scholarly journals Omnipresence of Partitiviruses in Rice Aggregate Sheath Spot Symptom-Associated Fungal Isolates from Paddies in Thailand

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2269
Author(s):  
Sokty Neang ◽  
Santiti Bincader ◽  
Sansern Rangsuwan ◽  
Pisut Keawmanee ◽  
Soriya Rin ◽  
...  
Keyword(s):  
Pathogenic Fungi ◽  
Colony Growth ◽  
Rna Seq ◽  
Rt Pcr ◽  
Cdna Library Construction ◽  
Double Stranded Rna ◽  
Potential Source ◽  
Rhizoctonia Oryzae ◽  
Synthetic Media ◽  
Shed Light

Partitiviruses are one of the most prevalent double-stranded RNA viruses that have been identified mostly in filamentous fungi and plants. Partitiviruses generally infect host fungi asymptomatically but infrequently exert significant effect(s) on morphology and virulence, thus being considered a potential source of biological control agents against pathogenic fungi. In this study, we performed a screening for mycoviruses of a collection of Thai isolates of rice fungal pathogen Rhizoctonia oryzae-sativae, a causal agent of rice aggregated sheath spot disease. As a result, 36% of tested isolates carried potentially viral double-stranded RNAs with sizes ranging from 2 to 3 kbp. By conventional cDNA library construction and RNA-seq, we determined six new alphapartitiviruses that infected three isolates: tentatively named Rhizoctonia oryzae-sativae partitivirus 1 to 6 (RosPV1-6). Furthermore, RT-PCR detection of each virus revealed their omnipresent nature in different R. oryzae-sativae isolates. Although virus-curing of basidiomycetous fungi is generally difficult, our repeated attempts successfully obtained virus-free (for RosPV1, RosPV2, and uncharacterized partitiviruses), isogenic strain of R. oryzae-sativae TSS190442. The virus-cured strain showed slightly faster colony growth on the synthetic media and severe symptom development on the rice sheath compared to its virus-infected counterpart. Overall, this study shed light on the distribution of partitiviruses in R. oryzae-sativae in a paddy environment and exemplified a virus-curing protocol that may be applicable for other basidiomycetous fungi.

scholarly journals Simultaneous enterovirus EV-D68 and CVA6 infections causing acute respiratory distress syndrome and hand, foot and mouth disease

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Ivanildo Pedro de Sousa ◽  
Heloísa Ihle Giamberardino ◽  
Sonia Mara Raboni ◽  
Maria Carmo Debur ◽  
Maria de Lourdes Aguiar Oliveira ◽  
...  
Keyword(s):  
Respiratory Distress ◽  
Clinical Symptoms ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Rt Pcr ◽  
Double Infection ◽  
Chinese Strain ◽  
Case Presentation ◽  
Foot And Mouth ◽  
Shed Light

Abstract Background Although most enterovirus (EV) infections can be asymptomatic, these viral agents can cause serious conditions associated with central nervous system, respiratory disease and uncommon manifestations of hand, foot and mouth disease (HFMD). EV-coinfections have been rarely reported with development of complications and severe clinical outcome. An atypical case of a child presenting HFMD and severe acute respiratory syndrome, co-infected with EV-D68 and CVA6, is reported herein. Case presentation A 3-year-old boy was admitted in the emergency department unit showing fever, abdominal pain and tachycardia. Twenty-four hours after hospitalization the child developed severe clinical symptoms associated with HFMD and was discharged after recovery. Two days later, the child was readmitted with fever, cough and respiratory distress. RT-PCR and Sanger sequencing confirmed positivity for EV-D68 and CVA6 in oro and nasopharynges swabs and vesicles fluid, respectively. Phylogenetic analysis based on VP1 gene sequences suggested that CVA6 was closely related with HFMD viruses circulating in Turkey, while EV-D68 was genetically related to a Chinese strain. Conclusions To the best of our knowledge, this case is the first report of a double infection caused by CVA6 and EV-D68, which shed light on the pathogenesis of enterovirus infections. Further studies must be conducted to ascertain the role and clinical significance of EV co-infections, as well as a potential synergistic pathway between these viruses.

