Newts have the incredible ability to regenerate many different organs and tissues as adults, including the limbs. Limb regeneration occurs via the dedifferentiation of stump tissue and the formation of a blastema, which provides the majority of cells for the regenerate. Despite all that we have learned about dedifferentiation and blastema formation, the cellular and molecular mechanisms underlying these processes are still poorly understood. We used representational difference analysis (RDA) to identify genes involved in the early dedifferentiation process in newt forelimb regeneration. Our analysis identified approximately 410 unique genes that were differentially regulated during this process. Microarray analysis was used to determine the expression profile of these genes throughout limb and tail regeneration. We used quantitative PCR (qPCR) to validate the expression of a subset of these genes [β-catenin, wntless, dapper, thymosin-β 4 (Tβ4), and thymosin-β 10/15 (Tβ10/15)] in regenerating limb and tail tissue, as well as in differentiating newt myoblasts. We also verified the expression of these genes in the regenerating newt limb using immunohistochemistry (IHC) and in situ hybridization (ISH). Finally, we performed a functional analysis on β-catenin, wntless, dapper, and Tβ4 by overexpressing these genes in mouse myoblasts to examine their effects on differentiation and potential roles in dedifferentiation. Quantitative PCR verified the expression of β-catenin, wntless, dapper, and Tβ4 during limb regeneration and IHC/ISH localized the β-catenin and Tβ4 proteins to the blastema during regeneration. Tβ10/15 was shown by qPCR to be expressed in the tail during regeneration. Overexpression of newt β-catenin, wntless, dapper, and Tβ4 in mouse myoblasts showed that each of these genes has an inhibitory effect on the differentiation of myoblasts into myotubes and, therefore, may play a role in promoting or maintaining the dedifferentiated state. Our work has identified a large number of genes with potential roles in regulating the dedifferentiation process during newt forelimb regeneration. We have also laid a framework from which much more work can be done by drawing on the genes we have identified and the microarray data, which indicate ideal follow-up candidates. Our analysis of specific genes has also increased our understanding of the molecular events occurring during the dedifferentiation process in the regenerating newt limb.

The present thesis is a contribution to unravel the molecular mechanisms that underlie urodele regeneration. Urodele amphibians (newts and salamanders) are among the few vertebrates with the remarkable ability to regenerate lost body appendages, like the limbs and the tail. Urodele tail and limb regeneration occurs via blastemal epimorphic regeneration. A blastema is a mound of progenitor cells that accumulates at the amputation plane and eventually gives rise to the missing structures. It is known today that dedifferentiating muscle fibers at the amputation plane contribute to the blastema cell pool, but how this process occurs on the cellular and molecular level is hardly understood, which is in part due to the lack of molecular methods to test gene function in urodeles. Furthermore, little is known about how coordinated growth and patterning occurs during urodele regeneration, and if the patterning mechanisms in regeneration are related to the ones in development. The goal of this study was to better understand these processes on the molecular level. To address these questions, I first established several methods in our model systems, which are the mexican salamander Ambystoma mexicanum (axolotl) and a cell line derived from the newt Notophthalmus viridescens. In order to monitor gene expression on a cellular level during regeneration, I worked out a good in situ hybridization protocol on axolotl tissue cryosections. To be able to test gene function, I established electroporation conditions to both overexpress genes in the cultured newt cells and to deliver morpholinos into axolotl cells in vivo and newt cells in culture. I demonstrate here that morpholinos are an effective tool to downregulate protein expression in urodele cells in vivo and in culture. Testing the role of two candidate genes in muscle fiber dedifferentiation, the homeobox containing transcription factor Msx1 and Rad, a GTP-binding protein of a new Ras-related protein family, revealed that neither seems to play a major role in muscle dedifferentiation, both in culture and in vivo. In addition to testing gene function I have examined the muscle dedifferentiation process in more detail. I show here that dedifferentiating muscle fiber nuclei undergo morphological changes that are likely due to chromatin remodeling events. I also demonstrate that the axolotl spinal cord expresses embryonic dorsoventral (d/v) patterning markers of the neural tube. The transcription factors Msx1, Pax7 and Pax6 are expressed in their respective d/v domains in both the differentiated and the regenerating axolotl spinal cord. Furthermore, the secreted signaling molecule sonic hedgehog (Shh) is expressed in the floor plate in both the differentiated and the regenerating cord. Using a chemical inhibitor (cyclopamine) and an activator of the hedgehog pathway, I discovered that hedgehog signaling is required for overall tail regeneration. Blocking hedgehog signaling does not only result in d/v patterning defects of the regenerating spinal cord, but it also strongly reduces blastema cell proliferation. In addition, I identified cartilage and putative muscle progenitor cells in the blastema, marked by the expression of the transcription factors Sox9 and Pax7, respectively. Both progenitor populations are reduced in the blastema in the absence of hedgehog signaling. The continuous expression of marker genes for embryonic progenitor cell domains in the mature axolotl may be related to their ability to regenerate.

