Increase in Full-Length Dystrophin by Exon Skipping in Duchenne Muscular Dystrophy Patients with Single Exon Duplications: An Open-label Study

Single exon duplications account for disease in a minority of Duchenne muscular dystrophy patients. Exon skipping in these patients has the potential to be highly therapeutic through restoration of full-length dystrophin expression. We conducted a 48-week open label study of casimersen and golodirsen in 3 subjects with an exon 45 or 53 duplication. Two subjects (aged 18 and 23 years) were non-ambulatory at baseline. Upper limb, pulmonary, and cardiac function appeared stable in the 2 subjects in whom they could be evaluated. Dystrophin expression increased from 0.94 % ±0.59% (mean±SD) of normal to 5.1% ±2.9% by western blot. Percent dystrophin positive fibers also rose from 14% ±17% at baseline to 50% ±42% . Our results provide initial evidence that the use of exon-skipping drugs may increase dystrophin levels in patients with single-exon duplications.

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity

BACKGROUND

Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms.

RESULTS

In sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms.

CONCLUSION

This work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.

CRISPR-Cas9 homology-independent targeted integration of exons 1-19 restores full-length dystrophin in mice

Duchenne muscular dystrophy is an X-linked disorder typically caused by out-of-frame mutations in the DMD gene. Most of these are deletions of one or more exons, which can theoretically be corrected through CRISPR-Cas9-mediated knockin. Homology-independent targeted integration is a mechanism for achieving such a knockin without reliance on homology-directed repair pathways, which are inactive in muscle. We designed a system based on insertion into intron 19 of a DNA fragment containing a pre-spliced mega-exon encoding DMD exons 1-19, along with the MHCK7 promoter, and delivered it via a pair of AAV9 vectors in mice carrying a Dmd exon 2 duplication. Maximal efficiency was achieved using a Cas9:donor adeno-associated virus (AAV) ratio of 1:5, with Cas9 under the control of the SPc5-12 promoter. This approach achieved editing of 1.4% of genomes in the heart, leading to 30% correction at the transcript level and restoration of 11% of normal dystrophin levels. Treatment efficacy was lower in skeletal muscles. Sequencing additionally revealed integration of fragmentary and recombined AAV genomes at the target site. These data provide proof of concept for a gene editing system that could restore full-length dystrophin in individuals carrying mutations upstream of intron 19, accounting for approximately 25% of Duchenne muscular dystrophy patients.

Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis

The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome and low-pass whole-genome sequencing and global DNA methylation microarrays. Expression subtype changes were observed in ~30% of samples and were coincident with DNA clonality shifts, especially involving HER2. Downregulation of estrogen receptor (ER)-mediated cell-cell adhesion genes through DNA methylation mechanisms was observed in metastases. Microenvironment differences varied according to tumor subtype; the ER+/luminal subtype had lower fibroblast and endothelial content, while triple-negative breast cancer/basal metastases showed a decrease in B and T cells. In 17% of metastases, DNA hypermethylation and/or focal deletions were identified near HLA-A and were associated with reduced expression and lower immune cell infiltrates, especially in brain and liver metastases. These findings could have implications for treating individuals with metastatic breast cancer with immune- and HER2-targeting therapies.

Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity

Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and RNA. However, given the frequent occurrence of structural variation in cancer, molecular profiling using long-read sequencing improves the resolution of such events. For example, the Pacific Biosciences long-read RNA-sequencing (Iso-Seq) transcriptome protocol provides full-length isoform characterization, discernment of allelic phasing, and isoform discovery, and identifies expressed fusion partners. The Pacific Biosciences Fusion and Long Isoform Pipeline (PB_FLIP) incorporates a suite of RNA-sequencing software analysis tools and scripts to identify expressed fusion partners and isoforms. In addition, sequencing of a commercial reference (Spike-In RNA Variants) with known isoform complexity was performed and demonstrated high recall of the Iso-Seq and PB_FLIP workflow to benchmark our protocol and analysis performance. This study describes the utility of Iso-Seq and PB_FLIP analysis in improving deconvolution of complex structural variants and isoform detection within an institutional pediatric and adolescent/young adult translational cancer research cohort. The exemplar case studies demonstrate that Iso-Seq and PB_FLIP discover novel expressed fusion partners, resolve complex intragenic alterations, and discriminate between allele-specific expression profiles.

High early death rates, treatment resistance, and short survival of Black adolescents and young adults with AML

Survival of patients with acute myeloid leukemia (AML) is inversely associated with age, but the impact of race on outcomes of adolescent and young adult (AYA; range, 18-39 years) patients is unknown. We compared survival of 89 non-Hispanic Black and 566 non-Hispanic White AYA patients with AML treated on frontline Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology protocols. Samples of 327 patients (50 Black and 277 White) were analyzed via targeted sequencing. Integrated genomic profiling was performed on select longitudinal samples. Black patients had worse outcomes, especially those aged 18 to 29 years, who had a higher early death rate (16% vs 3%; P=.002), lower complete remission rate (66% vs 83%; P=.01), and decreased overall survival (OS; 5-year rates: 22% vs 51%; P<.001) compared with White patients. Survival disparities persisted across cytogenetic groups: Black patients aged 18 to 29 years with non-core-binding factor (CBF)-AML had worse OS than White patients (5-year rates: 12% vs 44%; P<.001), including patients with cytogenetically normal AML (13% vs 50%; P<.003). Genetic features differed, including lower frequencies of normal karyotypes and NPM1 and biallelic CEBPA mutations, and higher frequencies of CBF rearrangements and ASXL1, BCOR, and KRAS mutations in Black patients. Integrated genomic analysis identified both known and novel somatic variants, and relative clonal stability at relapse. Reduced response rates to induction chemotherapy and leukemic clone persistence suggest a need for different treatment intensities and/or modalities in Black AYA patients with AML. Higher early death rates suggest a delay in diagnosis and treatment, calling for systematic changes to patient care.

