• ParaSAM: a parallelized version of the significance analysis of microarrays algorithm.

      Sharma, Ashok; Zhao, Jieping; Podolsky, Robert H.; McIndoe, Richard A; Department of Pathology (2010-05-20)
      MOTIVATION: Significance analysis of microarrays (SAM) is a widely used permutation-based approach to identifying differentially expressed genes in microarray datasets. While SAM is freely available as an Excel plug-in and as an R-package, analyses are often limited for large datasets due to very high memory requirements. SUMMARY: We have developed a parallelized version of the SAM algorithm called ParaSAM to overcome the memory limitations. This high performance multithreaded application provides the scientific community with an easy and manageable client-server Windows application with graphical user interface and does not require programming experience to run. The parallel nature of the application comes from the use of web services to perform the permutations. Our results indicate that ParaSAM is not only faster than the serial version, but also can analyze extremely large datasets that cannot be performed using existing implementations. AVAILABILITY: A web version open to the public is available at http://bioanalysis.genomics.mcg.edu/parasam. For local installations, both the windows and web implementations of ParaSAM are available for free at http://www.amdcc.org/bioinformatics/software/parasam.aspx.
    • Pediatric primary intramedullary spinal cord glioblastoma

      Lober, Robert M.; Sharma, Suash; Bell, Beverly; Free, Alan; Figueroa, Ramon; Sheils, Chris W; Lee, Mark R.; Cowell, John K.; Department of Pathology; Department of Pediatrics; et al. (2010-09-30)
      Spinal cord tumors in pediatric patients are rare, representing less than 1% of all central nervous system tumors. Two cases of pediatric primary intramedullary spinal cord glioblastoma at ages 14 and 8 years are reported. Both patients presented with rapid onset paraparesis and quadraparesis. Magnetic resonance imaging in both showed heterogeneously enhancing solitary mass lesions localized to lower cervical and upper thoracic spinal cord parenchyma. Histopathologic diagnosis was glioblastoma. Case #1 had a small cell component (primitive neuroectodermal tumor-like areas), higher Ki67, and p53 labeling indices, and a relatively stable karyotype with only minimal single copy losses involving regions: Chr8;pter-30480019, Chr16;pter-29754532, Chr16;56160245â 88668979, and Chr19;32848902-qter on retrospective comparative genomic hybridization using formalin-fixed, paraffin-embedded samples. Case #2 had relatively bland histomorphology and negligible p53 immunoreactivity. Both underwent multimodal therapy including gross total resection, postoperative radiation and chemotherapy. However, there was no significant improvement in neurological deficits, and overall survival in both cases was 14 months.This report highlights the broad histological spectrum and poor overall survival despite multi modality therapy. The finding of relatively unique genotypic abnormalities resembling pediatric embryonal tumors in one case may highlight the value of genome-wide profiling in development of effective therapy. The differences in management with intracranial and low-grade spinal cord gliomas and current management issues are discussed.
    • Primary mucinous adenocarcinoma in a defunctionalized urinary bladder: a case report.

      Taneous, Mary; Ramalingam, Preetha; Mode, Donald G; Heiner, Jared G; Terris, Martha K; Lee, Jeffrey R.; Department of Pathology; Department of Surgery (2010-01-11)
      INTRODUCTION: Malignancies are rare in defunctionalized bladders and are thought to arise from metaplasia secondary to chronic inflammation. Transitional cell and squamous cell carcinomas are the most common but there are three reported cases of mucinous adenocarcinoma. CASE PRESENTATION: We report a 57-year-old Caucasian man presenting with penile discharge for 30 years following ileal conduit surgery for neurogenic bladder, and who was found to have primary mucinous adenocarcinoma of his defunctionalized bladder. CONCLUSION: Although urinary diversion without cystectomy is less common in current urologic practice, there are many patients with longstanding defunctionalized bladders. While there are no established surveillance protocols, defunctionalized bladder patients with urethral discharge should be evaluated.
    • Switched alternative splicing of oncogene CoAA during embryonal carcinoma stem cell differentiation.

      Yang, Zheqiong; Sui, Yang; Xiong, Shiqin; Liour, Sean S; Phillips, Andrew C; Ko, Lan; Department of Pathology (2007-04-23)
      Alternative splicing produces functionally distinct proteins participating in cellular processes including differentiation and development. CoAA is a coactivator that regulates transcription-coupled splicing and its own pre-mRNA transcript is alternatively spliced. We show here that the CoAA gene is embryonically expressed and alternatively spliced in multiple tissues to three splice variants, CoAA, CoAM and CoAR. During retinoic-acid-induced P19 stem cell differentiation, the expression of CoAA undergoes a rapid switch to its dominant negative splice variant CoAM in the cavity of the embryoid body. CoAM functionally inhibits CoAA, and their switched expression up-regulates differentiation marker Sox6. Using a CoAA minigene cassette, we find that the switched alternative splicing of CoAA and CoAM is regulated by the cis-regulating sequence upstream of the CoAA basal promoter. Consistent to this, we show that p54(nrb) and PSF induce CoAM splice variant through the cis-regulating sequence. We have previously shown that the CoAA gene is amplified in human cancers with a recurrent loss of this cis-regulating sequence. These results together suggest that the upstream regulatory sequence contributes to alternative splicing of the CoAA gene during stem cell differentiation, and its selective loss in human cancers potentially deregulates CoAA alternative splicing and alters stem cell differentiation.
    • Transcriptional Coactivator and Oncoprotein CoAA

