Malignant A-to-I RNA editing by ADAR1 drives T cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing

Leukemia-initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches. Here, we show that the RNA-editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine editing is a common attribute of relapsed T cell acute lymphoblastic leukemia (T-ALL) regardless of molecular subtype. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL patient-derived xenograft models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA to avoid detection by the innate immune sensor melanoma differentiation-associated protein 5 (MDA5). Moreover, we uncover that the cell-intrinsic level of MDA5 dictates the dependency on the ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents an effective therapeutic strategy for eliminating T-ALL LICs.

Lipopolysaccharide-induced chronic inflammation increases female serum gonadotropins and shifts the pituitary transcriptomic landscape

Introduction

Female reproductive function depends on a choreographed sequence of hormonal secretion and action, where specific stresses such as inflammation exert profound disruptions. Specifically, acute LPS-induced inflammation inhibits gonadotropin production and secretion from the pituitary, thereby impacting the downstream production of sex hormones. These outcomes have only been observed in acute inflammatory stress and little is known about the mechanisms by which chronic inflammation affects reproduction. In this study we seek to understand the chronic effects of LPS on pituitary function and consequent luteinizing and follicle stimulating hormone secretion.

Methods

A chronic inflammatory state was induced in female mice by twice weekly injections with LPS over 6 weeks. Serum gonadotropins were measured and bulk RNAseq was performed on the pituitaries from these mice, along with basic measurements of reproductive biology.

Results

Surprisingly, serum luteinizing and follicle stimulating hormone was not inhibited and instead we found it was increased with repeated LPS treatments.

Discussion

Analysis of bulk RNA-sequencing of murine pituitary revealed paracrine activation of TGFβ pathways as a potential mechanism regulating FSH secretion in response to chronic LPS. These results provide a framework with which to begin dissecting the impacts of chronic inflammation on reproductive physiology.

A Network Landscape of HPVOPC Reveals Methylation Alterations as Significant Drivers of Gene Expression via an Immune-Mediated GPCR Signal

HPV-associated oropharynx carcinoma (HPVOPC) tumors have a relatively low mutational burden. Elucidating the relative contributions of other tumor alterations, such as DNA methylation alterations, alternative splicing events (ASE), and copy number variation (CNV), could provide a deeper understanding of carcinogenesis drivers in this disease. We applied network propagation analysis to multiple classes of tumor alterations in a discovery cohort of 46 primary HPVOPC tumors and 25 cancer-unaffected controls and validated our findings with TCGA data. We identified significant overlap between differential gene expression networks and all alteration classes, and this association was highest for methylation and lowest for CNV. Significant overlap was seen for gene clusters of G protein-coupled receptor (GPCR) pathways. HPV16-human protein interaction analysis identified an enriched cluster defined by an immune-mediated GPCR signal, including CXCR3 cytokines CXCL9, CXCL10, and CXCL11. CXCR3 was found to be expressed in primary HPVOPC, and scRNA-seq analysis demonstrated CXCR3 ligands to be highly expressed in M2 macrophages. In vivo models demonstrated decreased tumor growth with antagonism of the CXCR3 receptor in immunodeficient but not immunocompetent mice, suggesting that the CXCR3 axis can drive tumor proliferation in an autocrine fashion, but the effect is tempered by an intact immune system. In conclusion, methylation, ASE, and SNV alterations are highly associated with network gene expression changes in HPVOPC, suggesting that ASE and methylation alterations have an important role in driving the oncogenic phenotype. Network analysis identifies GPCR networks, specifically the CXCR3 chemokine axis, as modulators of tumor-immune interactions that may have proliferative effects on primary tumors as well as a role for immunosurveillance; however, CXCR3 inhibition should be used with caution, as these agents may both inhibit and stimulate tumor growth considering the competing effects of this cytokine axis. Further investigation is needed to explore opportunities for targeted therapy in this setting.

Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing

Leukemia initiating cells (LICs) are regarded as the origin of leukemia relapse and therapeutic resistance. Identifying direct stemness determinants that fuel LIC self-renewal is critical for developing targeted approaches to eliminate LICs and prevent relapse. Here, we show that the RNA editing enzyme ADAR1 is a crucial stemness factor that promotes LIC self-renewal by attenuating aberrant double-stranded RNA (dsRNA) sensing. Elevated adenosine-to-inosine (A-to-I) editing is a common attribute of relapsed T-ALL regardless of molecular subtypes. Consequently, knockdown of ADAR1 severely inhibits LIC self-renewal capacity and prolongs survival in T-ALL PDX models. Mechanistically, ADAR1 directs hyper-editing of immunogenic dsRNA and retains unedited nuclear dsRNA to avoid detection by the innate immune sensor MDA5. Moreover, we uncovered that the cell intrinsic level of MDA5 dictates the dependency on ADAR1-MDA5 axis in T-ALL. Collectively, our results show that ADAR1 functions as a self-renewal factor that limits the sensing of endogenous dsRNA. Thus, targeting ADAR1 presents a safe and effective therapeutic strategy for eliminating T-ALL LICs.

Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome

BACKGROUND

Disabling pansclerotic morphea (DPM) is a rare systemic inflammatory disorder, characterized by poor wound healing, fibrosis, cytopenias, hypogammaglobulinemia, and squamous-cell carcinoma. The cause is unknown, and mortality is high.

METHODS

We evaluated four patients from three unrelated families with an autosomal dominant pattern of inheritance of DPM. Genomic sequencing independently identified three heterozygous variants in a specific region of the gene that encodes signal transducer and activator of transcription 4 (STAT4). Primary skin fibroblast and cell-line assays were used to define the functional nature of the genetic defect. We also assayed gene expression using single-cell RNA sequencing of peripheral-blood mononuclear cells to identify inflammatory pathways that may be affected in DPM and that may respond to therapy.

RESULTS

Genome sequencing revealed three novel heterozygous missense gain-of-function variants in STAT4. In vitro, primary skin fibroblasts showed enhanced interleukin-6 secretion, with impaired wound healing, contraction of the collagen matrix, and matrix secretion. Inhibition of Janus kinase (JAK)-STAT signaling with ruxolitinib led to improvement in the hyperinflammatory fibroblast phenotype in vitro and resolution of inflammatory markers and clinical symptoms in treated patients, without adverse effects. Single-cell RNA sequencing revealed expression patterns consistent with an immunodysregulatory phenotype that were appropriately modified through JAK inhibition.

CONCLUSIONS

Gain-of-function variants in STAT4 caused DPM in the families that we studied. The JAK inhibitor ruxolitinib attenuated the dermatologic and inflammatory phenotype in vitro and in the affected family members. (Funded by the American Academy of Allergy, Asthma, and Immunology Foundation and others.).