Molecular Heterogeneity in Pediatric Malignant Rhabdoid Tumors in Patients With Multi-Organ Involvement

Rhabdoid tumors (RTs) of the brain (atypical teratoid/rhabdoid tumor; AT/RT) and extracranial sites (most often the kidney; RTK) are malignant tumors predominantly occurring in children, frequently those with SMARCB1 germline alterations. Here we present data from seven RTs from three pediatric patients who all had multi-organ involvement. The tumors were analyzed using a multimodal molecular approach, which included exome sequencing of tumor and germline comparator and RNA sequencing and DNA array-based methylation profiling of tumors. SMARCB1 germline alterations were identified in all patients and in all tumors. We observed a second hit in SMARCB1 via chr22 loss of heterozygosity. By methylation profiling, all tumors were classified as rhabdoid tumors with a corresponding subclassification within the MYC, TYR, or SHH AT/RT subgroups. Using RNA-seq gene expression clustering, we recapitulated the classification of known AT/RT subgroups. Synchronous brain and kidney tumors from the same patient showed different patterns of either copy number variants, single-nucleotide variants, and/or genome-wide DNA methylation, suggestive of non-clonal origin. Furthermore, we demonstrated that a lung and abdominal metastasis from two patients shared overlapping molecular features with the patient’s primary kidney tumor, indicating the likely origin of the metastasis. In addition to the SMARCB1 events, we identified other whole-chromosome events and single-nucleotide variants in tumors, but none were found to be prognostic, diagnostic, or offer therapeutic potential for rhabdoid tumors. While our findings are of biological interest, there may also be clinical value in comprehensive molecular profiling in patients with multiple rhabdoid tumors, particularly given the potential prognostic and therapeutic implications for different rhabdoid tumor subgroups demonstrated in recent clinical trials and other large cohort studies.

Abstract LB176: Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network identifies microenvironment features as drivers of metastasis

Background: Metastatic breast cancer (MBC) patients often have short survival, and successful treatment represents one of the most challenging aspects of cancer care. This poor prognosis is likely multifactorial, including increased clonal heterogeneity, drug resistance mechanisms, and alterations of the tumor microenvironment.

Methods: The primary data source was multi-platform data coming from the AURORA US Project that includes RNAseq, DNAseq, and DNA methylation arrays, which assayed 55 MBC patients representing 51 primary cancers and 102 linked metastatic specimens. In addition, RNA sequencing data from two other datasets of primary tumor-metastasis pairs were also used (i.e. UNC Tumor Donation Program/RAP dataset (24 primary and 74 metastasis specimens), and the GEICAM/2009-03 ConvertHER trial dataset (102 primaries and 102 metastatic pairs)). In total, this combined RNAseq dataset contained 177 primary tumors and 278 metastases, including 28 liver, 18 lung, 12 brain, and 24 lymph node metastases. We used these data to address two pressing questions, namely: 1) do gene expression features vary in primary tumors vs metastases according to PAM50 expression subtype, and 2) do gene expression features vary according to site of metastasis.

Results: Using the AURORA multi-platform data, we determined that 17% of metastatic tumors (mainly TNBC/Basal-like) showed reduced expression of HLA-A that was associated with DNA methylation and/or focal DNA deletions near the HLA-A locus; these methylated tumors also showed concomitant lower immune cell infiltrates. Reduced expression of HLA-A gene and immune cell infiltrates were also validated at the RNA level in RAP dataset. Next, RNA expression differences were examined using the combined data set and varied according to tumor subtype. ER+/Luminal metastases had lower fibroblast and endothelial cell content, while triple negative (TNBC)/Basal-like metastases showed a dramatic decrease in T cell and B cell signatures/features. Comparative analyses between primary and site-specific metastasis (i.e., primary vs liver metastasis) or between sites of metastases (i.e., liver vs lung metastasis) revealed that both liver and brain, on average, had low immune cell features regardless of the primary tumor phenotype. Even within the same patient, we detected low immune cell features in brain and liver metastases compared to lung and lymph node metastases. Lastly, liver metastases showed a gain of Luminal B/HER2E gene expression features and MYC targets, and brain TNBC metastasis showed a gain of cell differentiation/Luminal-related gene signatures.

Conclusions: These findings could have direct implications for the treatment of MBC patients with immune-based therapies and suggest new therapeutic avenues depending upon the tumor metastasis phenotype, and site of metastasis.

Citation Format: Susana Garcia Recio, Toshinori Hinoue, Gregory L. Wheeler, Benjamin J. Kelly, Justin M. Balko, Katherine A. Hoadley, Peter W. Laird, Elaine R. Mardis, Charles M. Perou. Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network identifies microenvironment features as drivers of metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB176.

Detection of brain somatic variation in epilepsy-associated developmental lesions

OBJECTIVE

Epilepsy-associated developmental lesions, including malformations of cortical development and low-grade developmental tumors, represent a major cause of drug-resistant seizures requiring surgical intervention in children. Brain-restricted somatic mosaicism has been implicated in the genetic etiology of these lesions; however, many contributory genes remain unidentified.

METHODS

We enrolled 50 children who were undergoing epilepsy surgery into a translational research study. Resected tissue was divided for clinical neuropathologic evaluation and genomic analysis. We performed exome and RNA sequencing to identify somatic variation and we confirmed our findings using high-depth targeted DNA sequencing.

RESULTS

We uncovered candidate disease-causing somatic variation affecting 28 patients (56%), as well as candidate germline variants affecting 4 patients (8%). In agreement with previous studies, we identified somatic variation affecting solute carrier family 35 member A2 (SLC35A2) and mechanistic target of rapamycin kinase (MTOR) pathway genes in patients with focal cortical dysplasia. Somatic gains of chromosome 1q were detected in 30% (3 of 10) of patients with Type I focal cortical dysplasia (FCD)s. Somatic variation in mitogen-activated protein kinase (MAPK) pathway genes (i.e., fibroblast growth factor receptor 1 [FGFR1], FGFR2, B-raf proto-oncogene, serine/threonine kinase [BRAF], and KRAS proto-oncogene, GTPase [KRAS]) was associated with low-grade epilepsy-associated developmental tumors. RNA sequencing enabled the detection of somatic structural variation that would have otherwise been missed, and which accounted for more than one-half of epilepsy-associated tumor diagnoses. Sampling across multiple anatomic regions revealed that somatic variant allele fractions vary widely within epileptogenic tissue. Finally, we identified putative disease-causing variants in genes not yet associated with focal cortical dysplasia.

SIGNIFICANCE

These results further elucidate the genetic basis of structural brain abnormalities leading to focal epilepsy in children and point to new candidate disease genes.

Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery

Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant’s effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes.

Congenital heart disease is a common group of birth defects that are a leading cause of death in children under one year of age. There is strong evidence that genetics plays a role in causing congenital heart disease. While studies using individual cases have identified causative genes for those with a heart defect when accompanied by other birth defects or intellectual disabilities, for individuals who have only a heart defect without other problems, a genetic cause can be found in fewer than 10%. In this study, we enrolled families where there was more than one individual with a heart defect. This allowed us to take advantage of inheritance by searching for potential disease-causing genetic variants in common among all affected individuals in the family. Among 19 families studied, we were able to find a plausible disease-causing variant in eight of them and identified new genes that may cause or contribute to the presence of a heart defect. Two families had potential disease-causing variants in two different genes. We designed assays to test if the variants led to altered function of the protein coded by the gene, demonstrating a functional consequence that support the gene and variant as contributing to the heart defect. These findings show that studying families may be more effective than using individuals to find causes of heart defects. In addition, this family-based method suggests that changes in more than one gene may be required for a heart defect to occur.

