Down syndrome acute lymphoblastic leukemia, a highly heterogeneous disease in which aberrant expression of CRLF2 is associated with mutated JAK2: a report from the International BFM Study Group

We report gene expression and other analyses to elucidate the molecular characteristics of acute lymphoblastic leukemia (ALL) in children with Down syndrome (DS). We find that by gene expression DS-ALL is a highly heterogeneous disease not definable as a unique entity. Nevertheless, 62% (33/53) of the DS-ALL samples analyzed were characterized by high expression of the type I cytokine receptor CRLF2 caused by either immunoglobulin heavy locus (IgH@) translocations or by interstitial deletions creating chimeric transcripts P2RY8-CRLF2. In 3 of these 33 patients, a novel activating somatic mutation, F232C in CRLF2, was identified. Consistent with our previous research, mutations in R683 of JAK2 were identified in 10 specimens (19% of the patients) and, interestingly, all 10 had high CRLF2 expression. Cytokine receptor-like factor 2 (CRLF2) and mutated Janus kinase 2 (Jak2) cooperated in conferring cytokine-independent growth to BaF3 pro-B cells. Intriguingly, the gene expression signature of DS-ALL is enriched with DNA damage and BCL6 responsive genes, suggesting the possibility of B-cell lymphocytic genomic instability. Thus, DS confers increased risk for genetically highly diverse ALLs with frequent overexpression of CRLF2, associated with activating mutations in the receptor itself or in JAK2. Our data also suggest that the majority of DS children with ALL may benefit from therapy blocking the CRLF2/JAK2 pathways

Nanog transforms NIH3T3 cells and targets cell-type restricted genes

The transcription factor Nanog is uniquely expressed in embryonic stem (ES) cells and in germ cell tumors and is important for selfrenewal. To understand the relation between this and cell transformation, we expressed Nanog in NIH3T3 cells, and these cells showed an increased growth rate and a transformed phenotype as demonstrated by foci formation and colony growth in soft agar. This suggests that Nanog possesses an oncogenic potential that may be related to the role it plays in germ cell tumors and to its function in self renewal of ES cells. We studied the transcription targets of Nanog using microarrays to identify Nanog regulated genes. The list of genes regulated by Nanog was unique for each cell type and more than 10 % of the Nanog regulated genes, including transcription factors, are primary Nanog targets since their promoters bind Nanog in ES cells. Some of these target genes can explain the transformation o

Snord 3A: a molecular marker and modulator of prion disease progression.

Since preventive treatments for prion disease require early identification of subjects at risk, we searched for surrogate peripheral markers characterizing the asymptomatic phases of such conditions. To this effect, we subjected blood mRNA from E200K PrP CJD patients and corresponding family members to global arrays and found that the expression of Snord3A, a non-coding RNA transcript, was elevated several times in CJD patients as compared to controls, while asymptomatic carriers presented intermediate Snord3A levels. In the brains of TgMHu2ME199K mice, a mouse model mimicking for E200K CJD, Snord 3A levels were elevated in an age and disease severity dependent manner, as was the case for brains of these mice in which disease was exacerbated by copper administration. Snord3A expression was also elevated in scrapie infected mice, but not in PrP(0/0) mice, indicating that while the expression levels of this transcript may reflect diverse prion etiologies, they are not related to the loss of PrP(C)'s function. Elevation of Snord3A was consistent with the activation of ATF6, representing one of the arms of the unfolded protein response system. Indeed, SnoRNAs were associated with reduced resistance to oxidative stress, and with ER stress in general, factors playing a significant role in this and other neurodegenerative conditions. We hypothesize that in addition to its function as a disease marker, Snord3A may play an important role in the mechanism of prion disease manifestation and progression

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats

Identification of Snord3A and Aldh1A1 as disease specific markers.

<p>a: Gene expression heat map representing the levels of transcripts expressed in blood from E200KCJD patients, carriers and non-carriers control. b: Snord3A expression level in microarrays of patients and healthy mutation carriers as compared to non-carrier controls. C: Aldh1A1 expression level in patients and healthy mutation carriers as compared to non-carrier controls (P value <0.005).</p

Differential gene expression profile of E200KCJD patients and carriers compared with non carriers control.

<p>Differential gene expression profile of E200KCJD patients and carriers compared with non carriers control.</p

Elevation of Snord3A expression in Tg MHu2M E199K MEFs and in copper treated mice.

<p>Total RNA from brains of TgMHu2ME199K and wild-type mice as described, as well as from designated MEFs were amplified for Snord3A by Real time PCR. Relative RNA expression levels were normalized in reference to UBC and <i>β-actin</i> (Respectively). a: Scheme of accumulation of PrP and MEF survival during copper treatment (as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054433#pone.0054433-Canello2" target="_blank">[32]</a>). b: Snord3A levels in designated MEFs (wt: cells from wt mice; tg: cells from TgMHu2ME199K mice; KO: cells from PrP^0/0 mice. c: Snord3A levels in TgMHu2ME199K and wild-type mice brain after 75 days of copper treatment versus age-matched control (** P value <0.001).</p

Expression of Snord3A in scrapie-infected brain’s.

<p><u>Main picture</u>: Total RNA from brains of scrapie infected mice (6 and 24 months old mice, 4 in each group) and age matched wt controls were amplified for Snord3A by real time PCR as described. Relative RNA expression levels were normalized in reference to UBC. Relative Snord3A expression level in scrapie infected mice is indicated by fold change versus age-matched controls. <u>Insert</u>: Immunoblotting of PrP^Sc in brains of infected mice (2 young, two old). (** P value <0.001).</p