SUMMARY While molecular subgrouping has revolutionized medulloblastoma classification, the extent of heterogeneity within subgroups is unknown. Similarity network fusion (SNF) applied to genome-wide DNA methylation and gene expression data across 763 primary samples identifies very homogeneous clusters of patients, supporting the presence of medulloblastoma subtypes. After integration of somatic copy-number alterations, and clinical features specific to each cluster, we identify 12 different subtypes of medulloblastoma. Integrative analysis using SNF further delineates group 3 from group 4 medulloblastoma, which is not as readily apparent through analyses of individual data types. Two clear subtypes of infants with Sonic Hedgehog medulloblastoma with disparate outcomes and biology are identified. Medulloblastoma subtypes identified through integrative clustering have important implications for stratification of future clinical trials.

Summary: The study of the origin and development of cerebellar tumors has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. Sonic Hedgehog medulloblastoma transcriptionally mirrors the granule cell hierarchy as expected, whereas Group3 MB resemble Nestin+ve stem cells, Group 4 MB resemble unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the pre-natal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumors demonstrates that many bulk tumors contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumors as a disorder of early brain development, and provide a proximate explanation for the peak incidence of cerebellar tumors in early childhood.

Idiopathic pulmonary fibrosis is a progressive and fatal fibrotic disease of the lungs with unclear etiology. Prior efforts to treat idiopathic pulmonary fibrosis that focused on anti-inflammatory therapy have not proven to be effective. Recent insight suggests that the pathogenesis is mediated through foci of dysregulated fibroblasts driven by profibrotic cytokine signaling. TGF-β and PDGF are 2 of the most potent of these cytokines. In the current study, we investigated the role of TGF-β-induced fibrosis mediated by activation of the Abelson (Abl) tyrosine kinase. Our data indicate that fibroblasts respond to TGF-β by stimulating c-Abl kinase activity independently of Smad2/3 phosphorylation or PDGFR activation. Moreover, inhibition of c-Abl by imatinib prevented TGF-β-induced ECM gene expression, morphologic transformation, and cell proliferation independently of any effect on Smad signaling. Further, using a mouse model of bleomycin-induced pulmonary fibrosis, we found a significant inhibition of lung fibrosis by imatinib. Thus, Abl family members represent common targets for the modulation of profibrotic cytokine signaling.

Idiopathic pulmonary fibrosis is a progressive and fatal fibrotic disease of the lungs with unclear etiology. Prior efforts to treat idiopathic pulmonary fibrosis that focused on anti-inflammatory therapy have not proven to be effective. Recent insight suggests that the pathogenesis is mediated through foci of dysregulated fibroblasts driven by profibrotic cytokine signaling. TGF-β and PDGF are 2 of the most potent of these cytokines. In the current study, we investigated the role of TGF-β-induced fibrosis mediated by activation of the Abelson (Abl) tyrosine kinase. Our data indicate that fibroblasts respond to TGF-β by stimulating c-Abl kinase activity independently of Smad2/3 phosphorylation or PDGFR activation. Moreover, inhibition of c-Abl by imatinib prevented TGF-β-induced ECM gene expression, morphologic transformation, and cell proliferation independently of any effect on Smad signaling. Further, using a mouse model of bleomycin-induced pulmonary fibrosis, we found a significant inhibition of lung fibrosis by imatinib. Thus, Abl family members represent common targets for the modulation of profibrotic cytokine signaling.

