Tobias A. Beyer

Functional Genomics Reveals a BMP-Driven Mesenchymal-to-Epithelial Transition in the Initiation of Somatic Cell Reprogramming

Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by expression of defined embryonic factors. However, little is known of the molecular mechanisms underlying the reprogramming process. Here we explore somatic cell reprogramming by exploiting a secondary mouse embryonic fibroblast model that forms iPSCs with high efficiency upon inducible expression of Oct4, Klf4, c-Myc, and Sox2. Temporal analysis of gene expression revealed that reprogramming is a multistep process that is characterized by initiation, maturation, and stabilization phases. Functional analysis by systematic RNAi screening further uncovered a key role for BMP signaling and the induction of mesenchymal-to-epithelial transition (MET) during the initiation phase. We show that this is linked to BMP-dependent induction of miR-205 and the miR-200 family of microRNAs that are key regulators of MET. These studies thus define a multistep mechanism that incorporates a BMP-miRNA-MET axis during somatic cell reprogramming. PAPERCLIP:

Impaired liver regeneration in Nrf2 knockout mice: role of ROS‐mediated insulin/IGF‐1 resistance

The liver is frequently challenged by surgery‐induced metabolic overload, viruses or toxins, which induce the formation of reactive oxygen species. To determine the effect of oxidative stress on liver regeneration and to identify the underlying signaling pathways, we studied liver repair in mice lacking the Nrf2 transcription factor. In these animals, expression of several cytoprotective enzymes was reduced in hepatocytes, resulting in oxidative stress. After partial hepatectomy, liver regeneration was significantly delayed. Using in vitro and in vivo studies, we identified oxidative stress‐mediated insulin/insulin‐like growth factor resistance as an underlying mechanism. This deficiency impaired the activation of p38 mitogen‐activated kinase, Akt kinase and downstream targets after hepatectomy, resulting in enhanced death and delayed proliferation of hepatocytes. Our results reveal novel roles of Nrf2 in the regulation of growth factor signaling and in tissue repair. In addition, they provide new insight into the mechanisms underlying oxidative stress‐induced defects in liver regeneration. These findings may provide the basis for the development of new strategies to improve regeneration in patients with acute or chronic liver damage.

The Nrf2 transcription factor protects from toxin-induced liver injury and fibrosis

The liver is frequently exposed to insults, including toxic chemicals and alcohol, viral infection or metabolic overload. Although it can fully regenerate after acute injury, chronic liver damage causes liver fibrosis and cirrhosis, which can result in complete liver failure. In this study, we demonstrate that the NF-E2-related factor 2 (Nrf2) transcription factor protects the liver from acute and chronic toxin-mediated damage. Repair of the liver injury that occurs after a single treatment with the hepatotoxin carbon tetrachloride (CCl4) was severely delayed in Nrf2-deficient mice. The defect in repair was accompanied by an enhanced and prolonged inflammatory and profibrotic response. After long-term CCl4 treatment, liver fibrosis was strongly aggravated in the Nrf2 knockout mice and inflammation was enhanced. We demonstrate that these abnormalities are at least in part due to the reduced expression of known and novel Nrf2 target genes in hepatocytes, which encode enzymes involved in the detoxification of CCl4 and its metabolites. These results suggest that activation of Nrf2 may be a novel strategy to prevent or ameliorate toxin-induced liver injury and fibrosis.

Nrf transcription factors in keratinocytes are essential for skin tumor prevention but not for wound healing.

ABSTRACT The Nrf2 transcription factor is a key player in the cellular stress response through its regulation of cytoprotective genes. In this study we determined the role of Nrf2-mediated gene expression in keratinocytes for skin development, wound repair, and skin carcinogenesis. To overcome compensation by the related Nrf1 and Nrf3 proteins, we expressed a dominant-negative Nrf2 mutant (dnNrf2) in the epidermis of transgenic mice. The functionality of the transgene product was verified in vivo using mice doubly transgenic for dnNrf2 and an Nrf2-responsive reporter gene. Surprisingly, no abnormalities of the epidermis were observed in dnNrf2-transgenic mice, and even full-thickness skin wounds healed normally. However, the onset, incidence, and multiplicity of chemically induced skin papillomas were strikingly enhanced, whereas the progression to squamous cell carcinomas was unaltered. We provide evidence that the enhanced tumorigenesis results from reduced basal expression of cytoprotective Nrf target genes, leading to accumulation of oxidative damage and reduced carcinogen detoxification. Our results reveal a crucial role of Nrf-mediated gene expression in keratinocytes in the prevention of skin tumors and suggest that activation of Nrf2 in keratinocytes is a promising strategy to prevent carcinogenesis of this highly exposed organ.

Roles and mechanisms of action of the Nrf2 transcription factor in skin morphogenesis, wound repair and skin cancer

Roles and mechanisms of action of the Nrf2 transcription factor in skin morphogenesis, wound repair and skin cancer

Fibroblast growth factor 22 and its potential role during skin development and repair.