scholarly journals EPEN-30. C11ORF95-RELA FUSION PROTEIN ENGAGES NOVEL GENOMIC LOCI TO DRIVE MURINE EPENDYMOMA GROWTH

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii314-iii314
Author(s):  
Amir Arabzade ◽  
Yanhua Zhao ◽  
Srinidhi Varadharajan ◽  
Hsiao-Chi Chen ◽  
Austin Stuckert ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Molecular Targets ◽  
Lead Target ◽  
Open Chromatin ◽  
Rna Seq ◽  
In Utero Electroporation ◽  
Pathway Activation ◽  
Mouse Cells ◽  
Shed Light

Abstract RATIONALE Over 70% of supratentorial (ST) ependymoma are characterized by an oncogenic fusion between C11ORF95 and RELA. C11ORF95-RELA fusion is frequently the sole genetic driver detected in ST ependymoma, thus ranking this genomic event as a lead target for therapeutic investigation. RELA is a transcription factor (TF) central to mediating NF-kB pathway activation in processes such as inflammation, cellular metabolism, and chemotaxis. HYPOTHESIS: We posited that C11ORF95-RELA acts as an oncogenic TF that aberrantly shapes the tumor epigenome to drive aberrant transcription. Approach: To this end we developed an in utero electroporation (IUE) mouse model of ependymoma to express C11ORF95-RELA during embryonic development. Our IUE approach allowed us to develop C11ORF95-RELA driven tumor models and cell lines. We comprehensively characterized the epigenome and transcriptome of C11ORF95-RELA fusion driven mouse cells by H3K27ac ChIP-seq, ATAC-seq, and RNA-seq. RESULTS This data revealed that: 1) C11ORF95-RELA directly engages ‘open’ chromatin and is enriched at regions with known RELA TF binding sites as well as novel genomic loci/motifs, 2) C11ORF95-RELA preferentially binds to both H3K27ac (active) enhancers and promoters, and 3) Bound C11ORF95-RELA promoter loci are associated with increased transcription of genes shared with human ependymoma. CONCLUSION Our findings shed light on the transcriptional mechanisms of C11ORF95-RELA, and reveal downstream targets that may represent cancer dependency genes and molecular targets.

scholarly journals Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

2012 ◽  
Vol 22 (9) ◽  
pp. 1698-1710 ◽  
Author(s):  
C. Howald ◽  
A. Tanzer ◽  
J. Chrast ◽  
F. Kokocinski ◽  
T. Derrien ◽  
...  
Keyword(s):  
Human Genome ◽  
Rna Seq ◽  
Rt Pcr

scholarly journals Transcriptome analyses reveal anthocyanin biosynthesis in eggplants

2018 ◽  
Author(s):  
Xi Ou Xiao ◽  
Wen qiu Lin ◽  
Ke Li ◽  
Xue Feng Feng ◽  
Hui Jin ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Negative Regulation ◽  
Anthocyanin Content ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Wild Type ◽  
Rt Pcr ◽  
Total Anthocyanin ◽  
Total Anthocyanin Content ◽  
Cumulative Knowledge

We obtained a white-peel eggplant (L6-5) by EMS mutation in our previous study, whose total anthocyanin content was significantly decreased as compared with that of wild-type (WT). To analyse the anthocyanin biosynthesis mechanism in eggplants, we analysed the eggplant peel by RNA-seq in this study. The transcript results revealed upregulation of 465 genes and downregulation of 525 genes in L6-5 as compared with the WT eggplant. A total of 11 anthocyanin biosynthesis structure genes were significantly downregulated in L6-5 as compared with that in WT. Meanwhile, on the basis of the RT-PCR results of four natural eggplant cultivars, the expression pattern of 11 anthocyanin biosynthesis structure genes was consistent with the anthocyanin content. Thus, we speculated the anthocyanin biosynthesis pathway in eggplant peel. The transcript and RT-PCR results suggested positive regulation of MYB1, MYB108 and TTG8 and negative regulation of bHLH36 in anthocyanin biosynthesis. This study enhanced our cumulative knowledge about anthocyanin biosynthesis in eggplant peels.