Background: Limited data exist regarding the population-based epidemiology of idiopathic pulmonary fi brosis (IPF). The objective of the study was to describe the trends in the incidence, prevalence, and clinical course of IPF in the community. Methods:We conducted a population-based study of adult patients with IPF in Olmsted County, Minnesota, from 1997 to 2005. Two methods were used to identify IPF cases, as defi ned by the 2002 American Thoracic Society/European Respiratory Society consensus statement: (1) usual interstitial pneumonia (UIP) on a surgical lung biopsy specimen or a defi nite UIP pattern on a high-resolution CT image (narrow criteria) and (2) UIP on a surgical lung biopsy specimen or a defi nite or possible UIP pattern on CT image (broad criteria). Results: Of 596 patients screened for the possibility of pulmonary disease or pulmonary fi brosis over 9 years of follow-up, 47 cases had IPF. Of these, 24 met the narrow criteria. The age-and sex-adjusted incidence was 8.8/100,000 and 17.4/100,000 person-years, for narrow and broad criteria, respectively. The age-adjusted incidence was higher in men than in women, and among patients aged 70-79 years. During the study period, the incidence of IPF decreased ( P , .001). On December 31, 2005, the age-and sex-adjusted prevalence was 27.9/100,000 and 63/100,000 persons by narrow and broad criteria, respectively. Thirty-seven patients experienced a total of 53 respiratory exacerbations (26 IPF related, 27 non-IPF related), and 34 (72%) patients died. The primary cause of death was IPF related in 16 (47%) patients. Median survival for narrow-criteria and broad-criteria incidence cases was 3.5 and 4.4 years, respectively. Conclusions: The incidence of IPF in Olmsted County decreased over the study period. Nonprimary IPF respiratory exacerbations are as frequent as primary IPF respiratory exacerbations and an important cause of death.CHEST 2010; 137( 1 ):129-137Abbreviations: ATS/ERS 5 American Thoracic Society and European Respiratory Society; HRCT 5 high-resolution computed tomography; IPF 5 idiopathic pulmonary fi brosis; REP 5 Rochester Epidemiology Project; UIP 5 usual interstitial pneumonia

OBJECTIVE:To determine the biochemical parameters of chylous pleural fluids and better inform current clinical practice in the diagnosis of chylothorax. PATIENTS AND METHODS:We retrospectively reviewed 74 patients with chylothorax (defined by the presence of chylomicrons) who underwent evaluation during a 10-year period from January 1, 1997, through December 31, 2006. The biochemical parameters and appearance of the fluid assessed during diagnostic evaluation were analyzed. RESULTS:The study consisted of 37 men (50%) and 37 women (50%), with a median age of 61.5 years (range, 20-93 years). Chylothorax was caused by surgical procedures in 51%. The chylous pleural fluid appeared milky in only 44%. Pleural effusion was exudative in 64 patients (86%) and transudative in 10 patients (14%). However, pleural fluid protein and lactate dehydrogenase levels varied widely. Transudative chylothorax was present in all 4 patients with cirrhosis but was also seen with other causes. The mean ± SD triglyceride level was 728±797 mg/dL, and the mean ± SD cholesterol value was 66±30 mg/dL. The pleural fluid triglyceride value was less than 110 mg/dL in 10 patients (14%) with chylothorax, 2 of whom had a triglyceride value lower than 50 mg/dL.

SummaryThe modal length or degree of polymerization (dp) of the Shigella¯exneri O-antigen is determined in an unknown manner by the Wzz/Rol protein. The Wzz protein is anchored into the cytoplasmic membrane by two transmembrane domains (TM1 amino acids 32±52; TM2 amino acids 295±315) with the central loop of the protein located in the periplasm. Plasmids were constructed encoding hybrid Wzz proteins consisting of regions of S.¯exneri Wzz (Wzz SF ) and Salmonella typhimurium Wzz (Wzz ST ). These imparted O-antigen modal chain lengths that implied that the carboxy-terminal region of Wzz was involved in chain length determination. Site-directed mutagenesis was undertaken to investigate the functional signi®-cance of highly conserved residues in amino-/carboxy-terminal domains of Wzz SF . Some of the Wzz SF variants resulted in O-antigen modal chain lengths much shorter than those of wild-type Wzz SF , whereas other mutants inactivated Wzz SF function entirely and a third class had a longer O-antigen chain length distribution. The data indicate that amino acids throughout the length of the Wzz SF protein are important in determination of O-antigen modal chain length. In vivo cross-linking experiments were performed to investigate the interactions between Wzz proteins. The experiments indicated that the Wzz SF protein is able to form dimers and oligomers of at least six Wzz SF proteins. A carboxy-terminal-truncated Wzz SF protein having the amino terminal 194 amino acids was able to oligomerize, indicating that the aminoterminal region is suf®cient for the Wzz±Wzz interaction observed. Shortened Wzz SF proteins having internal deletions in the amino-terminal region were also able to oligomerize, suggesting that residues 59±194 are not essential for oligomerization. Crosslinking of Wzz SF proteins with mutationally altered residues showed that loss of Wzz SF function may be correlated to a reduced/altered ability to form oligomers, and that mutational alteration of glycine residues in the TM2 segment affects Wzz SF ±Wzz SF dimer mobility in SDS polyacrylamide gels. These results provide the ®rst evidence of protein±protein interactions for proteins involved in O-antigen polysaccharide biosynthesis.

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