Detection and targeting of splicing deregulation in pediatric acute myeloid leukemia stem cells

Pediatric acute myeloid leukemia (pAML) is typified by high relapse rates and a relative paucity of somatic DNA mutations. Although seminal studies show that splicing factor mutations and mis-splicing fuel therapy-resistant leukemia stem cell (LSC) generation in adults, splicing deregulation has not been extensively studied in pAML. Herein, we describe single-cell proteogenomics analyses, transcriptome-wide analyses of FACS-purified hematopoietic stem and progenitor cells followed by differential splicing analyses, dual-fluorescence lentiviral splicing reporter assays, and the potential of a selective splicing modulator, Rebecsinib, in pAML. Using these methods, we discover transcriptomic splicing deregulation typified by differential exon usage. In addition, we discover downregulation of splicing regulator RBFOX2 and CD47 splice isoform upregulation. Importantly, splicing deregulation in pAML induces a therapeutic vulnerability to Rebecsinib in survival, self-renewal, and lentiviral splicing reporter assays. Taken together, the detection and targeting of splicing deregulation represent a potentially clinically tractable strategy for pAML therapy.

Transient genomic instability drives tumorigenesis through accelerated clonal evolution

In this study, Shoshani et al. tested the role of aneuploidy in tumor initiation and progression, and generated mice with random aneuploidies by transient induction of polo-like kinase 4 (Plk4), a master regulator of centrosome number. Their findings show how transient CIN generates cells with random aneuploidies from which ones that acquire a karyotype with specific chromosome gains are sufficient to drive cancer formation, and that distinct CIN mechanisms can lead to similar karyotypic cancer-causing outcomes.

Abnormal numerical and structural chromosome content is frequently found in human cancer. To test the role of aneuploidy in tumor initiation and progression, we generated mice with random aneuploidies by transient induction of polo-like kinase 4 (Plk4), a master regulator of centrosome number. Short-term chromosome instability (CIN) from transient Plk4 induction resulted in formation of aggressive T-cell lymphomas in mice with heterozygous inactivation of one p53 allele and accelerated tumor development in the absence of p53. Transient CIN increased the frequency of lymphoma-initiating cells with a specific karyotype profile, including trisomy of chromosomes 4, 5, 14, and 15 occurring early in tumorigenesis. Tumor development in mice with chronic CIN induced by an independent mechanism (through inactivation of the spindle assembly checkpoint) gradually trended toward a similar karyotypic profile, as determined by single-cell whole-genome DNA sequencing. Overall, we show how transient CIN generates cells with random aneuploidies from which ones that acquire a karyotype with specific chromosome gains are sufficient to drive cancer formation, and that distinct CIN mechanisms can lead to similar karyotypic cancer-causing outcomes.

Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution

Inflammation-dependent base deaminases promote therapeutic resistance in many malignancies. However, their roles in human pre-leukemia stem cell (pre-LSC) evolution to acute myeloid leukemia stem cells (LSCs) had not been elucidated. Comparative whole-genome and whole-transcriptome sequencing analyses of FACS-purified pre-LSCs from myeloproliferative neoplasm (MPN) patients reveal APOBEC3C upregulation, an increased C-to-T mutational burden, and hematopoietic stem and progenitor cell (HSPC) proliferation during progression, which can be recapitulated by lentiviral APOBEC3C overexpression. In pre-LSCs, inflammatory splice isoform overexpression coincides with APOBEC3C upregulation and ADAR1p150-induced A-to-I RNA hyper-editing. Pre-LSC evolution to LSCs is marked by STAT3 editing, STAT3β isoform switching, elevated phospho-STAT3, and increased ADAR1p150 expression, which can be prevented by JAK2/STAT3 inhibition with ruxolitinib or fedratinib or lentiviral ADAR1 shRNA knockdown. Conversely, lentiviral ADAR1p150 expression enhances pre-LSC replating and STAT3 splice isoform switching. Thus, pre-LSC evolution to LSCs is fueled by primate-specific APOBEC3C-induced pre-LSC proliferation and ADAR1-mediated splicing deregulation.

Abstract 5726: A-to-I RNA deaminase deregulation in pre-leukemia stem cell evolution

While inflammation induced ADAR1 RNA deaminases protect the human genome from retroviral integration, deregulation promotes therapeutic resistance in many malignancies. However, the combinatorial role of these deaminases in pre-leukemia stem cell (pre-LSC) evolution to therapy resistant LSC had not been elucidated. Thus, we performed whole genome sequencing (WGS) analysis of 43 CD34+pre-leukemic myeloproliferative neoplasm (MPN) samples compared with matched saliva and non-MPN controls andwhole transcriptome sequencing (RNA-seq) analysis of 113 FACS-purified hematopoietic stem cells (HSC) and hematopoietic progenitor cells (HPC) from MPN, acute myeloid leukemia (AML) and healthy young and aged samples. During MPN progression, inflammation-driven ADAR1 isoform p150 upregulation corresponded with increased Adenosine-to-Inosine (A-to-I) transitions in both MPN stem and progenitor populations. We identified unique A-to-I editing events in coding regions that are associated with either normal stem progenitors or with MPN progenitors. In addition, STAT3 transcript hyper-editing leads to STAT3beta splice isoform expression. Moreover, lentiviral ADAR1p150 overexpression enhanced replating as well as beta-catenin activation, which was reversed by lentiviral shRNA ADAR1 knockdown. In summary, innate immune deaminase deregulation fuels pre-LSC evolution to LSC and may represent a vital LSC therapeutic vulnerability.

Citation Format: Qingfei Jiang, Frida Holm, Jane Isquith, Adam Mark, Cayla Mason, Eduardo Reynoso, Isabella Morris, Wenxue Ma, Raymond Diep, Jessica Pham, Chanond Nasamran, Guorong Xu, Roman Sasik, Sara Brin Rosenthal, Amanda Birmingham, Leslie Crews, Gabriel Pineda, Thomas Whisenant, Kathleen Fisch, Catriona Jamieson. A-to-I RNA deaminase deregulation in pre-leukemia stem cell evolution [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5726.

