Requirement for the orphan steroid receptor Nur77 in apoptosis of T-cell hybridomas

Apoptosis is a phenomenon observed during development of many cell types in many organisms. It is an internal, programmed cell death characterized by DNA fragmentation into nucleosome-size pieces. Anti-CD3-induced apoptosis in T-cell hybridomas and immature thymocytes requires new gene transcription and may be related to negative selection during T-cell development. Using subtractive hybridization, we isolated a complementary DNA clone encoding the orphan steroid receptor Nur77 (refs 7-9). It shows different patterns of messenger RNA induction between apoptotic and stimulated T cells. We report here the use of gel shift analysis to demonstrate that the Nur77 protein is present at high levels in apoptotic T-cell hybridomas and apoptotic thymocytes, but not in growing T cells or stimulated splenocytes. A Nur77 dominant negative protected T-cell hybridomas from activation-induced apoptosis. Hence Nur77 is necessary for induced apoptosis in T-cell hybridomas.

A library of gene expression signatures to illuminate normal and pathological lymphoid biology

Genomics has provided a lever to pry open lymphoid cells and examine their regulatory biology. The large body of available gene expression data has also allowed us to define the of coordinately expressed genes, termed gene expression signatures, which characterize the states of cellular physiology that reflect cellular differentiation, activation of signaling pathways, and the action of transcription factors. Gene expression signatures that reflect the action of individual transcription factors can be defined by perturbing transcription factor function using RNA interference (RNAi), small-molecule inhibition, and dominant-negative approaches. We have used this methodology to define gene expression signatures of various transcription factors controlling B-cell differentiation and activation, including BCL-6, B lymphocyte-induced maturation protein-1 (Blimp-1), X-box binding protein-1 (XBP1), nuclear factor-kappaB (NF-kappaB), and c-myc. We have also curated a wide variety of gene expression signatures from the literature and assembled these into a signature database. Statistical methods can define whether any signature in this database is differentially expressed in independent biological samples, an approach we have used to gain mechanistic insights into the origin and clinical behavior of B-cell lymphomas. We also discuss the use of genomic-scale RNAi libraries to identify genes and pathways that may serve as therapeutic targets in B-cell malignancies.

Identification of FGFR4-activating mutations in human rhabdomyosarcomas that promote metastasis in xenotransplanted models

Rhabdomyosarcoma (RMS) is a childhood cancer originating from skeletal muscle, and patient survival is poor in the presence of metastatic disease. Few determinants that regulate metastasis development have been identified. The receptor tyrosine kinase FGFR4 is highly expressed in RMS tissue, suggesting a role in tumorigenesis, although its functional importance has not been defined. Here, we report the identification of mutations in FGFR4 in human RMS tumors that lead to its activation and present evidence that it functions as an oncogene in RMS. Higher FGFR4 expression in RMS tumors was associated with advanced-stage cancer and poor survival, while FGFR4 knockdown in a human RMS cell line reduced tumor growth and experimental lung metastases when the cells were transplanted into mice. Moreover, 6 FGFR4 tyrosine kinase domain mutations were found among 7 of 94 (7.5%) primary human RMS tumors. The mutants K535 and E550 increased autophosphorylation, Stat3 signaling, tumor proliferation, and metastatic potential when expressed in a murine RMS cell line. These mutants also transformed NIH 3T3 cells and led to an enhanced metastatic phenotype. Finally, murine RMS cell lines expressing the K535 and E550 FGFR4 mutants were substantially more susceptible to apoptosis in the presence of a pharmacologic FGFR inhibitor than the control cell lines expressing the empty vector or wild-type FGFR4. Together, our results demonstrate that mutationally activated FGFR4 acts as an oncogene, and these are what we believe to be the first known mutations in a receptor tyrosine kinase in RMS. These findings support the potential therapeutic targeting of FGFR4 in RMS.

Cutting Edge: IL-36 Receptor Promotes Resolution of Intestinal Damage

IL-1 family members are central mediators of host defense. In this article, we show that the novel IL-1 family member IL-36γ was expressed during experimental colitis and human inflammatory bowel disease. Germ-free mice failed to induce IL-36γ in response to dextran sodium sulfate (DSS)-induced damage, suggesting that gut microbiota are involved in its induction. Surprisingly, IL-36R-deficient (Il1rl2(-/-)) mice exhibited defective recovery following DSS-induced damage and impaired closure of colonic mucosal biopsy wounds, which coincided with impaired neutrophil accumulation in the wound bed. Failure of Il1rl2(-/-) mice to recover from DSS-induced damage was associated with a profound reduction in IL-22 expression, particularly by colonic neutrophils. Defective recovery of Il1rl2(-/-) mice could be rescued by an aryl hydrocarbon receptor agonist, which was sufficient to restore IL-22 expression and promote full recovery from DSS-induced damage. These findings implicate the IL-36/IL-36R axis in the resolution of intestinal mucosal wounds.