scholarly journals Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Wenshuai Liu ◽  
Hanxing Tong ◽  
Chenlu Zhang ◽  
Rongyuan Zhuang ◽  
He Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sanger Sequencing ◽  
Immune Cell ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Rna Seq ◽  
Loss Of Function ◽  
Rt Pcr ◽  
The Difference ◽  
Histologic Types

Abstract Background Treating patients with advanced sarcomas is challenging due to great histologic diversity among its subtypes. Leiomyosarcoma (LMS) and de-differentiated liposarcoma (DDLPS) are two common and aggressive subtypes of soft tissue sarcoma (STS). They differ significantly in histology and clinical behaviors. However, the molecular driving force behind the difference is unclear. Methods We collected 20 LMS and 12 DDLPS samples and performed whole exome sequencing (WES) to obtain their somatic mutation profiles. We also performed RNA-Seq to analyze the transcriptomes of 8 each of the LMS and DDLPS samples and obtained information about differential gene expression, pathway enrichment, immune cell infiltration in tumor microenvironment, and chromosomal rearrangement including gene fusions. Selected gene fusion events from the RNA-seq prediction were checked by RT-PCR in tandem with Sanger sequencing. Results We detected loss of function mutation and deletion of tumor suppressors mostly in LMS, and oncogene amplification mostly in DDLPS. A focal amplification affecting chromosome 12q13–15 region which encodes MDM2, CDK4 and HMGA2 is notable in DDLPS. Mutations in TP53, ATRX, PTEN, and RB1 are identified in LMS but not DDLPS, while mutation of HERC2 is only identified in DDLPS but not LMS. RNA-seq revealed overexpression of MDM2, CDK4 and HMGA2 in DDLPS and down-regulation of TP53 and RB1 in LMS. It also detected more fusion events in DDLPS than LMS (4.5 vs. 1, p = 0.0195), and the ones involving chromosome 12 in DDLPS stand out. RT-PCR and Sanger sequencing verified the majority of the fusion events in DDLPS but only one event in LMS selected to be tested. The tumor microenvironmental signatures are highly correlated with histologic types. DDLPS has more endothelial cells and fibroblasts content than LMS. Conclusions Our analysis revealed different recurrent genetic variations in LMS and DDLPS including simultaneous upregulation of gene expression and gene copy number amplification of MDM2 and CDK4. Up-regulation of tumor related genes is favored in DDLPS, while loss of suppressor function is favored in LMS. DDLPS harbors more frequent fusion events which can generate neoepitopes and potentially targeted by personalized immune treatment.

scholarly journals BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Paulo Rapazote-Flores ◽  
Micha Bayer ◽  
Linda Milne ◽  
Claus-Dieter Mayer ◽  
John Fuller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Splice Junction ◽  
Rna Seq ◽  
Rt Pcr ◽  
High Quality ◽  
Transcript Quantification ◽  
Reference Transcript ◽  
Alternatively Spliced ◽  
Time Required ◽  
Comprehensive Reference

Abstract Background The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants. Results A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts – BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427–433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20–28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5′ and 3′ UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage. Conclusion A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.

130 A CATALOG OF REFERENCE GENES WITH HIGH, MEDIUM, AND LOW LEVELS OF EXPRESSION DURING BOVINE IN VIVO PRE-IMPLANTATION DEVELOPMENT

2017 ◽  
Vol 29 (1) ◽  
pp. 173
Author(s):  
Z. Jiang ◽  
J. Sun ◽  
S. Marjani ◽  
H. Dong ◽  
X. Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Target Genes ◽  
Stable Expression ◽  
Bovine Embryo ◽  
Rna Seq ◽  
Rt Pcr ◽  
Data Set ◽  
Low Expression