Discovery of clinically relevant fusions in pediatric cancer

Background

Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and specific detection of gene fusions through the analysis of next-generation-based RNA sequencing (RNA-Seq) data is computationally challenging and may be confounded by low tumor cellularity or underlying genomic complexity. Furthermore, numerous computational tools are available to identify fusions from supporting RNA-Seq reads, yet each algorithm demonstrates unique variability in sensitivity and precision, and no clearly superior approach currently exists. To overcome these challenges, we have developed an ensemble fusion calling approach to increase the accuracy of identifying fusions.

Results

Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless technology. This method uses paired end RNA-Seq sequence reads as input, and the output from each algorithm is examined to identify fusions detected by a consensus of at least three algorithms. These consensus fusion results are filtered by comparison to an internal database to remove likely artifactual fusions occurring at high frequencies in our internal cohort, while a “known fusion list” prevents failure to report known pathogenic events. We have employed the EnFusion pipeline on RNA-Seq data from 229 patients with pediatric cancer or blood disorders studied under an IRB-approved protocol. The samples consist of 138 central nervous system tumors, 73 solid tumors, and 18 hematologic malignancies or disorders. The combination of an ensemble fusion-calling pipeline and a knowledge-based filtering strategy identified 67 clinically relevant fusions among our cohort (diagnostic yield of 29.3%), including RBPMS-MET, BCAN-NTRK1, and TRIM22-BRAF fusions. Following clinical confirmation and reporting in the patient’s medical record, both known and novel fusions provided medically meaningful information.

Conclusions

The EnFusion pipeline offers a streamlined approach to discover fusions in cancer, at higher levels of sensitivity and accuracy than single algorithm methods. Furthermore, this method accurately identifies driver fusions in pediatric cancer, providing clinical impact by contributing evidence to diagnosis and, when appropriate, indicating targeted therapies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08094-z.

Endogenous retrovirus envelope as a tumor-associated immunotherapeutic target in murine osteosarcoma

Osteosarcoma remains one of the deadliest cancers in pediatrics and young adults. We administered two types of immunotherapies, oncolytic virotherapy and immune checkpoint inhibition, to two murine osteosarcoma models and observed divergent results. Mice bearing F420 showed no response, whereas those with K7M2 showed prolonged survival in response to combination therapy. K7M2 had higher expression of immune-related genes and higher baseline immune cell infiltrates, but there were no significant differences in tumor mutational burden or predicted MHC class I binding of nonsynonymous mutations. Instead, we found several mouse endogenous retrovirus sequences highly expressed in K7M2 compared with F420. T cell tetramer staining for one of them, gp70, was detected in mice with K7M2 but not F420, suggesting that endogenous retrovirus proteins are targets for the anti-tumor immune reaction. Given prior observations of endogenous retrovirus expression in human osteosarcomas, our findings may be translatable to human disease.

Evidence of pioneer factor activity of an oncogenic fusion transcription factor

Recent characterizations of pioneer transcription factors provide insights into their structures and patterns of chromatin recognition associated with their roles in cell fate commitment and transformation. Intersecting with these basic science concepts, identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. This study defines the cellular and chromatin localization of PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a ChIP-seq workflow with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal insights into inactive chromatin localization of PAX3-FOXO1. Taken together, our studies are consistent with pioneer function for a driver oncoprotein in RMS, with repressed chromatin binding and nucleosome-motif targeting.

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The fusion oncoprotein PAX3-FOXO1 binds to both active and repressed chromatin

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PAX3-FOXO1-binding sites are adjacent to H3K9me3 domains

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PAX3-FOXO1 engages partial DNA motifs at early timepoints

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PAX3-FOXO1 can bind stably to inaccessible chromatin without inducing accessibility

Gastroblastoma with a novel EWSR1-CTBP1 fusion presenting in adolescence

Gastroblastomas are rare tumors with a biphasic epithelioid/spindle cell morphology that typically present in early adulthood and have recurrent MALAT1-GLI1 fusions. We describe an adolescent patient with Wiskott-Aldrich syndrome who presented with a large submucosal gastric tumor with biphasic morphology. Despite histologic features consistent with gastroblastoma, a MALAT1-GLI1 fusion was not found in this patient's tumor; instead, comprehensive molecular profiling identified a novel EWSR1-CTBP1 fusion and no other significant genetic alterations. The tumor also overexpressed NOTCH and FGFR by RNA profiling. The novel fusion and expression profile suggest a role for epithelial-mesenchymal transition in this tumor, with potential implications for the pathogenesis of biphasic gastric tumors such as gastroblastoma.

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population

Background

The role of synonymous single-nucleotide variants in human health and disease is poorly understood, yet evidence suggests that this class of “silent” genetic variation plays multiple regulatory roles in both transcription and translation. One mechanism by which synonymous codons direct and modulate the translational process is through alteration of the elaborate structure formed by single-stranded mRNA molecules. While tools to computationally predict the effect of non-synonymous variants on protein structure are plentiful, analogous tools to systematically assess how synonymous variants might disrupt mRNA structure are lacking.

Results

We developed novel software using a parallel processing framework for large-scale generation of secondary RNA structures and folding statistics for the transcriptome of any species. Focusing our analysis on the human transcriptome, we calculated 5 billion RNA-folding statistics for 469 million single-nucleotide variants in 45,800 transcripts. By considering the impact of all possible synonymous variants globally, we discover that synonymous variants predicted to disrupt mRNA structure have significantly lower rates of incidence in the human population.

Conclusions

These findings support the hypothesis that synonymous variants may play a role in genetic disorders due to their effects on mRNA structure. To evaluate the potential pathogenic impact of synonymous variants, we provide RNA stability, edge distance, and diversity metrics for every nucleotide in the human transcriptome and introduce a “Structural Predictivity Index” (SPI) to quantify structural constraint operating on any synonymous variant. Because no single RNA-folding metric can capture the diversity of mechanisms by which a variant could alter secondary mRNA structure, we generated a SUmmarized RNA Folding (SURF) metric to provide a single measurement to predict the impact of secondary structure altering variants in human genetic studies.