Deciphering the genetic code of DNA methylation

DNA methylation plays crucial roles in many biological processes and abnormal DNA methylation patterns are often observed in diseases. Recent studies have shed light on cis-acting DNA elements that regulate locus-specific DNA methylation, which involves transcription factors, histone modification and DNA secondary structures. In addition, several recent studies have surveyed DNA motifs that regulate DNA methylation and suggest potential applications in diagnosis and prognosis. Here, we discuss the current biological foundation for the cis-acting genetic code that regulates DNA methylation. We review the computational models that predict DNA methylation with genetic features and discuss the biological insights revealed from these models. We also provide an in-depth discussion on how to leverage such knowledge in clinical applications, particularly in the context of liquid biopsy for early cancer diagnosis and treatment.

Elemental and configural learning and the perception of odorant mixtures by the spiny lobster Panulirus argus

The present study used a conditioning assay to investigate if the type of learning task that spiny lobsters (Panulirus argus) were required to perform influenced the way that they perceived odorant mixtures. Mixtures were composed of 2 food-related compounds (adenosine-5'-monophosphate, betaine, or L-glutamate) at concentrations that produced the same duration of searching behavior in unconditioned animals. Aversive conditioning of search behavior coupled with generalization testing was used to evaluate perceptual similarity between related mixtures. When animals were conditioned to stop searching to a binary mixture AX, they did not generalize significantly from this mixture to either of its components (A or X), or to a binary mixture containing one novel component (AY). However, when lobsters were conditioned to avoid AX but to continue responding to AY, they generalized between AX and X and between AY and Y. The results support the hypothesis that altering the salience of a mixture's components by giving them different reinforcement contingencies changed the way that the mixtures were perceived. As a result of such conditioning, animals perceived the mixture's components as separate elements, rather than as a configuration, and, as a consequence, animals generalized between binary mixtures and their most salient or predictive components.

Identification of DNA motifs that regulate DNA methylation

DNA methylation is an important epigenetic mark but how its locus-specificity is decided in relation to DNA sequence is not fully understood. Here, we have analyzed 34 diverse whole-genome bisulfite sequencing datasets in human and identified 313 motifs, including 92 and 221 associated with methylation (methylation motifs, MMs) and unmethylation (unmethylation motifs, UMs), respectively. The functionality of these motifs is supported by multiple lines of evidence. First, the methylation levels at the MM and UM motifs are respectively higher and lower than the genomic background. Second, these motifs are enriched at the binding sites of methylation modifying enzymes including DNMT3A and TET1, indicating their possible roles of recruiting these enzymes. Third, these motifs significantly overlap with "somatic QTLs" (quantitative trait loci) of methylation and expression. Fourth, disruption of these motifs by mutation is associated with significantly altered methylation level of the CpGs in the neighbor regions. Furthermore, these motifs together with somatic mutations are predictive of cancer subtypes and patient survival. We revealed some of these motifs were also associated with histone modifications, suggesting a possible interplay between the two types of epigenetic modifications. We also found some motifs form feed forward loops to contribute to DNA methylation dynamics.

Developmental partitioning of SYK and ZAP70 prevents autoimmunity and cancer

Even though SYK and ZAP70 kinases share high sequence homology and serve analogous functions, their expression in B and T cells is strictly segregated throughout evolution. Here, we identified aberrant ZAP70 expression as a common feature in a broad range of B cell malignancies. We validated SYK as the kinase that sets the thresholds for negative selection of autoreactive and premalignant clones. When aberrantly expressed in B cells, ZAP70 competes with SYK at the BCR signalosome and redirects SYK from negative selection to tonic PI3K signaling, thereby promoting B cell survival. In genetic mouse models for B-ALL and B-CLL, conditional expression of Zap70 accelerated disease onset, while genetic deletion impaired malignant transformation. Inducible activation of Zap70 during B cell development compromised negative selection of autoreactive B cells, resulting in pervasive autoantibody production. Strict segregation of the two kinases is critical for normal B cell selection and represents a central safeguard against the development of autoimmune disease and B cell malignancies.

Finding de novo methylated DNA motifs

MOTIVATION

Increasing evidence has shown that nucleotide modifications such as methylation and hydroxymethylation on cytosine would greatly impact the binding of transcription factors (TFs). However, there is a lack of motif finding algorithms with the function to search for motifs with modified bases. In this study, we expand on our previous motif finding pipeline Epigram to provide systematic de novo motif discovery and performance evaluation on methylated DNA motifs.