Appropriate reference genes for accurate normalization in RT-PCR are essential for the study of gene expression. Ideal reference genes should not only have stable expression across stages of embryo development, but also be expressed at comparable levels to the target genes. Using RNA-seq data from in vivo-produced bovine oocytes and embryos from the 2-cell to blastocyst stage (Jiang et al., 2014 BMC Genomics 15, 756), we tried to establish a catalogue of all reference genes for RT-PCR analysis. One-way ANOVA generated 4055 genes that did not differ across stages. To reduce this list, we used the entire RNA-seq data set and first removed genes with a FPKM (fragments per kilobase of transcript per million mapped reads) of <1, and then rescaled each gene’s expression values within a range of 0 to 1. We subsequently calculated the expression variance for each gene across all stages. By assuming that the calculated variances follow a Gaussian distribution and that the majority of the genes do not have a stable expression level, a gene was classified as a reference if its variance significantly deviated (P < 0.05) from these assumptions. We identified 346 potential reference genes, all of which were among the candidates from the ANOVA analysis. We arbitrarily assigned genes in this list to high (FPKM ≥ 100), medium (10 < FPKM < 100), and low expression levels (FPKM ≤ 10), and 37, 154, and 155 genes, respectively, fell into these groups. Surprisingly, none of the commonly used reference genes, such as GAPDH, PPIA, ACTB, PRL15, GUSB, and H3F2A, were identified as being stably expressed across in vivo development. This is consistent with findings of prior RT-PCR studies (Robert et al. 2002 Biol. Reprod. 67, 1465–1472; Ross et al. 2010 Cell Reprogram. 12, 709–717). The following gene ontology terms were significantly enriched for the 346 genes: cell cycle, translation, transport, chromatin, cell division, and metabolic process, indicating that the early embryos maintained constant levels of genes involved in fundamental biological functions. Finally, we performed RT-PCR to validate the RNA-seq results using different bovine in vivo-derived oocytes and embryos (n = 3/stage). We successfully validated 10 selected genes, including those in the high (CS, PGD, and ACTR3), medium (CCT5, MRPL47, COG2, CRT9, and HELLS), and low expression groups (CDC23 and TTF1). In conclusion, we recommend the use of reference genes that are expressed at comparable levels to target genes. This study offers a useful resource to aid in the appropriate selection of reference genes, which will improve the accuracy of quantitative gene expression analyses across bovine embryo pre-implantation development.

scholarly journals First Identification of RNA-Binding Proteins That Regulate Alternative Exons in the Dystrophin Gene

2020 ◽  
Vol 21 (20) ◽  
pp. 7803
Author(s):  
Julie Miro ◽  
Anne-Laure Bougé ◽  
Eva Murauer ◽  
Emmanuelle Beyne ◽  
Dylan Da Cunha ◽  
...  
Keyword(s):  
Large Scale ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Dystrophin Gene ◽  
Rna Seq ◽  
Spatio Temporal ◽  
Dmd Gene ◽  
Shed Light

The Duchenne muscular dystrophy (DMD) gene has a complex expression pattern regulated by multiple tissue-specific promoters and by alternative splicing (AS) of the resulting transcripts. Here, we used an RNAi-based approach coupled with DMD-targeted RNA-seq to identify RNA-binding proteins (RBPs) that regulate splicing of its skeletal muscle isoform (Dp427m) in a human muscular cell line. A total of 16 RBPs comprising the major regulators of muscle-specific splicing events were tested. We show that distinct combinations of RBPs maintain the correct inclusion in the Dp427m of exons that undergo spatio-temporal AS in other dystrophin isoforms. In particular, our findings revealed the complex networks of RBPs contributing to the splicing of the two short DMD exons 71 and 78, the inclusion of exon 78 in the adult Dp427m isoform being crucial for muscle function. Among the RBPs tested, QKI and DDX5/DDX17 proteins are important determinants of DMD exon inclusion. This is the first large-scale study to determine which RBP proteins act on the physiological splicing of the DMD gene. Our data shed light on molecular mechanisms contributing to the expression of the different dystrophin isoforms, which could be influenced by a change in the function or expression level of the identified RBPs.