Urodele amphibians have the remarkable ability to re-grow lost body parts. This regenerative response after injury in urodeles involves dedifferentiation of fully differentiated cells into proliferative cells. One well-studied example of this is the dedifferentiation of multinucleated muscle cells into mononucleate cells resembling their precursors, the myoblasts. To form these mononucleate cells the differentiated myotubes in vivo must re-enter and complete the cell cycle; they again proliferate and produce progeny. A key question is what factors induce the myotubes to re-enter the cell cycle and proliferate. Early events of cell cycle re-entry can be studied in the A1 cell line, a myogenic cell line isolated from the Notophthalmus viridescens hindlimb, which traverses cell cycle until G2 in response to serum. In particular, it was found that thrombin cleavage induces a factor in serum of all animals tested so far to promote S phase re-entry in A1 myotubes. We have used this S phase re-entry of the A1 cell line to purify the serum activity and developed a 5-step purification protocol that enriches the activity almost 2 000 fold over the starting material, or 40 000 fold over serum. To conveniently produce and test potential candidates for their ability to induce S phase re-entry in A1 myotubes, we also developed an overexpression- and purification system for emerging candidates. Candidates were then tested for this activity with or without prior incubation with thrombin. We identified Bmp proteins as the first pure molecules that were found in fractions across the purification of the activity and that could also induce cell cycle re-entry in a dose-dependent manner when recombinantly added to the A1 myotubes. Furthermore, this response could be blocked in a dose-dependent manner by the known bmp-inhibitor noggin. Finally, we showed that inhibition of Bmp signaling in vivo causes defects in axolotl tail regeneration.

Somatic cells could be reprogrammed into an ES-like state called induced pluripotent stem cells (iPSCs) by expression of four transcriptional factors: Oct4, Sox2, Klf4 and cMyc. iPSCs have full potentials to generate cells of all lineages and have become a valuable tool to understand human development and disease pathogenesis. However, reprogramming process suffers from extremely low efficiency and the molecular mechanism remains poorly understood. This dissertation is focused on studying the role of small non-coding RNAs (microRNAs) and kinases during the reprogramming process in order to understand how it is regulated and why only a small percentage of cells could achieve fully reprogrammed state. We demonstrate that loss of microRNA biogenesis pathway abolished the potential of mouse embryonic fibroblasts (MEFs) to be reprogrammed and revealed that several clusters of mES-specific microRNAs were highly induced by four factors during early stage of reprogramming. Among them, miR-93 and 106b were further confirmed to enhance iPSC generation by promoting mesenchymal-to-epithelial transition (MET) and targeting key p53 and TGFβ pathway components: p21 and Tgfbr2, which are important barrier genes to the process. To expand our view of microRNAs function during reprogramming, a systematic approach was used to analyze microRNA expression profile in iPSC-enriched early cell population. From a list of candiate microRNAs, miR-135b was found to be most highly induced and promoted reprogramming. Subsequent analysis revealed that it targeted an extracellular matrix network by directly modulating key regulator Wisp1. By regulating several downstream ECM genes including Tgfbi, Nov, Dkk2 and Igfbp5, Wisp1 coordinated IGF, TGFβ and Wnt signaling pathways, all of which were strongly involved in the reprogramming process. Therefore, we have identified a microRNA-regulated network that modulates somatic cell reprogramming, involving both intracellular and extracellular networks. In addition to microRNAs, in order to identify new regulators and signaling pathways of reprogramming, we utilized small molecule kinase inhibitors. A collection of 244 kinase inhibitors were screened for both enhancers and inhibitors of the process. We identified that inhibition of several novel kinases including p38, IP3K and Aurora kinase could significantly enhance iPSC generation, the effects of which were also confirmed by RNAi of specific target genes. Further characterization revealed that inhibition of Aurora A kinase enhanced phosphorylation and inactivation of GSK3β, a process mediated by Akt kinase. All together, in this dissertation, we have identified novel role of both small non-coding RNAs and kinases in regulating the reprogramming of MEFs to iPSCs.