YAP1-FAM118B Fusion Defines a Rare Subset of Childhood and Young Adulthood Meningiomas

Meningiomas are a central nervous system tumor primarily afflicting adults, with <1% of cases diagnosed during childhood or adolescence. Somatic variation in NF2 may be found in ∼50% of meningiomas, with other genetic drivers (eg, SMO, AKT1, TRAF7) contributing to NF2 wild-type tumors. NF2 is an upstream negative regulator of YAP signaling and loss of the NF2 protein product, Merlin, results in YAP overexpression and target gene transcription. This mechanism of dysregulation is described in NF2-driven meningiomas, but further work is necessary to understand the NF2-independent mechanism of tumorigenesis. Amid our institutional patient-centric comprehensive molecular profiling study, we identified an individual with meningioma harboring a YAP1-FAM118B fusion, previously reported only in supratentorial ependymoma. The tumor histopathology was remarkable, characterized by prominent islands of calcifying fibrous nodules within an overall collagen-rich matrix. To gain insight into this finding, we subsequently evaluated the genetic landscape of 11 additional pediatric and adolescent/young adulthood meningioma patients within the Children's Brain Tumor Tissue Consortium. A second individual harboring a YAP1-FAM118B gene fusion was identified within this database. Transcriptomic profiling suggested that YAP1-fusion meningiomas are biologically distinct from NF2-driven meningiomas. Similar to other meningiomas, however, YAP1-fusion meningiomas demonstrated overexpression of EGFR and MET. DNA methylation profiling further distinguished YAP1-fusion meningiomas from those observed in ependymomas. In summary, we expand the genetic spectrum of somatic alteration associated with NF2 wild-type meningioma to include the YAP1-FAM118B fusion and provide support for aberrant signaling pathways potentially targetable by therapeutic intervention.

Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience

Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.

Abstract GS3-08: Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network

Background: It has become increasingly clear that effective treatment of metastatic breast cancer (MBC) requires an in-depth understanding of the molecular differences between primary tumors and metastases. The AURORA US Network was established to collect primary breast cancer-metastasis pairs for multi-platform genomic profiling in order to identify the molecular drivers of metastatic disease. AURORA US has both a retrospective and prospective phase. This is the first report of the retrospective phase.

Methods: Archived tissue samples from the primary tumor and at least one distant metastasis were retrospectively collected from 83 MBC patients. Following internal quality assessment, samples from 55 pts, including 105 distinct metastatic lesions, were subject to DNA low pass whole genome and exome sequencing, DNA methylation arrays, and RNA sequencing. Early analyses of these multi-platform data include: DNA methylation, tumor gene expression and microenvironmental signatures, somatic and germline variants, DNA copy number changes, and structural variants between breast primaries and matched metastases.

Results: Median age at diagnosis was 49 years (25-76); 32 (58%) were Stage I or II at presentation, 27 (49%) had a family history of breast cancer, and 20 (36%) had a second breast primary. Median disease-free interval before developing MBC was 2 years (range 0-36, 5 patients presented with Stage IV). Median overall survival from initial presentation was 4 years (range 0-37). Median survival after developing MBC was 1 year (range 0-13), with a median of three treatments. Primary tissue samples were banked from 1977-2017 and metastases were banked from 1999-2017. Clinical phenotypes of the primaries included 27 HR+ (49%), 15 triple negative (TNBC, 27%), and 11 HER2+ (20%, 12 missing HER2 status). Intrinsic subtype distribution of the primaries included 17 Basal-like (31%), 17 Luminal A (31%), 7 Normal-like (13%), 5 HER2-enriched (9%), and 1 Luminal B, with 8 pending. All metastases from the Basal-like cases remained Basal-like, while metastases from luminal primaries tended to gain HER2-Enriched subtype features (5/18, p = 0.01). Overall, we identified significant metastasis-enriched alterations in metabolism pathways, an increase in proliferation, and the loss of differentiation signatures and immune infiltrates with progression; the latter being the most pronounced in brain metastases. The most frequent somatic mutations in this cohort were in TP53, NCOR1, and RUNX1. Interestingly, ERBB2, EGFR, and ATM were also mutated in ≥10% of the tumors sequenced. In almost all cases, CpG island hypermethylation was clonally present in the primary tumor and persisted stably in the majority of metastatic lesions. Promoter CpG island hypermethylation was also identified in some metastatic lesions at JAM3, an important cellular adhesion molecule,and this was accompanied by reduced mRNA expression.

CONCLUSIONS: Collection of banked primary and metastatic tissue pairs identified a young MBC cohort with a high frequency of breast cancer family history and second breast primaries. Molecular characterization of luminal tumor pairs highlighted acquisition of aggressive traits including increased proliferation and loss of differentiation in the metastases. In contrast, basal-like pairs remained relatively unchanged, except for the loss of immune activation. Ongoing analyses to be presented include clonal heterogeneity and phylogeny, novel metastasis signature discovery, gene fusion, and endogenous retrovirus detection.

Citation Format: Tari A King, Minetta C Liu, Marni B McClure, Toshinori Hinoue, Benjamin J Kelly, Chad J Creighton, Jay Bowen, Kristen Leraas, Robyn T Burns, Sara Coppens, Salma Rezk, Amy L Garrett, Justin M Balko, Joel S Parker, Ben H Park, Ian Krop, Carey Anders, Katherine A Hoadley, Julie Gastier-Foster, Mothaffar F Rimawi, Rita Nanda, Nancy U Lin, Claudine Isaacs, P. Kelly Marcom, Anna Maria Storniolo, Fergus J Couch, Elaine R Mardis, Adrian V Lee, Uma Chandran, Peter W Laird, Susan G Hilsenbeck, Larry Norton, Andrea L Richardson, W. Fraser Symmans, Lisa A Carey, Antonio C Wolff, Nancy E Davidson, Charles M Perou, the AURORA US Network. Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr GS3-08.

Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder

RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.

Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads

Linked-read sequencing enables greatly improves haplotype assembly over standard paired-end analysis. The detection of mosaic single-nucleotide variants benefits from haplotype assembly when the model is informed by the mapping between constituent reads and linked reads. Samovar evaluates haplotype-discordant reads identified through linked-read sequencing, thus enabling phasing and mosaic variant detection across the entire genome. Samovar trains a random forest model to score candidate sites using a dataset that considers read quality, phasing, and linked-read characteristics. Samovar calls mosaic single-nucleotide variants (SNVs) within a single sample with accuracy comparable with what previously required trios or matched tumor/normal pairs and outperforms single-sample mosaic variant callers at minor allele frequency 5%-50% with at least 30X coverage. Samovar finds somatic variants in both tumor and normal whole-genome sequencing from 13 pediatric cancer cases that can be corroborated with high recall with whole exome sequencing. Samovar is available open-source at https://github.com/cdarby/samovar under the MIT license.