We have isolated, using RT-PCR, a cDNA from mouse skin wounds that encodes fibroblast growth factor (FGF) 22, a recently discovered member of the FGF family, which is closely related to FGF-7 and FGF-10. Transient expression of tagged FGF-22 protein in COS-1 and MCF-7 cells revealed that the protein was present within the cell and at the cell surface but was not apparently released from the cell. Analysis of RNA expression revealed that FGF-22 transcripts were not detected in the developing mouse embryo until day E16.5 and in the adult mouse it was expressed in the brain, tongue, and skin, but not in other tissues examined. After skin injury, FGF-22 mRNA levels were slightly down-regulated within the first 5 days after wounding, but expression increased strongly at the later stages of the repair process. In situ hybridization revealed the presence of FGF-22 mRNA throughout the epidermis and hair follicle keratinocytes of E16.5 embryos, as well as in adult skin and keratinocytes of the hyperthickened wound epithelium. This expression pattern suggests a potential role for FGF-22 in cutaneous development and repair.

The TGFβ superfamily in stem cell biology and early mammalian embryonic development

BACKGROUND Members of the Transforming Growth Factor-beta (TGFβ) superfamily of cytokines are essential for early embryonic development and play crucial roles in pluripotency and differentiation of embryonic stem cells in vitro. SCOPE OF REVIEW In this review, we discuss how TGFβ family signals are read by cells and how they are modulated by the cellular context. Furthermore, we review recent advances in our understanding of TGFβ function in embryonic stem cells and point out hot topics at the intersection of TGFβ signaling and stem cell biology fields. MAJOR CONCLUSION TGFβ family signals are essential for early mammalian development and the importance of this pathway is reflected in pluripotent stem cells derived from the mammalian embryo. GENERAL SIGNIFICANCE Understanding signaling pathways underlying pluripotency and cell fate specification holds promises for the advent of personalized regenerative medicine. This article is part of a Special Issue entitled Biochemistry of Stem Cells.

The cytoprotective Nrf2 transcription factor controls insulin receptor signaling in the regenerating liver

The Nrf2 transcription factor is a crucial regulator of the cellular redox homeostasis through its capacity to induce the expression of enzymes, which detoxify reactive oxygen species, and of other antioxidant proteins. Therefore, it plays an important role in the protection from carcinogenesis induced by various insults. In addition, recent results identified a novel role of Nrf2 in tissue repair. In the liver, regeneration after partial hepatectomy was strongly delayed in the absence of Nrf2. This defect was shown to result from transient resistance to insulin and insulin-like growth factor 1 that was caused by chronic oxidative stress in hepatocytes. These results demonstrate a link between Nrf2 deficiency, oxidative stress and insulin resistance, and suggest that activation of this transcription factor could be a novel strategy to improve liver regeneration in patients with acute or chronic liver injury. In addition, it may help to alleviate oxidative stress-induced insulin resistance in the liver and potentially also in other organs.

Fibroblast growth factor receptor 1-IIIb is dispensable for skin morphogenesis and wound healing.

Alternative splicing in the extracellular domain is a characteristic feature of members of the fibroblast growth factor receptor (FGFR) family. This splicing event generates receptor variants, which differ in their ligand binding specificities. A poorly characterized splice variant is FGFR1-IIIb, recently found to be a functional FGF receptor predominantly expressed in the skin. Here we show that FGFR1-IIIb is expressed in normal and wounded mouse skin. Reduced expression of this type of receptor was found in wounds of healing-impaired genetically diabetic mice, suggesting that downregulation of FGFR1-IIIb is associated with wound healing defects. To address this possibility, we deleted the IIIb exon of FGFR1 in mice. The lack of FGFR-IIIb did not alter the expression of either FGFR1-IIIc, other FGF receptor genes or of FGFR1-IIIb ligands in normal and wounded skin. Histological analysis of the skin of FGFR1-IIIb knockout animals did not reveal any obvious abnormalities. Furthermore, full-thickness excisional skin wounds in these mice healed normally and no defects could be observed at the macroscopic or histological level. Finally, several genes that encode key players in wound repair were normally expressed in these animals. These data demonstrate that FGFR1-IIIb is dispensable for skin development and wound repair.

Comparative analysis of differential gene expression tools for RNA sequencing time course data

Abstract RNA sequencing (RNA‐seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past decades, RNA‐seq time course (TC) DE analysis algorithms are still in their early stages. In this study, we compare, for the first time, existing TC RNA‐seq tools on an extensive simulation data set and validated the best performing tools on published data. Surprisingly, TC tools were outperformed by the classical pairwise comparison approach on short time series (<8 time points) in terms of overall performance and robustness to noise, mostly because of high number of false positives, with the exception of ImpulseDE2. Overlapping of candidate lists between tools improved this shortcoming, as the majority of false‐positive, but not true‐positive, candidates were unique for each method. On longer time series, pairwise approach was less efficient on the overall performance compared with splineTC and maSigPro, which did not identify any false‐positive candidate.