Nuclear Parkin Activates the ERRα Transcriptional Program and Drives Widespread Changes in Gene Expression Following Hypoxia

Parkin is an E3 ubiquitin ligase well-known for facilitating clearance of damaged mitochondria by ubiquitinating proteins on the outer mitochondrial membrane. However, knowledge of Parkin's functions beyond mitophagy is still limited. Here, we demonstrate that Parkin has functions in the nucleus and that Parkinson's disease-associated Parkin mutants, ParkinR42P and ParkinG430D, are selectively excluded from the nucleus. Further, Parkin translocates to the nucleus in response to hypoxia which correlates with increased ubiquitination of nuclear proteins. The serine-threonine kinase PINK1 is responsible for recruiting Parkin to mitochondria, but translocation of Parkin to the nucleus occurs independently of PINK1. Transcriptomic analyses of HeLa cells overexpressing wild type or a nuclear-targeted Parkin revealed that during hypoxia, Parkin contributes to both increased and decreased transcription of genes involved in regulating multiple metabolic pathways. Furthermore, a proteomics screen comparing ubiquitinated proteins in hearts from Parkin-/- and Parkin transgenic mice identified the transcription factor estrogen-related receptor α (ERRα) as a potential Parkin target. Co-immunoprecipitation confirmed that nuclear-targeted Parkin interacts with and ubiquitinates ERRα. Further analysis uncovered that nuclear Parkin increases the transcriptional activity of ERRα. Overall, our study supports diverse roles for Parkin and demonstrates that nuclear Parkin regulates transcription of genes involved in multiple metabolic pathways.

Cognitive biases and knowledge deficits leading to delayed recognition of cryptococcal meningitis

Cryptococcal meningitis is a potentially devastating infectious complication of immunosuppression best characterized in individuals with HIV. Early recognition of and appropriate antifungal therapy for cryptococcal meningitis has a profound effect on outcomes, but with more varied presentations in well-resourced countries recognition may be delayed. We present four cases of cryptococcal meningitis in immunosuppressed patients, each with significant delays in diagnosis. Pulling from recollections of providers and the documented chart assessments, we discuss and tabulate the cognitive biases and diagnostic errors that contributed to delay. We further explore the knowledge deficits regarding cryptococcal meningitis that appeared in these cases. Once meningitis was considered, each of these cases of cryptococcal meningitis was rapidly diagnosed. Diagnostic delay was driven by knowledge deficits, followed by common biases such as availability heuristics and premature closing. These delays could be countered by maintaining broad differential diagnoses, re-evaluating the patient presentation after recognition of immunosuppression, and early consultation of specialists. Delay in diagnosis of cryptococcal meningitis is associated with high morbidity and mortality. By exploring the various case presentations and errors made, we hope to provide a counter to some of the knowledge deficits associated with cryptococcal meningitis, and to provide actionable advice for early consultation to infectious disease specialists in order to improve outcomes.

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

The original version of this Article contained an error in the author affiliations. Trey Ideker was incorrectly associated with 'Department of Medicine (Oncology), Stanford University School of Medicine, 875 Blake Wilbur Dr, Palo Alto, CA 94304, USA.' This has now been corrected in both the PDF and HTML versions of the Article.

Mutation of chromatin regulators and focal hotspot alterations characterize human papillomavirus-positive oropharyngeal squamous cell carcinoma

BACKGROUND

Human papillomavirus (HPV)-associated oropharyngeal cancer is a disease clinically and biologically distinct from smoking-related head and neck squamous cell carcinoma (HNSCC). Despite its rapidly increasing incidence, the mutational landscape of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) remains understudied.

METHODS

This article presents the first mutational analysis of the 46 HPV+ OPSCC tumors within the newly expanded cohort of 530 HNSCC tumors from The Cancer Genome Atlas. A separate exome sequencing analysis was also performed for 46 HPV+ OPSCCs matched to their normal lymphocyte controls from the Johns Hopkins University cohort.

RESULTS

There was a strikingly high 33% frequency of mutations within genes associated with chromatin regulation, including mutations in lysine methyltransferase 2C (KMT2C), lysine methyltransferase 2D (KMT2D), nuclear receptor binding SET domain protein 1 (NSD1), CREB binding protein (CREBBP), E1A-associated protein p300 (EP300), and CCCTC-binding factor (CTCF). In addition, the commonly altered genes phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA) and fibroblast growth factor receptor 3 (FGFR3) showed distinct domain-specific hotspot mutations in comparison with their HPV- counterparts. PIK3CA showed a uniquely high rate of mutations within the helicase domain, and FGFR3 contained a predominance of hotspot S249C alterations that were not found in HPV- HNSCC.

CONCLUSIONS

This analysis represents one of the largest studies to date of HPV+ OPSCC and lends novel insight into the genetic landscape of this biologically distinct disease, including a high rate of mutations in histone- and chromatin-modifying genes, which may offer novel therapeutic targets.

WITHDRAWN: Fighting for access: Research at the National Abortion Federation's 43rd Annual Meeting

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RNA based individualized drug selection in breast cancer patients without patient-matched normal tissue

Background

While standard RNA expression tests stratify patients into risk groups, RNA-Seq can guide personalized drug selection based on expressed mutations, fusion genes, and differential expression (DE) between tumor and normal tissue. However, patient-matched normal tissue may be unavailable. Additionally, biological variability in normal tissue and technological biases may confound results. Therefore, we present normal expression reference data for two sequencing methods that are suitable for breast biopsies.

Results

We identified breast cancer related and drug related genes that are expressed uniformly across our normal samples. Large subsets of these genes are identical for formalin fixed paraffin embedded samples and fresh frozen samples. Adipocyte signatures were detected in frozen compared to formalin samples, prepared by surgeons and pathologists, respectively. Gene expression confounded by adipocytes was identified using fat tissue samples. Finally, immune repertoire statistics were obtained for healthy breast, tumor and fat tissues.

Conclusions

Our reference data can be used with patient tumor samples that are asservated and sequenced with a matching aforementioned method. Coefficients of variation are given for normal gene expression. Thus, potential drug selection can be based on confidently overexpressed genes and immune repertoire statistics.

Materials and Methods

Normal expression from formalin and frozen healthy breast tissue samples using Roche Kapa RiboErase (total RNA) (19 formalin, 9 frozen) and Illumina TruSeq RNA Access (targeted RNA-Seq, aka TruSeq RNA Exome) (11 formalin, 1 frozen), and fat tissue (6 frozen Access). Tumor DE using 10 formalin total RNA tumor samples and 1 frozen targeted RNA tumor sample.