Abstract 484: Molecular profiling identifies a second malignancy in a patient with medulloblastoma

Medulloblastoma is a pediatric embryonal tumor that can be classified into four molecular subgroups, each derived from a different progenitor cell. It is estimated that about 30-40% of patients will relapse, typically with recurrence at the primary site and of the same molecular subgroup. We present paired tumor/normal genomic analysis of an 18 year-old male who presented with non-Wnt/non-SHH medulloblastoma at age 12 and relapsed with metastatic disease of the falx cerebri 3 years later. Combination surgery, chemotherapy, and radiation were used in treatment of the primary and recurrent tumor. At a timepoint 6 years from original diagnosis, the patient presented with a cerebellar tumor histologically described as “consistent with recurrent medulloblastoma” with comment recommending genomics to confirm. The diagnosis was made based on near identifical morphology and retention of Neu-N and Synaptophysin in the tumor (confirmed by subsequent genetic analysis). The primary tumor and the tumor occurring 6 years after the primary diagnosis were analyzed by whole exome sequencing (blood and tumor tissues) to assess for germline variants, somatic mutation, and copy number variation. We observed no pathogenic germline variants in cancer predisposition genes. The tumor mutational profiles were distinct, with only 6 (1.8%) shared somatic variants between tumors. Specimen provenance was verified by germline variation and SRY coverage. Two targetable mutations within the RAS-MAPK pathway (PTPN11 p.Glu76Lys and PIK3CA p.Gly1007Arg) were present only in the new CNS tumor. Although the primary tumor harbored isochromosome 17q and a gain of chromosome 4, these somatic chromosomal aberrations were not detected in the new CNS tumor. RNA-seq was performed on both tumors and compared to pediatric CNS tumors from the University of California Santa Cruz Treehouse Initiative (n=434). The primary tumor clustered with the medulloblastoma patients by principal component analysis while the new CNS tumor clustered with a group of gliomas and non-medulloblastoma embryonal tumors. The primary tumor displayed evidence of overexpression of Group 4 medulloblastoma genes (e.g. EOMES, RBM24, SNCAIP, and UNC5D). These genes were not overexpressed in the new CNS tumor. Enrichment of genes commonly found in gliomas (e.g. BCAN, CHI3L2, PDGFRA, and SOX2) were noted in the new CNS tumor only. In summary, tumor genomic profiling of a primary medulloblastoma and the new CNS tumor arising 6 years later revealed two distinct sets of somatic mutations suggestive of second malignancy rather than recurrence in this patient. While second malignancy in the setting of medulloblastoma is a rare event, it has been documented, both in a time period consistent with that described in our patient and in the form of glioma. Thus, tumor profiling refined diagnosis in this patient allowing for a more accurate assessment of treatment and management options.

Citation Format: Kathleen M. Schieffer, Katherine E. Miller, Daniel R. Boue, Daniel C. Koboldt, Patrick Brennan, Benjamin J. Kelly, Gregory Wheeler, Vincent Magrini, Amy Wetzel, Elizabeth Varga, Devon Dishman, Kristen Leraas, Vibhuti Agarwal, Mohamed S. AbdelBaki, Jonathan L. Finlay, Jeffrey R. Leonard, Peter White, Julie M. Gastier-Foster, Catherine E. Cottrell, Elaine R. Mardis, Richard K. Wilson. Molecular profiling identifies a second malignancy in a patient with medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 484.

In-frame de novo mutation in BICD2 in two patients with muscular atrophy and arthrogryposis

We describe two unrelated patients, a 12-yr-old female and a 6-yr-old male, with congenital contractures and severe congenital muscular atrophy. Exome and genome sequencing of the probands and their unaffected parents revealed that they have the same de novo deletion in BICD2 (c.1636_1638delAAT). The variant, which has never been reported, results in an in-frame 3-bp deletion and is predicted to cause loss of an evolutionarily conserved asparagine residue at position 546 in the protein. Missense mutations in BICD2 cause autosomal dominant spinal muscular atrophy, lower-extremity predominant 2 (SMALED2), a disease characterized by muscle weakness and arthrogryposis of early onset and slow progression. The p.Asn546del clusters with four pathogenic missense variants in a region that likely binds molecular motor KIF5A. Protein modeling suggests that removing the highly conserved asparagine residue alters BICD2 protein structure. Our findings support a broader phenotypic spectrum of BICD2 mutations that may include severe manifestations such as cerebral atrophy, seizures, dysmorphic facial features, and profound muscular atrophy.

A de novo nonsense mutation in ASXL3 shared by siblings with Bainbridge-Ropers syndrome

Two sisters (ages 16 yr and 15 yr) have been followed by our clinical genetics team for several years. Both girls have severe intellectual disability, hypotonia, seizures, and distinctive craniofacial features. The parents are healthy and have no other children. Oligo array, fragile X testing, and numerous single-gene tests were negative. All four family members underwent research exome sequencing, which revealed a heterozygous nonsense mutation in ASXL3 (p.R1036X) that segregated with disease. Exome data and independent Sanger sequencing confirmed that the variant is de novo, suggesting possible germline mosaicism in one parent. The p.R1036X variant has never been observed in healthy human populations and has been previously reported as a pathogenic mutation. Truncating de novo mutations in ASXL3 cause Bainbridge–Ropers syndrome (BRPS), a developmental disorder with similarities to Bohring–Opitz syndrome. Fewer than 30 BRPS patients have been described in the literature; to our knowledge, this is the first report of the disorder in two related individuals. Our findings lend further support to intellectual disability, absent speech, autistic traits, hypotonia, and distinctive facial appearance as common emerging features of Bainbridge–Ropers syndrome.

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.

Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets

MOTIVATION

Common contemporary practice within the nuclear magnetic resonance (NMR) metabolomics community is to evaluate and validate novel algorithms on empirical data or simplified simulated data. Empirical data captures the complex characteristics of experimental data, but the optimal or most correct analysis is unknown a priori; therefore, researchers are forced to rely on indirect performance metrics, which are of limited value. In order to achieve fair and complete analysis of competing techniques more exacting metrics are required. Thus, metabolomics researchers often evaluate their algorithms on simplified simulated data with a known answer. Unfortunately, the conclusions obtained on simulated data are only of value if the data sets are complex enough for results to generalize to true experimental data. Ideally, synthetic data should be indistinguishable from empirical data, yet retain a known best analysis.

