanog is necessary for the natural induction of pluripotency in early mammalian development but dispensable for both i...

Direct cell conversion developed into an important paradigm for generating cells with enhanced differentiation capability. We combined a transcription factor-based cell fate conversion strategy with the use of pharmacological compounds to derive early neuroepithelial progenitor cells from developmentally more restricted radial glia type neural stem...

Generation of induced pluripotent stem cell (iPSCs) from adult skin fibroblasts and subsequent differentiation into somatic cells provides fascinating prospects for the derivation of autologous transplants that circumvent histocompatibility barriers. However, progression through a pluripotent state and subsequent complete differentiation into desir...

Cellular reprogramming holds immense potential for both, regenerative medicine and developmental biology. Transcription factor-driven reprogramming of somatic cells such as fibroblasts has been shown to allow derivation of induced pluripotent stem (iPS) cells and more recently also other somatic cells including neurons, cardiomyocytes, as well as h...

The biological phenomenon of cell fusion plays an important role in several physiological processes, like fertilization, placentation, or wound healing/tissue regeneration, as well as pathophysiological processes, such as cancer. Despite this fact, considerably less is still known about the factors and conditions that will induce the merging of two...

Various strategies have been published enabling cardiomyocyte differentiation of human induced pluripotent stem (iPS) cells. However the complex nature of signaling pathways involved as well as line-to-line variability compromises the application of a particular protocol to robustly obtain cardiomyocytes from multiple iPS lines. Hence it is necessa...

Recent data suggest that cell-cell fusion contributes to the development of hybrid cell clones showing genetic and behavioural alterations. But less is known about forces triggering cell fusion processes between breast cancer cells and tumor surrounding cells. The influence of chronic inflammation and tumor microenvironment is increasingly being re...

Integrating viruses represent robust tools for cellular reprogramming, however, the presence of viral transgenes in induced pluripotent stem cells (iPSCs) is deleterious as it holds the risk of insertional mutagenesis leading to malignant transformation. Here, we combine the robustness of lentiviral reprogramming with the efficacy of Cre recombinas...

A comprehensive understanding of the functional network of transcription factors establishing and maintaining pluripotency is key for the development of biomedical applications of stem cells. Nanog plays an important role in early development and is essential to induce natural pluripotency in embryonic stem cells (ESCs). Inducible gain-of-function...

Oct4 is a transcription factor that plays a major role for the preservation of the pluripotent state in embryonic stem cells as well as for efficient reprogramming of somatic cells to induced pluripotent stem cells (iPSC) or other progenitors. Protein-based reprogramming methods mainly rely on the addition of a fused cell penetrating peptide. This...

Recent studies demonstrate that mammalian cells can be artificially reprogrammed by ectopic expression of transcription factors in an unforeseen straightforward manner. Patient-derived reprogrammed cells hold great potential for biomedical applications such as cell replacement therapy, drug toxicity studies and disease modeling. Somatic cells such...

Recent reports demonstrate that the plasticity of mammalian somatic cells is much higher than previously assumed and that ectopic expression of transcription factors may have the potential to induce the conversion of any cell type into another. Fibroblast cells can be converted into embryonic stem cell-like cells, neurons, cardiomyocytes, macrophag...