H3K27 Methylation Dynamics during CD4 T Cell Activation: Regulation of JAK/STAT and IL12RB2 Expression by JMJD3

The changes to the epigenetic landscape in response to Ag during CD4 T cell activation have not been well characterized. Although CD4 T cell subsets have been mapped globally for numerous epigenetic marks, little has been done to study their dynamics early after activation. We have studied changes to promoter H3K27me3 during activation of human naive and memory CD4 T cells. Our results show that these changes occur relatively early (1 d) after activation of naive and memory cells and that demethylation is the predominant change to H3K27me3 at this time point, reinforcing high expression of target genes. Additionally, inhibition of the H3K27 demethylase JMJD3 in naive CD4 T cells demonstrates how critically important molecules required for T cell differentiation, such as JAK2 and IL12RB2, are regulated by H3K27me3. Our results show that H3K27me3 is a dynamic and important epigenetic modification during CD4 T cell activation and that JMJD3-driven H3K27 demethylation is critical for CD4 T cell function.

Metastatic triple-negative breast cancer patient with TP53 tumor mutation experienced 11 months progression-free survival on bortezomib monotherapy without adverse events after ending standard treatments with grade 3 adverse events

A triple-negative breast cancer patient had no hereditary BRCA1, BRCA2, or TP53 risk variants. After exhaustion of standard treatments, she underwent experimental treatments and whole-exome sequencing of tumor, blood, and a metastasis. Well-tolerated experimental bortezomib monotherapy was administered for a progression-free period of 11 mo. After progression, treatments were changed and the exome data were evaluated, expanded with RNA and exome sequencing of a late-stage metastasis. In the final stage, eribulin alone and in combination with anthracyclines were administered. While suffering from grade 3 adverse events, skin metastases progressed. She lived 51 mo after initial diagnosis.Toxicity from anthracyclines and cisplatin may have been due to associated germline variants CBR3 C4Y and V224M and GSTP1 I105V, respectively. Somatic mutations predicted or reported as pathogenic were detected in 38 genes in tumor tissues. All tumor samples harbored the heterozygous TP53 Y220C variant, known to destabilize p53 and down-regulate p53-mediated apoptosis. The success of bortezomib may be explained by the previously reported up-regulation of caspase-mediated apoptosis, which is p53-independent. Phylogenetic analysis of blood, primary tumor, and two metastases inferred an ancestral tumor cell with 12 expressed tumor mutations from which all three tumors may have evolved.Although our first urgent analysis could only include 40 genes, postmortem analysis uncovered the aggressiveness and suggested experimental therapies including 16 actionable targets, partly validated by immunohistochemistry. Exome and transcriptome analyses yielded comprehensive therapy-relevant information and should be considered for patients at first diagnosis.

Abstract 4156: Molecular and phenotypic characterization of breast and colorectal cancer cells selected for resistance to antibody-dependent cell-mediated cytotoxicity (ADCC)

Monoclonal antibody (mAb) therapy is limited by clinical resistance. For example, alterations in PI3K/Akt /Ras-MAPK signaling, over activation/expression of alternate receptor kinases (c-Met/ IGF-1R), or proteolysis of extracellular domains harboring target epitopes are postulated mechanisms of clinical resistance to trastuzumab. ADCC is a major mechanism of action for mAbs. Most studies have focused on cell models of resistance through in vitro selection, in presence of mAbs, in the absence of immune effector cells. We developed a unique model of immune selection, where target cells (HER2 +ve breast cancer cells SKBR3, BT474; and EGFR +ve colon cancer cells HT29, DLD1) were subjected to ADCC (>90% cell death) with saturating concentrations of trastuzumab or cetuximab (100 µg/ml), respectively, and human peripheral blood mononuclear cells (PBMCs). Selection (in triplicate) was continued for 10 consecutive passages and surviving cells were allowed to grow to confluence over a period of 8-10 weeks. Mock-treated parent cells, IgG1 isotype control, mAb-alone and PBMCs only were utilized as controls. Compared to parent controls, immune-selected DLD1 and SKBR3 cells demonstrated statistically significant increase in proliferation (WST viability assays, P<0.01), and significantly higher colony forming efficiency (soft agar assays, P<0.001); immune-selected HT29 and SKBR3 cells showed significantly higher motility (trans-well migration assays, P<0.05, and P<0.001 respectively). In vitro ADCC assays (calcein labeling) suggested significant reduction (max 20%, p<0.005) in cell lysis in all the immune-selected cell lines compared to parent. Immune-selected HT29 cells demonstrated a 5-fold reduction in gene copy number of EGFR by fluorescence in situ hybridization (FISH, p<0.0001), 2-fold reduction in mRNA levels (qPCR, p< 0.01) and 1.8-fold reduction in protein levels of EGFR (densitometry scans, western blot analyses, p<0.01). Transcriptome-wide next-generation RNA sequencing (Illumina NextSeq 500, 2 x 75 bp paired-end, with over 100 million paired-end reads/sample), coupled with bioinformatic analyses (Reactome pathway database) revealed gene expression changes in ADCC-selected cells. These involve changes in key immune signaling pathways such as class I/II MHC antigen processing, cell chemotaxis, inflammatory and immune regulatory pathways among others. Our data indicate immune-selection by effector cells contributes to ADCC resistance in vitro. Further investigation will determine whether mAb combination with an agonist antibody against CD137 (co-stimulatory NK cell receptor) or Fc-engineered MAbs (e.g. afucosylated) will sensitize the resistant cells. It is hoped that this investigation will better inform mAb therapy by elucidating potentially targetable pathways/ markers that emerge from immune-selection with therapeutic mAbs.

Citation Format: Tanuka Biswas, Rebecca Fritzemeier, Adam Mark, Tobias Meißner, Brandon Young, Brian-Leyland Jones, Mark Pegram. Molecular and phenotypic characterization of breast and colorectal cancer cells selected for resistance to antibody-dependent cell-mediated cytotoxicity (ADCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4156. doi:10.1158/1538-7445.AM2017-4156

Abstract 5355: PANCeq - Development and validation of a targeted sequencing assay for detection of mutations and copy number changes in most recurrently mutated driver genes

Next generation sequencing is becoming increasingly prevalent as a tool for the identification of genetic variation to aid diagnosis and support therapy decisions in routine clinical care. It has been shown that tumors are comprised of subpopulations of cells with distinct genomic alterations, and hence tumor heterogeneity is becoming an important factor in deciding treatment. Deep sequencing of tumor samples allows for the determination of number and proportions of low variant allele frequency tumor subclones. Currently, high costs for whole-exome deep sequencing (> 250X) limit its application in routine clinical care, and there is a need for more affordable targeted approaches. Here we present PAN Cancer Sequencing (PANCeq), a targeted deep sequencing panel for the detection of mutations and copy number variants (CNVs) in most recurrently mutated cancer driver genes. A platform-independent computational Docker-based pipeline for data analysis and automatic report generation was developed. PANCeq uses customized targeted enrichment, followed by next-generation sequencing of (FFPE) tumor and matched germline samples.