RESULTS

We have developed a technique for creating realistic synthetic metabolomics validation sets based on NMR spectroscopic data. The validation sets are developed by characterizing the salient distributions in sets of empirical spectroscopic data. Using this technique, several validation sets are constructed with a variety of characteristics present in 'real' data. A case study is then presented to compare the relative accuracy of several alignment algorithms using the increased precision afforded by these synthetic data sets.

AVAILABILITY

These data sets are available for download at http://birg.cs.wright.edu/nmr_synthetic_data_sets.

Aplasia cutis congenita of the trunk with fetus papyraceus

Aplasia cutis congenita (ACC) is the absence of localized or widespread areas of skin at birth. A frequently cited classification schema is based on location and the presence of associated anomalies. Histologically it is characterized by dermal fibrosis and absence of adenexal structures. We present a newborn female with extensive truncal ACC associated with fetus papyraceus.

Demoralisation, depression and desire for death: problems with the Dutch guidelines for euthanasia of the mentally ill

OBJECTIVE

Given the recent publication of Dutch guidelines for euthanasia of the mentally ill, our aim in this paper is to review the clinical role of the psychiatrist in assessing patients who seek euthanasia or physician-assisted suicide.

METHOD

Three areas are examined that are informative of the role of the psychiatrist in assessing patients who desire death: recent surveys of psychiatrists' attitudes, empirical and clinical studies, and treatment issues.

RESULTS

Demoralisation and depression emerge as pertinent clinical issues worthy of psychiatric intervention. The role of the psychiatrist is complex and includes issues of assessment, systems, countertransference and treatment.

CONCLUSIONS

Dutch guidelines for physician-assisted suicide in the mentally ill generate serious concern given the uncertainty of prognosis, potential range and variability of outcome of treatments of suicidality and the boundary violations that are involved for the psychiatrist. The guidelines have the potential to dangerously alter the practice of psychiatry and should be condemned.

Cisplatin-based therapy: a neurological and neuropsychological review

The present paper reviews research in the area of the broad-spectrum chemotherapeutic agent cisplatin (cis-diamminedichloro-platinum II) and examines the implications for clinical neuropsychology arising from the neurological disruption associated with cisplatin-based therapy. The paper begins with a brief review of cisplatin treatment in terms other than survival alone, and examines the side-effects and the potential central nervous system (CNS) dysfunction in terms of neurological symptoms and concomitant implications for neuropsychology. Two main implications for clinical neuropsychology arising from cisplatin therapy are identified. First, cisplatin therapy impacts upon the psychological well-being of the patient, particularly during and in the months following treatment. It is suggested that during this time, a primary role for neuropsychology is to focus upon the monitoring and the active enhancement of the patient's social, psychological and spiritual resources. Second, with regard to neurocognitive changes, the review suggests that (1) neurocognitive assessment may not yield stable results within 8 months following treatment and (2) while perceptual, memory, attentional and executive dysfunction may be predicted following cisplatin treatment, little systematic research has been carried out to investigate such a possibility. Future research might profitably address this issue and also specifically examine the effects of low dosage cisplatin-based therapy and the effects of recently developed neuroprotective agents. Finally, there is some evidence to suggest that women may be more susceptible to neurotoxicity during cisplatin therapy, but no gender-related cognitive effects are reported in the cisplatin literature. Future research could usefully investigate gender differences in association with cisplatin chemotherapy.

Progression in acute stroke: value of the initial NIH stroke scale score on patient stratification in future trials

BACKGROUND AND PURPOSE

The objective was to determine the occurrence of neurological changes during the first 48 hours after acute stroke as it relates to initial stroke severity.

METHODS

The National Institutes of Health Stroke Scale (NIHSS) was performed serially for the first 48 hours on 127 consecutive ischemic stroke patients (129 strokes) admitted to the neuroscience intensive care unit. Incidence of stroke progression (a >/=3-point increase on the NIHSS) was recorded and analysis performed to determine its association with initial stroke severity and other demographic and physiological variables. Deficit resolution by 48 hours, defined as an NIHSS score of 0 or 1, measured the frequency of functional recovery predicted by the initial deficit.

RESULTS

Overall progression was noted in 31% of events (40/129). Applying Bayes' solution to the observed frequency of worsening, the greatest likelihood of predicting future patient progression occurs with stratification at NIHSS scores of </=7 and >7. Patients with an initial NIHSS of </=7 experienced a 14.8% (13/88) worsening rate versus a those with a score of >7 with a 65.9% (27/41) worsening rate (P<0.000005). Forty-five percent (40/88) of those with an initial score of </=7 were functionally normal at 48 hours, whereas only 2.4% (1/41) of those with scores of >7 returned to a normal examination within this period (chi2, P<0.000005).

CONCLUSIONS

This study suggests that the early clinical course of the neurological deficit after acute stroke is dependent on the initial stroke severity and that a dichotomy in early outcome exists surrounding an initial NIHSS score of 7. These findings may have significant implications for the design and patient stratification in treatment protocols with respect to primary clinical outcome.

Managing HIV. Part 7: Professional issues. 7.7 HIV care: the impact on the doctor

Managing patients with HIV raises complex clinical, ethical and personal challenges. "Burnout" threatens the overcommitted doctor who is not prepared to take preventive measures.

Assisted suicide and euthanasia: what about the clinical issues?

This paper aims to address the clinical issues involved in a patient's request for assisted suicide. The psychiatric and broader psychosocial issues for the dying patient, their family and their treating doctor have been largely unaddressed in the debate concerning euthanasia to date. A range of the clinical issues that need to be incorporated in the ethical and legal considerations are reviewed. The reasons for a patient seeking suicide as a treatment are complex and go beyond questions of a patient's right to die. The request for euthanasia needs to be seen in the context of the patient's circumstances, including relationships with and attitudes of carers and health professionals, along with patterns of psychiatric disorder and psychiatric symptoms in the medically ill. The clinical issues involve not only the diagnosis or management of psychiatric disorder but also the acknowledgment of the factors influencing an individual's adjustment to the threat of illness and death. The dynamics of family interactions and doctor-patient relationships in this setting are factors that may impinge upon a request for assistance to die. These factors may be more important than the severity of a person's illness or their quality of life, and are less likely to be recognised and addressed in situations of professional isolation. There are critical issues facing psychiatry in new legislative developments.