Real-Time RT-PCR Analysis of Individual Osteolineage Cells within the Hematopoietic Stem Cell Niche

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2389-2389
Author(s):  
Lev Silberstein ◽  
Masatake Osawa ◽  
Charles Lin ◽  
Peter Kharchenko ◽  
Cristina Lo Celso ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Rt Pcr ◽  
Hematopoietic Stem ◽  
Chi Squared ◽  
The Individual ◽  
Osteolineage Cells ◽  
Angiopoietin 1

Abstract Abstract 2389 Osteolineage cells (OLCs) have been shown to participate in a regulatory bone marrow microenvironment for the hematopoietic stem and progenitor cells (HSPCs) – the endosteal niche. Our previous experiments using live animal imaging have demonstrated that single transplanted HSPCs preferentially home in close proximity to the individual OLCs. We hypothesized that these HSPC-proximal cells represent a distinct subpopulation of OLCs, which is specifically involved in a non-cell autonomous regulation of HSPC quiescence and self-renewal. To test this hypothesis, we developed a novel experimental platform, which allows visualization of HSPC-OLC cell pairs in-vivo and retrieval of the individual OLCs for molecular analysis. We intravenously injected DiI labeled adult bone marrow-derived FACS-sorted Lin−Sca1+c-kit+CD34−Flk2− HSPCs into irradiated newborn collagen 2.3GFP mouse recipients; in this transgenic strain, the majority of the OLCs are labeled with green fluorescent protein (GFP). 48 hours later, we sacrificed the animals and obtained fresh unfixed sections of femoral trabecular bone. Using a combination of differential interference contrast fluorescent microscopy, in-situ enzymatic digestion and micromanipulation, we harvested individual GFP-positive OLCs located within 2 cell diameters (“niche” OLCs) or greater than 5 cell diameters (“control” OLCs) from single DiI-bright HSPCs. Following reverse transcription and cDNA amplification with 29 cycles of PCR, as per the single cell RNA-Seq protocol (Tang et al, Nature Protocols 2010), we performed real-time RT-PCR analysis of 31 samples – 15 niche cells and 16 controls - for the OLC signature genes (osteocalcin, osterix) and for the genes implicated in playing a functional role in the HSPC-OLC cell interaction (osteopontin, CXCL12, angiopoietin 1). Transcripts for GAPDH, collagen 1 and GFP served as positive controls for the amplification. As expected, all cells were positive for GFP and over 85% cells expressed collagen 1. Osteopontin and CXCL12 were expressed at a similar level and frequency in the niche and control OLCs. However, we found that angiopoietin 1 transcripts were detected exclusively in the niche OLCs (3/15 versus 0/16, p <0.05 by Chi-squared). Moreover, niche OLCs were enriched for the osterix-positive cells (7/15 versus 2/16, p <0.05 by Chi-squared) and expressed a lower level of osteocalcin, as normalized for GAPDH expression (1.13 vs. 0.97, p< 0.05 by t-test). Our results suggest that niche OLCs may have a distinct molecular signature and reside within a population of very immature OLCs, as evidenced by the osterix + osteocalcin low phenotype. Further unbiased transcriptome characterization of these cells using genome-wide RNA-Seq assay is therefore likely to provide more evidence in support of our hypothesis and reveal novel non-cell autonomous regulators of HSPC quiescence. To our knowledge, this approach represents the first attempt to define molecular heterogeneity in-vivo at a single cell level using the micro-anatomical relationship between two heterologous cell types. Disclosures: Scadden: Fate Therapeutics: Equity Ownership.