We included 12 patient samples (breast, ovarian, kidney and prostate) as well as triplicates of 3 reference standards (HD200, HD753, HD733 - Horizon). These were sequenced on Illumina NextSeq o an average depth of 1000X. Sequencing data was aligned using BWA to hg19 human reference. Somatic variants and CNVs were identified using VarDict and CNVkit respectively.

We mined TCGA data across 26 tumor types, and selected known mutations from the most recurrently mutated genes, yielding 2849 mutations across 467 genes. In addition, we included 79 pharmacogenomic relevant and 218 sample tracking SNPs as well as 80 cancer relevant CNVs (whole exon), and designed a custom panel based on their genomic locations, resulting in a panel size of 708kb. To assess performance, we sequenced reference standards with known variants spiked-in at varying VAF (1 - 41.5%). Somatic variant calling was performed against a wildtype sample. For HD200, out of 21 covered mutations, 14 were correctly classified as germline, and 7 as somatic. For HD733, out of 21 mutations, 3 were correctly identified as germline, 18 as somatic. For HD753, all 6 germline and somatic mutations were correctly identified. The 2 CNVs spiked-in were also correctly identified. In all cases we found a good agreement between observed and expected VAF. Somatic variant results for 12 patient samples were compared with variants reported by a private vendor. While we found good agreement at VAF > 20%, our panel detected on average 7 additional clinically relevant mutations at < 20%.

We demonstrate that PANCeq is an accurate and sensitive method for timely identification of clinically actionable mutations and copy number variations across multiple cancer types.

Citation Format: Tobias Meissner, Anu Amallraja, Brandon Michael Young, Adam Mark, Cayce Conolly, Amanda Andrews, Casey Williams, Brian Leyland-Jones. PANCeq - Development and validation of a targeted sequencing assay for detection of mutations and copy number changes in most recurrently mutated driver genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5355. doi:10.1158/1538-7445.AM2017-5355

Abstract P1-05-23: Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting

Introduction

Variant calling based on DNA samples has been the gold standard of clinical testing since the advent of Sanger sequencing. The use of DNA variants has proved a great value to guide treatment in cancer patients. However, DNA based analysis will not inform about expression status of the gene harboring a particular variant. RNA has long been used to monitor expression. To this point RNA assays and analysis are confined to the research laboratory and rarely used clinically except in specifically defined gene signatures such as PAM50 and OncoType Dx. Beyond expression, RNA has the ability to confirm expression of DNA variants and identify fusion events. We hypothesize that the combination of DNA and RNA based data will allow the determination of variant specific expression status and improve clinical diagnostics. It has been previously shown that RNA sequencing (RNA-Seq) based variant calls are highly accurate and confirm DNA based variant calls. In this study we investigated the utility of RNA-Seq as a diagnostic assay integrated with DNA based sequencing data.

Materials and Methods

Targeted DNA sequencing of 321 genes was performed on 37 patient samples (FFPE), including 22 breast cancer samples by a commercial vendor. RNA-Seq on the same patient samples was performed using 100ng of total RNA. Libraries were run on the Illumina NextSeq 500 with a minimum of 75M paired 75bp reads. To evaluate RNA-seq expression reproducibility, replicates of 6 normal ovarian tissue samples (min. 50M reads) were run in sets of triplicates. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). RNA-Seq based variant calling was performed using the SNPiR pipeline. Based on the results of the commercial assay, DNA based variants were examined for expression of the corresponding genes and ability to confirm variants in the RNA-Seq data.

Results

RNA expression data showed no corresponding gene expression for at least one single nucleotide variant (SNV) in 9/37 patients analyzed (24.3%). In 18/37 patients (48.6%) SNV corresponding expression was in the lowest quartile of expression values. Variant calls could be confirmed by RNA-Seq for 95/455 SNVs, with adequate coverage in 263 of the remaining 360 variant locations (median coverage: 34). Of these, a homozygous reference call was made in 166/263 SNVs. Concordance for RNA-Seq gene level expression data between replicates was > 0.995.

Conclusions

These findings suggest that RNA-Seq based data can provide clinical value when using gene expression values in combination with DNA based variant calls. We found gene level expression to be highly reproducible and will further investigate the use of spike in controls to determine clinically usable expression ranges and lower limit of expression values. To our knowledge, it has not been shown that RNA-Seq based variant calls are reproducible which is the focus of our current research as this will be one requirement for usage in a regulated environment. While our use of RNA Seq is currently limited to gene expression level data, we have demonstrated a clinically relevant benefit to using RNA Seq data as an additive feature to the current standard of DNA variant calling.

Citation Format: Young B, Mark A, Meissner T, Amallraja A, Andrews A, Connolly C, Williams C, Leyland-Jones B. Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-23.

Abstract P3-03-06: Characterization of HER2-positive breast cancer (BC) cells selected for tolerance to trastuzumab-induced antibody-dependent cell-mediated cytotoxicity (ADCC)