Changes in acetylcholine receptor number in muscle from critically ill patients receiving muscle relaxants: an investigation of the molecular mechanism of prolonged paralysis

OBJECTIVE

Previous reports have described prolonged paralysis after the administration of muscle relaxants in critically ill patients. The purpose of this study was to examine possible pathophysiologic causes for this paralysis by measuring muscle-type, nicotinic acetylcholine receptor number in necropsy muscle specimens from patients who had received muscle relaxants to facilitate mechanical ventilation before death.

DESIGN

Prospective laboratory study of human muscle collected at autopsy.

SETTING

Medical and surgical intensive care units (ICUs) at a university hospital and a research laboratory.

PATIENTS

Fourteen critically ill patients, with a variety of diagnoses, all of whom required mechanical ventilatory support before their deaths in the ICU and who underwent post mortem examination. Patients were arbitrarily divided into three groups, according to their total vecuronium dose and number of days mechanically ventilated before death. Three patients were in the control group (defined as dying within 72 hrs of initiation of ventilatory support and receiving a total dose of < 5 mg of vecuronium). Six patients were in the low-dose group (defined as requiring ventilatory support for > 3 days before death and receiving a total vecuronium dose of < or = 200 mg). Five patients were in the high-dose group (defined as requiring ventilatory support for > 3 days before death and receiving a total vecuronium dose of > 200 mg).

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Nicotinic acetylcholine receptor numbers as measured by specific 125I-alpha-bungarotoxin binding to human rectus abdominis muscle obtained at autopsy were determined. In general, receptor number reflected the clinical requirements for the muscle relaxants of each patient. Patients who had increasing requirements for muscle relaxants before death had increases in receptor number, as compared with control values.

CONCLUSIONS

The increase in nicotinic acetylcholine receptor number in muscle from patients with an increasing requirement for muscle relaxants before death suggests that nicotinic acetylcholine receptor up-regulation may underlie the increased requirements for muscle relaxants seen in some patients. Furthermore, these findings suggest that muscle relaxant-induced, denervation-like changes may at least be partially responsible for prolonged muscle paralysis after the long-term administration of muscle relaxants. This study may provide the first information into the molecular mechanisms underlying prolonged paralysis.

Prevalence and severity of neurologic dysfunction in critically ill patients. Influence on need for continued mechanical ventilation

OBJECTIVE

The relative importance of neurologic dysfunction in critically ill mechanically ventilated patients has not been well studied. This study investigates the prevalence of neurologic dysfunction in critically ill mechanically ventilated patients and its influence on preventing the discontinuation of mechanical ventilation and patient outcome.

DESIGN

Prospective study.

SETTING

University-based, tertiary care center.

PATIENTS

All eligible adult patients mechanically ventilated for more than 48 h were included. A total of 66 patients were evaluated.

INTERVENTIONS

None.

MAIN OUTCOME MEASURES

Two independent questionnaires, one completed by the critical care attending physician documenting the major clinical factors necessitating continued mechanical ventilation, and a second questionnaire, completed by a critical-care trained neurologist documenting neurologic status and objective cardiopulmonary status formed the basis for outcome measurements. Respiratory and physiologic data, the patient's clinical conditions, and outcome (mortality) were also included in the database.

RESULTS

Pulmonary factors were the major reason for prolonged ventilation in only 51 percent of the patient evaluations. Neurologic status was the major factor necessitating continued mechanical ventilation in 32 percent of the patient evaluations and a significant contributing factor in an additional 41 percent. Of the neurologic factors, diminished level of consciousness was the major cause of continued ventilatory support. This was usually due to a systemic illness, rather than a primary central nervous system disorder. Mortality was significantly lower in patients who continued to require mechanical ventilation after 48 h because of neurologic factors as opposed to pulmonary factors (15 percent vs 72 percent, p = 0.002).

CONCLUSIONS

There is a high prevalence of neurologic dysfunction in critically ill patients and this problem plays a significant role in preventing the discontinuation of mechanical ventilation. Altered mental status is a major factor necessitating continued mechanical ventilation in combined medical-surgical intensive care units.

Attention deficits in children and adolescents with hearing loss. A survey

OBJECTIVES

To determine the prevalence of reported attention deficits in a sample of children who are deaf or hard of hearing and to examine associated variables.

DESIGN

Cross-sectional survey.

SETTING

Residential school for the deaf.

PARTICIPANTS

All students attending the school (n = 238; median age, 16.0 years; range, 4 to 21 years). Subjects were subgrouped by cause of deafness for further analyses.

INTERVENTION

None.

MEASUREMENTS/MAIN RESULTS

School personnel completed questionnaires that are commonly used in the assessment of attention problems. Teachers completed the Attention Deficit Disorder With Hyperactivity (ADD-H) Comprehensive Teacher Rating Scale (ACTeRS) and an abbreviated version of the Attention-Activity section of the ANSER (Aggregate Neurobehavioral Student Health and Education Review) System Questionnaires. Dormitory supervisors rated students on the Conners' Parent Rating Scale and the ANSER System Questionnaires. The mean factor scores for the total sample of deaf and hard-of-hearing students on the Attention and Hyperactivity scales of the ACTeRS and Conners' questionnaires did not differ from the normative data. The 64 students with hereditary deafness received significantly better ratings than the 75 with an acquired cause of deafness such as bacterial meningitis or congenital rubella. Raw scores on the ACTeRS were converted to percentile equivalents based on the normative sample. On the Attention Scale, 38.7% of those with acquired deafness were rated below the 20th percentile (indicative of problems); only 14.1% of the students with hereditary deafness were in this range (P = .002).

CONCLUSIONS

Ratings of attention for students with hearing loss, attending a residential school, did not differ from the normative data. However, the subgroup of children with acquired sensorineural deafness appear to be at increased risk for attention problems.

Current concepts in cerebral protection

In the past, physicians viewed ischemic injury as an irreversible event. Modern science has shown that this view is incorrect and that ischemic neuronal damage is an ongoing, active process that might be amenable to various therapies. Figure 2 illustrates some of the possible sites where these therapies might be active. Pending evidence of their effectiveness, cerebral protection can best be achieved by maintaining adequate CPP and CBF during periods when patients are at risk for cerebral ischemia, restoring perfusion after ischemia occurs, and optimizing the metabolic milieu of the ischemic penumbra.

Evaluation of techniques for the elimination of "hot" bladder artifacts in SPECT of the pelvis

The purpose of this study was to validate the usefulness of two digital filtering techniques used to eliminate the artifacts caused by rapid bladder filling during SPECT of the pelvis. A dynamic phantom model was used containing two hips and a bladder. The phantom was studied under three conditions--bladder empty, filling, and full. The ability of the pixel truncation and interpolative background replacement techniques to eliminate bladder artifacts was assessed. Both techniques gave similar results and resulted in significant (but not complete) recovery of activity in the hips. Quantitative analysis of pixel counts over each hip shows that the measured activity was variable and approximately 20%-30% less than that seen in the empty bladder study. The use of left/right ratio to quantitate differences in hip activity was highly inaccurate despite the use of these filtering techniques. In summary, while these techniques significantly improve image quality, caution should be exercised, particularly in the evaluation of the medial aspects of the hips.