Novel Chromosomal Rearrangements and Sequence Mutations in High-Risk Ph-Like Acute Lymphoblastic Leukemia

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 67-67
Author(s):  
Kathryn G. Roberts ◽  
Ryan D Morin ◽  
Jinghui Zhang ◽  
Martin Hirst ◽  
Richard C. Harvey ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
High Risk ◽  
Lymphoblastic Leukemia ◽  
Genetic Alterations ◽  
Cytokine Receptor ◽  
Negative Regulator ◽  
Rna Seq ◽  
Kinase Signaling ◽  
Rt Pcr ◽  
B Lineage

Abstract Abstract 67 Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, and relapsed B-lineage ALL remains a leading cause of cancer death in young people. Recent genomic analyses by our group and others identified a unique subtype of BCR-ABL-negative, high-risk B-ALL, with deletion or mutation of IKZF1 and a gene expression profile similar to BCR-ABL1-positive ALL (Ph-like ALL). Up to 50% of Ph-like patients harbor rearrangements of the cytokine receptor gene, CRLF2, with concomitant JAK mutations detected in ∼30%. However, the nature of genetic alterations activating kinase signaling in the remaining cases is unknown. To identify novel genetic alterations in Ph-like ALL, we performed transcriptome sequencing (RNA-seq) on 11 cases of Ph-like B-ALL (10 from the P9906 Children's Oncology Group trial and 1 from the St Jude Total XV study), and whole genome sequencing (WGS) on two of these. Using multiple complementary analysis pipelines including deFuse, Mosaik, CREST and CONSERTING, we identified novel rearrangements, structural variations and sequence mutations dysregulating cytokine receptor and kinase signaling in 10 cases. Putative rearrangements and sequence mutations were validated using RT-PCR, genomic PCR and Sanger sequencing. The spectrum of alterations included 3 cases with known IGH@CRLF2 rearrangement, 2 cases with the NUP214-ABL1 rearrangement, 1 case each with the in-frame fusions EBF1-PDGFRB, BCR-JAK2 or STRN3-JAK2, and 1 case with a cryptic IGH@-EPOR rearrangement. Detailed analysis of RNA-seq data revealed a 7.5 kb insertion of EPOR downstream of the enhancer domain in the IGH@ locus, which was not detected by fluorescence in situ hybridization. WGS identified an in-frame activating insertion in the transmembrane domain of IL7R (L242>FPGVC) in 1 index case, and recurrence screening identified similar IL7R sequence mutations in 8 cases from the P9906 cohort (N=188). This patient also harbored a focal homozygous deletion removing the first two exons of SH2B3 that was not evident by SNP array analysis. SH2B3 encodes LNK, a negative regulator of JAK2 signaling. Notably, all patients harbor genetic lesions affecting B-lymphoid development (e.g IKZF1), suggesting these events cooperate to drive B-lineage ALL. To determine the frequency of each fusion, candidate RT-PCR was performed on 231 cases from the COG AALL0232 trial of high-risk B-ALL, 40 (17%) of which were identified as Ph-like using Predictor Analysis of Microarrays (PAM). The EBF1-PDGFRB fusion was detected in 3 additional patients, each containing an intact PDGFRB kinase domain. No additional cases of NUP214-ABL1, BCR-JAK2, or STRN3-JAK2 were identified. Phosphoflow analysis on 3 primary ALL samples demonstrated increased CKRL phosphorylation in the NUP214-ABL1 case and tyrosine phosphorylation in the cases with BCR-JAK2 and STRN3-JAK2 fusions. Importantly, this activation was reduced with the tyrosine kinase inhibitors (TKI) imatinib, dasatinib and the T315I inhibitor XL228 in cells harboring the ABL1 fusion, and the JAK2 inhibitor, XL019, in the JAK2-rearranged samples. Furthermore, the novel EBF1-PDGFRB fusion transformed Ba/F3 cells to growth factor independence, induced constitutive activation of pSTAT5, pAkt, pERK1/2, and responded with low IC50 values to imatinib, dasatinib and the specific PDGFRB/FGFR inhibitor, dovitinib. Using complementary genomic approaches we show that rearrangements, sequence mutations and DNA copy number alterations dysregulating cytokine receptor and kinase signaling are a hallmark of Ph-like ALL. These data support the screening of patients at diagnosis to identify those with Ph-like ALL, characterize the genomic lesions driving this phenotype, and to determine those that may benefit from TKI treatment. Disclosures: Hunger: Bristol-Myers Squibb: Author's children own stock in BMS, Membership on an entity's Board of Directors or advisory committees.

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