SummaryRepair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair.

Four Hodgkin's lymphoma cell lines (KM-H2, HDLM-2, L428, L1236) were analyzed for cytogenetic aberrations, applying multiplex fluorescence in situ hybridization, chromosome banding and comparative genomic hybridization. Each line was characterized by a highly heterogeneous pattern of karyotypic changes with a large spectrum of different translocated chromosomes (range 22-57). A recurrent finding in all cell lines was the presence of chromosomal rearrangements of the short arm of chromosome 2 involving the REL oncogene locus. Furthermore, multiple translocated copies of telomeric chromosomal segments were frequently detected. This resulted in a copy number increase of putative oncogenes, e.g., JAK2 ( HL is characterized by the presence of only a small fraction of malignant cells, i.e., Hodgkin cells as well as the multinucleated Reed-Sternberg cells. 1 Due to their small number, low mitotic index and frequently poor chromosomal morphology, cytogenetic analyses of HRS cells are particularly difficult and do not reveal characteristic numerical or structural chromosomal changes. Nevertheless, various nonrandom changes have been described by chromosome banding (for review, see Atkin 2 and Fonatsch et al. 3 ) and studies using CGH have revealed recurrent numerical changes on chromosomal arms 2p, 9p, 12q and 16q. 4 -7 Because of the problems encountered in molecular and cytogenetic analyses of primary Hodgkin's tumors, cell lines derived from malignant HRS cells are of particular importance. However, due to the complexity of karyotypic changes in these cell lines, it remains difficult to thoroughly assess the entire spectrum of chromosomal aberrations. As in primary tumors, no specific chromosomal rearrangements have been observed. 2,3 In the present study, 4 HL cell lines were analyzed, applying M-FISH, which allows visualization of translocated parts from all human chromosomes in a comprehensive manner. This approach is therefore particularly suited for the rapid delineation of complex chromosomal aberrations. In addition, the M-FISH results were complemented by chromosome banding and conventional FISH analysis. Finally, we applied CGH to identify net chromosomal gains and losses of individual chromosomal subregions. By applying this combined cytogenetic strategy, we aimed at identifying characteristic chromosomal aberrations in HL cell lines, to gain further insight into the molecular mechanisms involved in the development of this disease. MATERIAL AND METHODS Cell linesCell lines KM-H2, HDLM-2 and L428 were obtained from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany); cell line L1236 was kindly provided by Dr. V. Diehl (University of Cologne). Selected clinicopathologic parameters of the patients and tumors from which the cell lines were derived were described by Drexler. 8 M-FISHMetaphase spreads from cell lines HDLM-2, KM-H2, L428 and L1236 were prepared as outlined previously. 9,10 M-FISH was performed as described, with minor modifications. 11,12 Briefly, 5 pools of WCP prob...

Copy number gains and high-level amplifications of the short arm of chromosome 5 are frequently observed in soft tissue sarcomas. To identify genes from this region possibly involved in tumor progression, we analyzed 34 soft tissue sarcomas (10 pleomorphic and 8 dedifferentiated liposarcomas, 6 malignant fibrous histiocytomas, and 10 malignant peripheral nerve sheath tumors (MPNST)) using a DNA microarray including 418 BAC clones representing 99% of chromosome arm 5p. In seven tumors, distinct high-level amplifications were identified affecting four different subregions. From these regions, genes TERT, TRIO, SKP2, FBXO32, NKD2, SLC6A3, IRX2, POLS, FYB, PTGER4, and FGF10 were selected for detailed quantitative expression analysis (RQ-PCR) based on their potential tumorigenic function. Of these, TRIO, coding for a guanidine nucleotide exchange factor, was consistently overexpressed in all cases, while IRX2 and NKD2, both involved in the regulation of developmental processes via the WNT pathway, showed a characteristic expression only in MPNSTs. Detailed nonparametric multidimensional scaling analysis further showed that the expression of TRIO, IRX2, and NKD2 strongly correlated with the gene copy number. In conclusion, we found TRIO, IRX2, and NKD2 frequently affected by high-level amplifications as well as up-regulated in a gene-dosage dependent manner. Thus, these genes represent candidate targets of 5p amplifications in soft tissue sarcomas and might play a crucial role during the progression of this disease.