Turkey muscle growth and focal myopathy

Muscle structure and blood enzyme activity were studied to 16 wk of age in lines of turkeys selected for rapid growth. The body and carcass weights were measured, frozen sections of breast and leg muscles examined, and plasma creatine kinase (CK) levels determined. Muscle weights were usually proportional to BW except for the relatively larger superficial pectoralis (SP) muscles in the most rapidly growing line. Damaged muscle fibers were found in all muscles examined, especially in the SP of the breast, the gastrocnemius (GA), and other muscles of the leg; these damages became more common from 10 to 16 wk of age. There were more degenerating muscle fibers and higher levels of plasma CK in the rapidly growing lines than in a slower growing unselected line. The findings support the idea that a focal myopathy, unrelated to deep pectoral myopathy or to inherited muscular dystrophy of the chicken, is associated with rapid growth of turkeys.

Some parental views on the Community Dental Service

A sample of 220 adults accompanying children to Community Dental Service (CDS) clinics in two adjacent health districts in the North Western Health Region of England were questioned to gain insight into their views about the service. Seventy-five per cent reported that they had a dentist of their own; 82% of these claimed to have visited him/her in the previous 12 months. They had chosen the CDS for four broad reasons: 51% saw it as providing a specialised service, 27% came as a result of a school inspection, 15% used it because it was convenient, and 7% had been unhappy with the care provided by a general dental practitioner. Seventy-six per cent thought that the CDS should be allowed to treat adults. There were no significant differences between those with dentists of their own and those without, or between those who gave the specialised nature of the CDS as the reason for attending and those who did not. Those who came by car were significantly less likely to believe that the CDS should treat adults; nevertheless, 69% of these were in favour.

Unilateral pursuit-induced congenital nystagmus

We describe two patients with a lifelong history of oscillopsia only when following objects moving toward their left side. Neurologic examination was normal except for eye movements. The patients showed nystagmus during any tasks that required visual following toward the left (ie, smooth pursuit, optokinetic nystagmus, and vestibulo-ocular-reflex-suppression), but had no nystagmus during fixation of stationary targets or visual following tasks to the right. Eye-movement recordings showed waveforms during pursuit to the left that were typical of congenital nystagmus.

Effect of tampon wraps on production of toxic shock syndrome toxin 1

The influence of tampon wraps on the production and distribution of toxic shock syndrome toxin 1 (TSST-1) was investigated with use of a disk-membrane-agar method. Filter membranes (45 micron) overlaying agar medium in 50-mm petri dishes were spread-inoculated with a TSST-1-producing strain of Staphylococcus aureus and covered with 0.5 mL of whole citrated rabbit blood. Disks of tampon core materials with and without wraps were placed on the inoculated membranes and incubated at 37 degrees C in 5% CO2 in air. Eight wraps with each of 14 tampon core materials were tested to determine the amount of toxin in the agar layer, a quantity considered an indicator of the relative amounts of toxin available for absorption in vivo. The average level of toxin in the agar layer with any particular wrap compared with that in the agar layer with no wrap was higher with five wraps, lower with two wraps, and essentially the same with one wrap. The lower levels of toxin were obtained with one wrap that had a starch binder and with one that contained the surfactant Standamul 1414-E. Standamul 1414-E has been reported to be an inhibitor of growth of and production of TSST-1 by S. aureus.

Abnormal gallium uptake in anticardiolipin syndrome: an unexplained phenomenon

A case of asymmetrical gallium uptake in the musculature of a young woman with anticardiolipin syndrome is reported. The patient was asymptomatic in the areas of involvement, muscle biopsy was normal, and the abnormal gallium accumulation was unchanged on repeat evaluation 7 months later. Possible causes for the abnormal gallium uptake are proposed, but the mechanisms of uptake in this case remain unclear. Nuclear physicians should be aware of this disorder and the potential for abnormal gallium uptake with this syndrome.

Pasteurella anatipestifer infection in commercial meat-type turkeys in California

A disease outbreak characterized by respiratory signs, occasional neurologic signs, and increased mortality in commercial meat turkeys from four separate companies in central California was investigated in the late summer and early fall of 1986. The disease syndrome affected turkeys from 6 to 15 weeks of age and caused a severe fibrinous pericarditis, perihepatitis, and airsacculitis. Bacteriologic and serologic examinations as well as virus- and chlamydia-isolation attempts initially failed to implicate an etiologic agent. Eventually culture attempts were made in a 5% CO2 incubator, resulting in isolation of Pasteurella anatipestifer. The disease syndrome was reproduced in young turkeys and broiler chicks inoculated with the organism.

Clinical outbreak of Bordetella avium infection in two turkey breeder flocks

An acute upper respiratory disease was observed in two broad-breasted white (BBW) turkey primary breeder flocks. Associated clinical signs included sneezing, depression, and a deep dry cough originating from large conducting airways. Morbidity reached approximately 15-20% of the hens in an affected house. None of the turkeys died, and total feed consumption was not affected. A minimal effect upon egg production was noticed. Sera from an acutely affected flock exhibited a marked rise in titer to Bordetella avium compared with preinfection sera samples. In Case 1, B. avium was isolated in pure culture from affected birds. In Case 2, B. avium was diagnosed by serological results and clinical signs; bacteriological examination was not attempted. The findings presented here are consistent with an acute clinical outbreak of B. avium-induced turkey rhinotracheitis (turkey coryza) in BBW turkey breeder hens.

Hemorrhagic enteritis of turkeys in California: serologic study of hemorrhagic enteritis virus antibody with an enzyme-linked immunosorbent assay

The incidence of hemorrhagic enteritis (HE) infection in California turkeys was studied by testing 2220 turkey blood samples from 173 flocks for HE virus (HEV) antibody by the enzyme-linked immunosorbent assay (ELISA). Maternal antibody was detected at 1 day of age in all flocks tested, and it vanished after 3 weeks. Acquired HEV antibody appeared at 8 to 10 weeks, and 100% of the meat and breeder turkey flocks were positive after 11 weeks of age. HEV infection occurred earlier in the meat flocks than in the breeder flocks, and it also occurred earlier during summer than during the fall and winter months.