Cellular mechanisms of trastuzumab resistance include alteration(s) in cell signaling pathways (PTEN loss, activation of PI3K/Akt signaling), steric hindrance of antibody binding (by Muc-1/Muc-3), over-activation of alternate receptor kinases (HER3/c-Met/IGF-1R), and proteolysis of HER2 extracellular domain harboring target epitopes for antibody-based therapeutics. Prior studies of trastuzumab resistance have focused largely on cells selected ex vivo with the antibody in absence of human immune effector cells. We developed a selection model, wherein human HER2 positive BC cells (BT474, SKBR3) were subjected to acute ADCC (>90% cell death), trastuzumab concentration 100ug/mL, effector-target ratio 100:1, using human peripheral blood mononuclear cells (PBMCs) as effectors. Surviving cells were allowed to recover to confluence over 8-10 weeks, for 10 total rounds of ADCC selection ex vivo. Mock-treated parent, IgG1 isotype control, trastuzumab, and PBMCs alone were used as controls. ADCC assays based on calcein fluorescent labeling of live target cells, revealed significant reduction (maximum 20%, p<0.005) in cell lysis in immune-selected BT474 cell lines compared to parental controls (immune-selected SKBR3 cells exhibited a non-significant trend towards reduced ADCC). Transcriptome-wide next-generation RNA sequencing (Illumina NextSeq 500, 2 x 75 bp paired-end, median of 46 million paired-end reads/sample), coupled with pathway enrichment analysis (Reactome), followed by q-PCR validation, confirmed significant changes in expression in immune-selected cells (compared to parent control) for genes including: ALDH1, ANK1, TMPRSS3, HINT1, DNM2, TNNC1, COL4A4 in BT474; and ALDH1, ANK1, CAMP1, CPE, IDO1 in SKBR3 cells. Whole-genome sequencing (Illumina HiSeq X, 150 bp paired end, 30x coverage) elucidated 180 genes with single nucleotide variations (SNVs) in immune-selected cells compared to parent in BT474 cells, and 215 genes in SKBR3 cells. Thirty-four SNVs were shared in both cell lines. Further screening and validation confirm genes with SNVs demonstrating significant transcript up-regulation. These include: COL4A3, LEP, SOX-9 in BT474; and HLA-B, TNFRSF10B, HLA-B, PSMA6 in SKBR3. In further phenotypic analysis, ADCC-conditioned BT474 cells exhibit an elongated fibroblast-like morphology with multiple processes, in contrast to control. Immune-selected SKBR3 cells (and not BT474 cells) demonstrate significantly increased motility compared to control in transwell migration assays (p<0.001), and demonstrated increased cell proliferation (MTT assay, 10-15%, 48h; p=0.0242) as compared to parent controls. Our data indicate immune-selection by effector cells contributes to ADCC tolerance in vitro, and is associated with distinct genotypic and phenotypic alterations. Future investigation will determine whether Fc-engineered MAbs (afucosylated), antibody drug conjugates (T-DM1), or potentiation of ADCC by co-stimulatory agonist CD137 antibodies will re-sensitize ADCC-tolerance. This investigation will help to elucidate potentially targetable pathways that emerge from immune-selection with trastuzumab.

Citation Format: Biswas T, Fritzemeier R, Mark A, Meißner T, Young B, Jones BL, Pegram M. Characterization of HER2-positive breast cancer (BC) cells selected for tolerance to trastuzumab-induced antibody-dependent cell-mediated cytotoxicity (ADCC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-03-06.

Abstract P1-05-22: The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis

Introduction

Next generation sequencing has facilitated the understanding of pathogenesis and molecular heterogeneity of breast cancer (BC) as well as accelerated the path towards precision medicine. DNA sequencing (DNA-Seq) based assays for the detection of mutations and alterations in solid and hematologic cancers are finding their way into clinical practice and are readily available as clinical products. RNA sequencing (RNA-Seq), so far being vastly applied in the research context, promises to expand the diagnostic, prognostic and therapeutic use of this technology in cancer. Beyond mutational status, RNA-Seq enables the detection of fusions, quantification of gene expression level, detection of differentially expressed genes, molecular based subtyping, and risk-stratification. In this study we analyzed RNA-Seq and copy number data from BC patients that had undergone DNA-Seq based diagnostics through commercial providers with the goal to detect additional actionable targets.

Materials and Methods

We included 18 BC patients (5/18 triple negative) that had previously undergone DNA-based targeted (321 genes) sequencing. RNA-Seq to a minimum of 75M reads (75pb) was performed using 100 ng of total RNA on the Illumina NextSeq 500 platform. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). Fusions were detected using STAR-Fusion. DESeq2 was utilized to identify patient specific differentially expressed genes by analyzing samples individually against a set of 13 controls from healthy breast tissue generated in-house. Copy number variations (CNVs) were detected using the Nanostring CNV Cancer panel (89 genes) on the Nanostring nCounter platform. Differentially upregulated or amplified genes were queried against DGIdb and Gene Drug Knowledge database for suitable drug matches, limiting the queries to clinically actionable antineoplastic drugs.

Results

Analyzing the cohort of 18 BC patients, we detected on average 26 BC relevant genes (526 total, log2 FC > 2) to be upregulated per patient. Querying the upregulated genes against DGIdb, we found a total of 18 genes that had drug matches and fulfilled the criteria of being actionable antineoplastic drugs, with 17/18 samples having a minimum of two gene targets (avg: 4). Most frequent upregulated genes were TOP2A (83%), AURKA (61%), AURKB (56%), RET (39%)and FGFR3 (28%). In the case of CNVs, 12/18 patients showed at least one gene target with clinically actionable drugs associated. This was observed across 12 gene targets that were amplified (avg: 3) and 4 gene targets that underwent deletions (avg: 1). Most frequent CNVs included MYC (14%) and CCND1 (12%). 4/7 patients having an AURKA overexpression also showed an AURKA amplification on the CNV assay. 10/18 patients had fusions events, with an average of three fusions per patient, including GAB2-WNT11, PAK1-TENM4 and FGFR2-CEP55 fusions.

Conclusions

We show that RNA-Seq and copy number assays provide additional clinical value by detecting suitable drug targets beyond traditional DNA-based approaches. We are conducting further analysis on how these additionally derived drug targets could improve the current treatment schedule of those patients.

Citation Format: Meissner T, Amallraja A, Mark A, Andrews A, Connolly C, Young B, De P, Williams C, Leyland-Jones B. The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-22.

High-performance web services for querying gene and variant annotation

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

A structurally distinct human mycoplasma protein that generically blocks antigen-antibody union

We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known protein structures, as does its mechanism of antibody binding. Protein M binds with high affinity to all types of human and nonhuman immunoglobulin G, predominantly through attachment to the conserved portions of the variable region of the κ and λ light chains. Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens. Similar to the other immunoglobulin-binding proteins such as Protein A, Protein M as well as its orthologs in other Mycoplasma species could become invaluable reagents in the antibody field.

H3K4 methylation profiling reveals distinct epigenetic signatures in CD4 T cell activation and memory formation. (P1146)

The roles of histone modifications in T cell activation and memory formation are poorly understood. Thus, we used RNAseq and ChIPseq in tandem to assess the impact of promoter H3K4 di- and trimethylation in naive vs memory human CD4 T cells at rest and 5 days after activation. Changes in H3K4me2 and me3 correlated strongly with changes in RNA expression when comparing naive and memory cells; e.g. increased H3K4 methylation with increased gene expression. These changes define unique signatures comprised of >200 genes at rest and >400 post-activation. Dramatically, activation of naïve CD4 resulted in differential H3K4 methylation of >4000 genes while only ~800 changed with activation of memory. In contrast, activation-induced changes in gene expression and methylation correlated nearly perfectly in memory but poorly for naïve CD4 T cells. These data suggest a higher level of H3K4 methylation-based commitment in the memory subset 5 days after activation. We are presently doing the same studies for days 1 and 14 after activation to understand how quickly activation-induced H3K4 methylation changes occur and how well H3K4 methylation signatures are reflected 14 days after activation of naive cells. In sum, naïve and memory CD4 T cells demonstrate specific H3K4 methylation signatures, T cell activation is clearly an epigenetically dynamic process, and profiling of H3K4 methylation provides important insight into the epigenetic mechanisms driving the commitment to memory.