RESULTS

mEpigram outperforms both MEME and DREME on finding modified motifs in simulated data that mimics various motif enrichment scenarios. Furthermore we were able to identify methylated motifs in Arabidopsis DNA affinity purification sequencing (DAP-seq) data that were previously demonstrated to contain such motifs. When applied to TF ChIP-seq and DNA methylome data in H1 and GM12878, our method successfully identified novel methylated motifs that can be recognized by the TFs or their co-factors. We also observed spacing constraint between the canonical motif of the TF and the newly discovered methylated motifs, which suggests operative recognition of these cis-elements by collaborative proteins.

AVAILABILITY AND IMPLEMENTATION

The mEpigram program is available at http://wanglab.ucsd.edu/star/mEpigram.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Atypical Presentation of Escherichia coli Monomicrobial Necrotizing Fasciitis in a Renal Transplant Patient: A Case Report

Skin and soft tissue infections (SSTIs) are one of most frequent infectious causes for referral to the emergency department and one of the most frequent infectious causes of hospital admissions. Escherichia coli, the most commonly occurring gram-negative pathogen involved in these infections, contributes to about 7% of all SSTIs cases where gram-positive organisms reign dominant. Patients are more susceptible to these gram-negative SSTIs if they are neutropenic, have hematologic malignancies, have undergone solid organ or hematopoietic transplantation, or have cirrhotic liver disease. Due to their immunocompromised state, the prognosis is very poor and not well understood. We report a case of an atypical presentation of an E coli monomicrobial necrotizing fasciitis in a renal transplant patient. Our findings support improved mortality with rapid aggressive interventions, such as amputation, in immunocompromised patients.

A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus

BACKGROUND

Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation.

RESULTS

To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF).

CONCLUSIONS

Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.

A bioinformatics screen reveals Hox and chromatin remodeling factors at the Drosophila histone locus

Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.

Abstract 3898: Octamer Binding Protein-2 (Oct-2): A non-oncogene addiction in germinal center derived lymphomas and a promising therapeutic target

To identify genes required for the proliferation and survival of Diffuse Large B Cell Lymphomas (DLBCL) we conducted an “Achilles Heel” RNA interference screen in cell lines model of ABC (Activated B Cell-like) and GCB (Germinal Center B-cell like) DLBCL subtypes. One of the most toxic shRNAs in this screen targeted Oct2, encoding a POU domain transcriptional activator, primarily lymphoid restricted. It was identified due its ability to bind the DNA octamer motif (ATGCAAAT) within immunoglobulin (Ig) genes promoters. The B cell specific coactivator OCA-B interacts with Oct-2 enhancing its transactivation potential. Although Oct2 and OCA-B are dipensable for Ig transcription, they are essential for germinal center (GC) development. To understand the apoptotic cell death of DLBCL cells following shRNA Oct2 induction we investigated the genetic pathways controlled by Oct2. We profiled gene expression changes in DLBCL cells upon Oct2 knocked down and merged this data with genome-wide assessment of Oct2 and OCA-B binding sites, coupling chromatin immunoprecipitation (ChiP) with high-throughput sequencing (ChIPSeq). More than 60% of the Oct2 target genes also showed OCA-B biding. The Oct2/OCA-B overlapping set of targets was enriched for genes selectively expressed in GC B cells. We found that Oct2/OCA-B lie upstream many transcription factors known to play critical roles in GC development such as BCL6, MTA3, PU.1, IRF8 and SpiB. Oct2 regulates these genes in DLBCL cells and in centroblasts. Among Oct-2 downstream effectors, BCL6 could rescue DLBCL cells from the Oct2 shRNA lethal effect. The Oct2/OCA-B binding of BCL6 promoter was confirmed by single locus ChIP in primary GC B-cells and derived lymphomas. Gel shifts experiments showed that Oct2 binds a non canonical octamer site at the BCL6 transcription start site. Our findings uncovered a novel aspect of the Oct2 biology believed to regulate the activity of octamer containing promoters. Interestingly, Oct2 controls the expression of GC specific genes that do not harbor a canonical octamer motif. By array CGH, amplification of Oct2 and OCA-B was found in less than 1% of non Hodgkin lymphoma (NHL) patient samples. Nonetheless, lymphoma cells become dependent on the Oct2 controlled network to survive, being an example of non oncogene addiction. This turns Oct2 into an attractive therapeutic target for NHL treatment. Oct2 and OCA-B lie upstream of BCL6, widely considered a master regulator of the GC response, suggesting that Oct2 directed therapy should kill the same DLBCLs as BCL6 Peptide Inhibitor. Furthermore, all GC and Post-GC B cells tested require Oct2 for survival, indicating that Oct2 directed therapy might have a broder activity spectrum than the BCL6 directed therapy. The Oct2/OCA-B binding interface would be amenable to attack with potential manageable toxicity since this interaction is exclusively required in GC B cells.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3898.