No description available.

In contrast to mammals, some fish and amphibians have retained the ability to regenerate complex body structures or organs, such as the limb, the tail, the eye lens or even parts of the heart. One major difference in the response to injury is the appearance of a mesenchymal growth zone or blastema in these regenerative species instead of the scarring seen in mammals. This blastema is thought to largely derive from the dedifferentiation of various functional cell types, such as skeletal muscle, skin and cartilage. In the case of multinucleated skeletal muscle fibres, cell cycle re-entry into S-phase as well as fragmentation into mononucleated progenitors is observed both in vitro and in vivo. In order to identify molecules that initiate dedifferentiation of cells at the wound site in amphibians we have established a cellular assay with a cultured newt myogenic cell line. Using this assay we have found a serum activity that stimulates cell cycle re-entry in differentiated multinucleated newt myotubes. The activity is present in serum of all mammalian species tested so far and, interestingly, thrombin proteolysis amplifies the activity from both serum and plasma. We think this serum factor provides a link between wounding and regeneration and its identification will be a key step in understanding the remarkable differences in wound healing between mammals and amphibians. In the course of this PhD thesis we have characterized the serum factor as a thermo-labile, pH- and proteinase K-sensitive, high molecular weight protein that is resistant to denaturing conditions such as SDS, urea or organic solvents. Surprisingly, under denaturing conditions the activity behaves as a low molecular weight protein that displays charge heterogeneity on isoelectric focusing. Using these characteristics of the serum factor we have performed a systematic investigation of commonly used protein chromatography modes and separation techniques to develop a successful purification procedure. After four column chromatography steps -- cation exchange, hydrophobic interaction, heparin affinity and size exclusion chromatography under denaturing conditions -- we have achieved a 2,000-fold purification starting from a commercially available Crude Bovine Thrombin preparation. This represents about 40,000-fold purification over bovine serum. Silver stained gels of the most purified fractions revealed ten major protein bands. In order to finally identify the cell cycle re-entry factor, we are currently analyzing the purification by quantitative mass spectrometry by correlating the abundance of tryptic peptides with activity in sequential fractions across a chromatography run.

In contrast to mammals, some fish and amphibians have retained the ability to regenerate complex body structures or organs, such as the limb, the tail, the eye lens or even parts of the heart. One major difference in the response to injury is the appearance of a mesenchymal growth zone or blastema in these regenerative species instead of the scarring seen in mammals. This blastema is thought to largely derive from the dedifferentiation of various functional cell types, such as skeletal muscle, skin and cartilage. In the case of multinucleated skeletal muscle fibres, cell cycle re-entry into S-phase as well as fragmentation into mononucleated progenitors is observed both in vitro and in vivo. In order to identify molecules that initiate dedifferentiation of cells at the wound site in amphibians we have established a cellular assay with a cultured newt myogenic cell line. Using this assay we have found a serum activity that stimulates cell cycle re-entry in differentiated multinucleated newt myotubes. The activity is present in serum of all mammalian species tested so far and, interestingly, thrombin proteolysis amplifies the activity from both serum and plasma. We think this serum factor provides a link between wounding and regeneration and its identification will be a key step in understanding the remarkable differences in wound healing between mammals and amphibians. In the course of this PhD thesis we have characterized the serum factor as a thermo-labile, pH- and proteinase K-sensitive, high molecular weight protein that is resistant to denaturing conditions such as SDS, urea or organic solvents. Surprisingly, under denaturing conditions the activity behaves as a low molecular weight protein that displays charge heterogeneity on isoelectric focusing. Using these characteristics of the serum factor we have performed a systematic investigation of commonly used protein chromatography modes and separation techniques to develop a successful purification procedure. After four column chromatography steps -- cation exchange, hydrophobic interaction, heparin affinity and size exclusion chromatography under denaturing conditions -- we have achieved a 2,000-fold purification starting from a commercially available Crude Bovine Thrombin preparation. This represents about 40,000-fold purification over bovine serum. Silver stained gels of the most purified fractions revealed ten major protein bands. In order to finally identify the cell cycle re-entry factor, we are currently analyzing the purification by quantitative mass spectrometry by correlating the abundance of tryptic peptides with activity in sequential fractions across a chromatography run.