A unique DNA methylation signature defines human CD4 memory T cells (P1148)

Memory CD4 T cells are “primed” for rapid responses to antigen; however, the molecular basis of this “priming” is incompletely understood. Methylation of CpG dinucleotides in gene promoters is an epigenetic modification known to regulate gene transcription. Using a new protocol we developed for targeted bisulfite sequencing (Genome Res, 2011), we assessed promoter methylation in human naïve and memory CD4 T cells of 2100 genes (56,000 CpG) linked to activation by deep RNAseq. 466 individual CpGs representing 132 genes are differentially methylated between resting naïve and memory cells. 21 genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 genes encode proteins closely studied in T cells while 15 genes represent novel targets for further study. 39 genes exhibited reduced methylation in resting memory cells coupled with increased gene expression with activation compared to naïve cells including 8 chemokines and cytokines. These data reveal specific genes more rapidly expressed in memory compared to naïve cells and regulated by DNA methylation. Our findings define a DNA methylation signature unique to memory CD4 T cells and correlated with activation-induced gene expression. We are just completing a new analysis of naïve vs. memory at 3 time points (day 0, 5, 14) using a new protocol for genome-wide CpG capture and deep bisulfite DNA sequencing to validate and extend this work.

Real-time observation of the swelling and hydrolysis of a single crystalline cellulose fiber catalyzed by cellulase 7B from Trichoderma reesei

The biodegradation of cellulose involves the enzymatic action of cellulases (endoglucanases), cellobiohydrolases (exoglucanases), and β-glucosidases that act synergistically. The rate and efficiency of enzymatic hydrolysis of crystalline cellulose in vitro decline markedly with time, limiting the large-scale, cost-effective production of cellulosic biofuels. Several factors have been suggested to contribute to this phenomenon, but there is considerable disagreement regarding the relative importance of each. These earlier investigations were hampered by the inability to observe the disruption of crystalline cellulose and its subsequent hydrolysis directly. Here, we show the application of high-resolution atomic force microscopy to observe the swelling of a single crystalline cellulose fiber and its-hydrolysis in real time directly as catalyzed by a single cellulase, the industrially important cellulase 7B from Trichoderma reesei. Volume changes, the root-mean-square roughness, and rates of hydrolysis of the surfaces of single fibers were determined directly from the images acquired over time. Hydrolysis dominated the early stage of the experiment, and swelling dominated the later stage. The high-resolution images revealed that the combined action of initial hydrolysis followed by swelling exposed individual microfibrils and bundles of microfibrils, resulting in the loosening of the fiber structure and the exposure of microfibrils at the fiber surface. Both the hydrolysis and swelling were catalyzed by the native cellulase; under the same conditions, its isolated carbohydrate-binding module did not cause changes to crystalline cellulose. We anticipate that the application of our AFM-based analysis on other cellulolytic enzymes, alone and in combination, will provide significant insight into the process of cellulose biodegradation and greatly facilitate its application for the efficient and economical production of cellulosic ethanol.

Induction of heme oxygenase-1 modulates the profibrotic effects of transforming growth factor-beta in human renal tubular epithelial cells

Transforming growth factor-beta (TGF-beta) is implicated in a variety of kidney diseases where it promotes extracellular matrix (ECM) deposition and pro-inflammatory events, but it also stabilizes and attenuates tissue injury through the activation of cytoprotective proteins, including heme oxygenase-1 (HO-1). HO-1 catalyzes the conversion of heme into carbon monoxide (CO), iron, and biliverdin, which is subsequently converted to bilirubin. The beneficial effects of HO-1 induction include decreasing pro-oxidants (heme), increasing anti-oxidants (biliverdin and bilirubin), and producing a vasodilator with anti-apoptotic and anti-inflammatory properties (CO). The reaction products of HO-1 may also have antifibrogenic properties. The purpose of this study is to explore the effects of HO-1 expression and its reaction products on fibronectin, an ECM protein, in the kidney. The results demonstrate that kidneys of HO-1 knockout mice express significantly more fibronectin protein as compared to heterozygote mice. A potent inducer of HO-1, hemin, significantly decreases fibronectin protein with a concomitant increase in HO-1 protein. Cells expressing HO-1, via TGF-beta1 induction, have reduced fibronectin expression. Bilirubin, a product of the heme oxygenase reaction, attenuates TGF-beta1-mediated increases in fibronectin expression. These results indicate that HO-1 induction and activity may modulate the production of ECM components and suggest a potential role for TGF-beta-mediated HO-1 induction in attenuating renal fibrosis.

Neurotrophic effects of bone morphogenetic protein-7 in a rat model of Parkinson's disease

Previous studies have demonstrated that pretreatment with bone morphogenetic protein-7 (BMP7) reduces ischemic neuronal injury in vivo. Moreover, exogenous application of BMP7 increases both the number of tyrosine hydroxylase (+) cells and dopamine (DA) uptake in rat mesencephalic cell cultures. The purpose of this study was to investigate the in vivo effects of BMP7 on 6-hydroxydopamine (6-OHDA) induced lesioning of midbrain DA neurons. Adult Fischer 344 rats were anesthetized and injected with BMP7 or vehicle into the left substantia nigra, followed by local administration of 9 microg of 6-OHDA into the left medial forebrain bundle. The lesioned animals that received BMP7 pretreatment, as compared to vehicle/6-OHDA controls, had a significant reduction in methamphetamine-induced rotation 1 month after the surgery. BMP7-pretreatment partially preserved KCl-induced dopamine release in the lesioned striatum and significantly increased TH immunoreactivity in the lesioned nigra and striatum. In summary, our data suggest that BMP7 has neuroprotective and/or neuroreparative effects against 6-OHDA lesioning of the nigrostriatal DA pathway in an animal model of Parkinson's disease (PD).

Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations

To evaluate the ability of molecular dynamics (MD) simulations using atomic force-fields to correctly predict stable folded conformations of a peptide in solution, we show results from MD simulations of the reversible folding of an octapeptide rich in alpha-aminoisobutyric acid (2-amino-2-methyl-propanoic acid, Aib) solvated in di-methyl-sulfoxide (DMSO). This solvent generally prevents the formation of secondary structure, whereas Aib-rich peptides show a high propensity to form secondary structural elements, in particular 3(10)- and alpha-helical structures. Aib is, moreover, achiral, so that Aib-rich peptides can form left- or right-handed helices depending on the overall composition of the peptide, the temperature, and the solvation conditions. This makes the system an interesting case to study the ensembles of peptide conformations as a function of temperature by MD simulation. Simulations involving the folding and unfolding of the peptide were performed starting from two initial structures, a right-handed alpha-helical structure and an extended structure, at three temperatures, 298 K, 340 K, and 380 K, and the results are compared with experimental nuclear magnetic resonance (NMR) data measured at 298 K and 340 K. The simulations generally reproduce the available experimental nuclear Overhauser effect (NOE) data, even when a wide range of conformations is sampled at each temperature. The importance of adequate statistical sampling in order to reliably interpret the experimental data is discussed.

Ultrasound-guided fine-needle aspiration and thyroid disease

BACKGROUND

Fine-needle aspiration represents a critical diagnostic test in determining proper management of thyroid disease and the use of ultrasound-guided fine-needle aspiration (USGFNA) has increased over the years.

METHODS

A retrospective chart review of patients undergoing USGFNA. Two hundred fifteen patients underwent 234 procedures with 362 nodules aspirated within a 2 (1/2)-year period.

RESULTS

The mean ages of women and men were 51.9 and 57.8, respectively. The average size of nodules was 2.1 cm. A difficult to assess gland or nodule was the most common indication for USGFNA (33%). The sensitivity was 88.2%, specificity was 80.0%, the PPV was 65.2%, the negative predictive value was 94.1%, and the accuracy was 82.5%. The cancer yield, inadequacy, and complication rates were 44%, 10.5%, and 8.5%, respectively.

CONCLUSIONS

USGFNA aspiration is a safe and effective diagnostic modality in the management of thyroid disease, especially for nodules that are difficult to palpate.

Aortic dissection after ingestion of "ecstasy" (MDMA)

The authors report a case of aortic dissection and cardiac tamponade in a 29-year-old man after ingestion of ecstasy (methylenedioxymethamphetamine, MDMA) at a "rave" party. There was no history of hypertension, myxoid heart disease, or other risk factors for aortic dissection in the deceased, although a minor degree of cystic medial necrosis was noted on histologic examination of the aorta. Autopsy toxicology revealed low residual levels of MDMA in the blood about 48 hours after ingestion of the drug. This case report describes a probable association between MDMA ingestion and aortic dissection in a previously well young adult. The likely mechanisms are discussed, and the difficulties in diagnosing this complication are highlighted.

Demanding healthcare

This paper describes and compares the development of strategies to manage demand in healthcare in the UK and the USA. It suggests that the development is revealing the need to include disciplines other than the traditional ones of economics and public health if its effects are to be understood. Using as an example the growth of telephone help lines and telephone triage, based on computer based decision support systems, it explores the idea of increasing choice and alleviating fear as a way of reducing demand. Organizational behaviour and consumer behaviour can provide wider understanding of these issues, particularly as they relate to the emotional aspects of this activity. Some convergence of the UK and USA approaches and outcomes are identified but demand is revealed as a relatively unexplored territory in the management of health care in both countries.

Chaos and complexity--the future for health care HRM

The need to understand chaos and complexity in organisations has particular importance for health which is bedevilled by the complexity of organisations and the sometimes chaotic nature of its core activities. This article seeks to explore these issues in the context of one of the key functions which is expected to hold together this diversity: Human Resource Management (HRM). An exploration of the nature of HRM in health care as it has evolved indicates that in order for it to have a pivotal role for the future it will need to rethink this role in the changing paradigm which is now emerging; in so doing it could develop as the organisational intelligence for health care in the future facilitating organisational learning and creativity.

Subcutaneous versus intramuscular injection for booster DT vaccination of adolescents

The importance of the injection technique in booster vaccination was investigated in an open randomized study with 252 10-year-old Swedish school-children receiving routine DT vaccination either by subcutaneous or by intramuscular route in the upper arm. The adolescents had previously been primed with DT vaccine at 3, 5 and 12 months of age. Adverse reactions, monitored for 2 weeks, showed the same low rates for systemic reactions in both groups, while the intramuscular administration gave significantly less redness (p < 0.001), swelling (p < 0.001), itching (p < 0.01) and pain (p < 0.05). These reactions were also of shorter duration (p < 0.01 to p < 0.001). Girls were found to have more pain and itching than boys (p < 0.001). No significant differences in antibody responses between the two administration routes were found in the 99 samples drawn 2 weeks after the booster. However, girls were found to have a lower response to diphtheria toxoid than boys (p = 0.009). Local reactions to a booster can thus be significantly reduced by choice of injection technique, which may be necessary if increased dosages and/or further valences are to be given to adolescents and adults.

Food habits in Swedish adolescents in relation to socioeconomic conditions

OBJECTIVE

To describe the food habits of Swedish adolescents 14-15 y of age. To analyse the connection between food habits and socioeconomic circumstances and background factors.

DESIGN

Cross-sectional survey using a Food Frequency Questionnaire including questions on meal patterns.

SETTING

The city of Göteborg and the County of Alvsborg, Sweden 1996.

SUBJECTS

Pupils in the 8th grade in all schools in the city of Göteborg and the County of Alvsborg were in February 1996 invited to participate. The study comprised 7605 pupils. The drop-out rate was 14.4% (n = 1280).

RESULTS

The adolescents had an infrequent consumption of vegetables and fruits and they had a daily consumption of sweets. Cereals, dairy products and snacks: buns, wafers, soft drinks, ice cream and potato crisps were consumed more than once a day. Thirty percent of the girls and 20% of the boys did not eat breakfast every day. The free school lunch was eaten daily by 50% of the boys and 30% of the girls, the remainder ate some type of snack. A negative correlation was found between smoking and the frequency of vegetable consumption. Pupils from areas with high socioeconomic status more often ate breakfast and lunch and the boys more often ate dinner compared to adolescents from areas with low socioeconomic status.

CONCLUSIONS

An irregular meal pattern as well as snack consumption and smoking were common, especially among girls in areas with low socioeconomic status.

Capture EIA for determination of IgE to diphtheria and tetanus toxins in comparison to RIA

A capture IgE assay in EIA with diphtheria toxin and tetanus toxoid as model systems was developed and evaluated in relation to RIA in a DT booster study. The EIA and the RIA gave very similar results, although the EIA determined IgE over a wider range of concentrations, without interference by other subclasses. The comparison to the capture EIA indicated that the RIA gave more reliable results when a toxin as antigen. Weak correlations between local side effects and IgE responses and differences between vaccine groups were noted by RIA but not by EIA, which correlated better with the clinical findings.