Abstract LB-239: An rnai sensitization screen identifies compensatory IKKα activation during IKKβ inhibition

Introduction: We previously described a subtype of diffuse large B-cell lymphoma (DLBCL) termed activated B-cell-like (ABC) DLBCL that depends on NF-κB activity for survival, and showed that a specific small molecule inhibitor of the upstream kinase IKKβ is selectively toxic to this subgroup of lymphoma.

Methods: To identify proteins or pathways whose inhibition may synergize with the toxicity of IKKβ inhibition in ABC DLBCL, we performed an “RNAi sensitization” screen with an RNA interference library, directed against 500 protein kinases, in the presence of the specific IKKβ inhibitor in an ABC DLBCL cell line.

Results: Short hairpin RNA (shRNAs) targeting IKKα, a component of the IKK complex, enhanced killing by the IKKβ inhibitor in ABC DLBCL cell lines but not other lymphoma cell lines. Gene expression profiling and NF-κB-specific reporter assays showed that IKKα shRNA affects the classical NF-κB pathway, further inhibiting the phosphorylation of IκBα only in the presence of the specific IKKβ inhibitor. Further studies in physiologic models of lymphocyte stimulation showed that compensatory IKKα activity occurs in other settings.

Conclusions: These results demonstrate that loss-of-function screens in the presence of a defined inhibitor can identify therapeutic targets in cancers, providing a rationale for combination therapies targeting multiple pathways critical to an individual cancer.

470 Financial and Efficacy Analysis of a Centralised Neck of Femur Fracture Service

Aim

Osteoporotic fractures are rising in incidence, costing the National Health Service up to £1.1 billion for hospital care. The implementation of the Best Practice Tariff (BPT) of fragility fractures in 2010 created a financial incentive to achieve standards of best practice. In June 2015, a dedicated hip fracture unit (HFU) was set up at Princess Royal Hospital (PRH). The aim of this study is (A) to assess changes in performance to the BPT after the introduction of a dedicated HFU, and (B) whether the performance of a HFU is affected by direct/indirect presentation to the HFU.

Method

The performance of Brighton and Sussex University Hospitals (BSUH) to BPT pre and post HFU was assessed by a retrospective review of BPT performance data between 2015 and 2016. 870 patients who were treated for NOFF at BSUH were reviewed to assess whether the performance of the HFU was impacted by patients presenting either directly (PRH) to the HFU or indirectly (presentation to Royal Sussex County Hospital). Appropriate statistical tests were used to analyse the significant differences between these outcome measures.

Results

The comparison between pre and post HFU showed there was a significant increase in the time between A&E admission to ward, theatre or orthogeriatric (OG) assessment (P < 0.001) in patients presenting indirectly to HFU compared to direct presentations.

Conclusions

Having a HFU is cost neutral, and advantages of HFU include focusing NOFF care which improves in patient care. BPT achievements could be improved by increasing the direct admission of NOFF to the HFU.

Predicting regional somatic mutation rates using DNA motifs

How the locus-specificity of epigenetic modifications is regulated remains an unanswered question. A contributing mechanism is that epigenetic enzymes are recruited to specific loci by DNA binding factors recognizing particular sequence motifs (referred to as epi-motifs). Using these motifs to predict biological outputs depending on local epigenetic state such as somatic mutation rates would confirm their functionality. Here, we used DNA motifs including known TF motifs and epi-motifs as a surrogate of epigenetic signals to predict somatic mutation rates in 13 cancers at an average 23kbp resolution. We implemented an interpretable neural network model, called contextual regression, to successfully learn the universal relationship between mutations and DNA motifs, and uncovered motifs that are most impactful on the regional mutation rates such as TP53 and epi-motifs associated with H3K9me3. Furthermore, we identified genomic regions with significantly higher mutation rates than the expected values in each individual tumor and demonstrated that such cancer-related regions can accurately predict cancer types. Interestingly, we found that the same mutation signatures often have different contributions to cancer-related and cancer-independent regions, and we also identified the motifs with the most contribution to each mutation signature.

Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss

Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus sequences. We name this representation as sequence Motto and have implemented an efficient algorithm with flexible options for converting motif PWMs into Motto from nucleotides, amino acids, and customized characters. We show that this representation provides a simple and efficient way to identify the binding sites of 1156 common transcription factors (TFs) in the human genome. The effectiveness of the method was benchmarked by comparing sequence matches found by Motto with PWM scanning results found by FIMO. On average, our method achieves a 0.81 area under the precision-recall curve, significantly (P-value < 0.01) outperforming all existing methods, including maximal positional weight, Cavener's method, and minimal mean square error. We believe this representation provides a distilled summary of a motif, as well as the statistical justification.