      Brooks, Yang Sui; Department of Pathology (2008)
      CoAA contains two copies of RNA recognition motifs (RRM) and an intrinsic transactivation domain rich in repetitive tyrosines and glutamines (YxxQ domain). Previously, CoAA has been shown to be a transcriptional coactivator that stimulates transcriptional activation and regulates alternative splicing. A pattern and profile search revealed that the YxxQ domain in CoAA shared significant pattern homology with the oncogenic EWS activation domains (EAD) in TET family proteins, including, TLS/FUS, EWS and TAFII 68. It was further demonstrated that CoAA’s YxxQ domain and EWS’ EAD also shared functional similarities. Based on these findings, this work investigated the aberration of CoAA in cancers and its pathophysiological significance. The results showed that the CoAA gene was amplified in a high percentage of inflammation-related human cancers with recurrent loss of the 5’ regulatory element upstream of its promoter. This genomic aberration resulted in CoAA protein overexpression, which in turn, induced the transformation of NIH3T3 cells. Subsequently, it was shown that the lost 5’ regulatory element could modulate the alternative splicing of the CoAA gene during stem cell differentiation and that the unbalanced expression of CoAA and its splice variant, CoAM could potentially impact the cell differentiation process. To further characterize the regulation of CoAA alternative splicing, two conserved trans-splicing events between CoAA and its downstream RBM4 were identified. These events yield a novel zinc finger- containing coactivator, CoAZ, and a non-coding splice variant, ncCoAZ. Both variants regulated their parental genes’ mRNA expression as well as activities, suggesting a linked control between CoAA and RBM4. Moreover, the expression patterns of CoAA, RBM4 and their trans-splicing variants switched during neural stem cell differentiation, resulting in lineage-specific expression of each variant. Our phylogenetic analysis suggests that mammalian CoAA and RBM4 share a common ancestor with the Drosophila melanogaster gene, Lark. In this regard, the trans-splicing events between CoAA and RBM4 represent a functional regulation preserved during evolution. This study established the connection between CoAA and human cancer and provides evidence for CoAA’s involvement in the regulation of cell differentiation. Moreover, this study is the first to report a functional trans-splicing variant in mammalian cells.
    • The Transcriptional Profile of Mesenchymal Stem Cell Populations in Primary Osteoporosis Is Distinct and Shows Overexpression of Osteogenic Inhibitors

      Benisch, Peggy; Schilling, Tatjana; Klein-Hitpass, Ludger; Frey, Sonke P.; Seefried, Lothar; Raaijmakers, Nadja; Krug, Melanie; Regensburger, Martina; Zeck, Sabine; Schinke, Thorsten; et al. (2012-09-24)
      Primary osteoporosis is an age-related disease characterized by an imbalance in bone homeostasis. While the resorptive aspect of the disease has been studied intensely, less is known about the anabolic part of the syndrome or presumptive deficiencies in bone regeneration. Multipotent mesenchymal stem cells (MSC) are the primary source of osteogenic regeneration. In the present study we aimed to unravel whether MSC biology is directly involved in the pathophysiology of the disease and therefore performed microarray analyses of hMSC of elderly patients (79â 94 years old) suffering from osteoporosis (hMSC-OP). In comparison to age-matched controls we detected profound changes in the transcriptome in hMSC-OP, e.g. enhanced mRNA expression of known osteoporosis-associated genes (LRP5, RUNX2, COL1A1) and of genes involved in osteoclastogenesis (CSF1, PTH1R), but most notably of genes coding for inhibitors of WNT and BMP signaling, such as Sclerostin and MAB21L2. These candidate genes indicate intrinsic deficiencies in self-renewal and differentiation potential in osteoporotic stem cells. We also compared both hMSC-OP and non-osteoporotic hMSC-old of elderly donors to hMSC of â ¼30 years younger donors and found that the transcriptional changes acquired between the sixth and the ninth decade of life differed widely between osteoporotic and non-osteoporotic stem cells. In addition, we compared the osteoporotic transcriptome to long term-cultivated, senescent hMSC and detected some signs for pre-senescence in hMSC-OP.