Children\u27s Books

Tony Blundell (1991). Beware of Boys; Eve Merriam (1992). Fighting Words; Marisabina Russo (1992). Alex is My Friend; James Stevenson (1992). Monty; Roland Edwards (1992). Tigers; Peter Sis (1992). An Ocean World; Ann Jonas (1992). The Thirteenth Clue; Elsa Marston (1992). Runaway Gazeb

Methodology and Application of Adaptive and Sequential Approaches

The clinical trial, a prospective study to evaluate the effect of interventions in humans under prespecified conditions, is a standard and integral part of modern medicine. Many adaptive and sequential approaches have been proposed for use in clinical trials to allow adaptations or modifications to aspects of a trial after its initiation without undermining the validity and integrity of the trial. The application of adaptive and sequential methods in clinical trials has significantly improved the flexibility, efficiency, therapeutic effect, and validity of trials. To further advance the performance of clinical trials and convey the progress of research on adaptive and sequential methods in clinical trial design, we review significant research that has explored novel adaptive and sequential approaches and their applications in Phase I, II, and III clinical trials and discuss future directions in this field of research

Id1 Promotes Tumor Cell Migration in Nonsmall Cell Lung Cancers

Id1, which belongs to the Id family of helix-loop-helix transcription factors has been most associated with tumor progression and metastatsis; however, its significance in lung cancers has not been extensively explored. Here we seek to evaluate the expression of Id1 in a pilot study of nonsmall-cell lung cancers (NSCLCs) and determine its diagnostic and functional significance in these tumors. Paired normal and malignant lung tissues as well as a panel of NSCLC primary tumors and cell lines were evaluated for Id1 expression using Western blotting and quantitative RT-PCR. Functional assays were performed to evaluate the role of Id1 in tumor cell growth, migration and progression. We find Id1 expression is upregulated in squamous cell carcinoma when compared to adenocarcinoma of the lung and that expression of Id1 versus the normal control is variable in NSCLCs. We also note that Id1 expression in NSCLC cells is largely growth factor dependant and constitutive expression of Id1 in NSCLC cells significantly increases tumor cell migration without affecting cell proliferation. We conclude that Id1, as a mediator of tumor cell migration, may be an indicator of aggressive potential in nonsmall-cell lung cancers

Structural Variant Detection Tools Struggle with Whole Exome Sequencing (WES) Data

Whole exome sequencing (WES) is a targeted sequencing technique that sequences only the protein-coding regions of the genome. As WES is significantly cheaper than whole genome sequencing (WGS) while still providing meaningful information, WES has become a respected tool in identifying small genetic variants underlying diseases. It is also used, but less commonly, to identify large-scale structural variants (SVs) which because of their size and complexity, are more difficult to detect using short-read sequencing data. SVs are genome alterations spanning fifty or more base pairs and have been linked to the onset or progression of certain diseases, such as Multiple Myeloma (MM). Multiple bioinformatics tools are available for the identification of structural variants from genomic data; however, it is important to benchmark their accuracies and efficiencies, particularly when dealing with exome data. Using exome sequencing data from 71 Multiple Myeloma cell lines, we benchmarked six established SV identification tools by comparing their results to each cell-line’s known SVs. We utilized the Texas Advanced Computing Center (TACC) to parallelly run our workflows on these samples. When comparing the SVs detected by each tool to the SVs expected in these cell lines, the results brought to light the challenges of detecting SVs using short read WES data. At the chromosomal level of these known SVs, only two of six tools had a recall greater than 25%. At the coordinate level, no tool had a recall greater than 20%. These tools have been used in published studies to identify SVs from WES data; their poor recall in these MM cell-lines may indicate the need for WES-specific SV detection tools in the future

From Cancer Sequencing Data to Neoantigen Prediction: A Reusable Pipeline using Snakemake

Neoantigens are newly formed peptides formed by somatic mutations that are capable of inducing tumor-specific T-cell recognition. Because neoantigens are expressed specifically in tumor cells, prediction of these neoantigens can lead to personalized immunotherapies for the treatment of cancers. This process involves many steps, the most crucial of which is identification of expressed somatic mutations (or variants) using next generation sequencing data. After evaluating multiple bioinformatics tools for somatic mutation calling, we selected GATK (Genome Analysis ToolKit) for its ability to accurately call expected mutations. There are other steps that need to be performed before and after identification of somatic mutations as well and these include mapping, duplicate marking, annotation of mutation calls, and filtering of mutation calls. We developed a pipeline using the workflow management system Snakemake to perform these steps in order to identify somatic mutations from whole exome and RNA-Seq data. By making this into a snakemake workflow, we are able to easily extend upon it and add more steps as was done for neoantigen prediction. Furthermore, Snakemake submits slurm jobs for each individual step and can intelligently adjust the runtime and processing load for those jobs. This makes it simple to run even very large samples through the pipeline. We have evaluated this pipeline using RNA sequencing and whole exome sequencing data from 46 Multiple Myeloma cell lines and have identified hundreds of expressed mutations per cell line. This reusable and expandable pipeline can serve as a useful resource for other researchers looking to identify expressed mutations and make neoantigen predictions from cancer sequencing data

Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers

PURPOSE Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and recurrence, the molecular mechanisms underlying TNBC metastasis remain unclear. We performed whole-exome sequencing (WES) analysis of primary TNBC and paired recurrent tumors to investigate the genetic profile of TNBC. METHODS Genomic DNA extracted from 35 formalin-fixed paraffin-embedded tissue samples from 26 TNBC patients was subjected to WES. Of these, 15 were primary tumors that did not have recurrence, and 11 were primary tumors that had recurrence (nine paired primary and recurrent tumors). Tumors were analyzed for single-nucleotide variants and insertions/deletions. RESULTS The tumor mutational burden (TMB) was 7.6 variants/megabase in primary tumors that recurred (n = 9); 8.2 variants/megabase in corresponding recurrent tumors (n = 9); and 7.3 variants/megabase in primary tumors that did not recur (n = 15). MUC3A was the most frequently mutated gene in all groups. Mutations in MAP3K1 and MUC16 were more common in our dataset. No alterations in PI3KCA were detected in our dataset. CONCLUSIONS We found similar mutational profiles between primary and paired recurrent tumors, suggesting that genomic features may be retained during local recurrence

Role of LAG-3 in Regulatory T Cells

AbstractRegulatory T cells (Tregs) limit autoimmunity but also attenuate the magnitude of antipathogen and antitumor immunity. Understanding the mechanism of Treg function and therapeutic manipulation of Tregs in vivo requires identification of Treg-selective receptors. A comparative analysis of gene expression arrays from antigen-specific CD4+ T cells differentiating to either an effector/memory or a regulatory phenotype revealed Treg-selective expression of LAG-3, a CD4-related molecule that binds MHC class II. Antibodies to LAG-3 inhibit suppression by induced Tregs both in vitro and in vivo. Natural CD4+CD25+ Tregs express LAG-3 upon activation, which is significantly enhanced in the presence of effector cells, whereas CD4+CD25+ Tregs from LAG-3−/− mice exhibit reduced regulatory activity. Lastly, ectopic expression of LAG-3 on CD4+ T cells significantly reduces their proliferative capacity and confers on them suppressor activity toward effector T cells. We propose that LAG-3 marks regulatory T cell populations and contributes to their suppressor activity

ETV2/ER71 regulates the generation of FLK1+ cells from mouse embryonic stem cells through miR-126-MAPK signaling

Previous studies including ours have demonstrated a critical function of the transcription factor ETV2 (ets variant 2; also known as ER71) in determining the fate of cardiovascular lineage development. However, the underlying mechanisms of ETV2 function remain largely unknown. In this study, we demonstrated the novel function of the miR (micro RNA)-126-MAPK (mitogen-activated protein kinase) pathway in ETV2-mediated FLK1 (fetal liver kinase 1; also known as VEGFR2)+ cell generation from the mouse embryonic stem cells (mESCs). By performing a series of experiments including miRNA sequencing and ChIP (chromatin immunoprecipitation)-PCR, we found that miR-126 is directly induced by ETV2. Further, we identified that miR-126 can positively regulate the generation of FLK1+ cells by activating the MAPK pathway through targeting SPRED1 (sprouty-related EVH1 domain containing 1). Further, we showed evidence that JUN/FOS activate the enhancer region of FLK1 through AP1 (activator protein 1) binding sequences. Our findings provide insight into the novel molecular mechanisms of ETV2 function in regulating cardiovascular lineage development from mESCs

A Case Series Exploration of Multi-Regional Expression Heterogeneity in Triple-Negative Breast Cancer Patients

Background: Extensive intratumoral heterogeneity (ITH) is believed to contribute to therapeutic failure and tumor recurrence, as treatment-resistant cell clones can survive and expand. However, little is known about ITH in triple-negative breast cancer (TNBC) because of the limited number of single-cell sequencing studies on TNBC. In this study, we explored ITH in TNBC by evaluating gene expression-derived and imaging-derived multi-region differences within the same tumor. Methods: We obtained tissue specimens from 10 TNBC patients and conducted RNA sequencing analysis of 2-4 regions per tumor. We developed a novel analysis framework to dissect and characterize different types of variability: between-patients (inter-tumoral heterogeneity), between-patients across regions (inter-tumoral and region heterogeneity), and within-patient, between-regions (regional intratumoral heterogeneity). We performed a Bayesian changepoint analysis to assess and classify regional variability as low (convergent) versus high (divergent) within each patient feature (TNBC and PAM50 subtypes, immune, stroma, tumor counts and tumor infiltrating lymphocytes). Results: Gene expression signatures were categorized into three types of variability: between-patients (108 genes), between-patients across regions (183 genes), and within-patients, between-regions (778 genes). Based on the between-patient gene signature, we identified two distinct patient clusters that differed in menopausal status. Significant intratumoral divergence was observed for PAM50 classification, tumor cell counts, and tumor-infiltrating T cell abundance. Other features examined showed a representation of both divergent and convergent results. Lymph node stage was significantly associated with divergent tumors. Conclusions: Our results show extensive intertumoral heterogeneity and regional ITH in gene expression and image-derived features in TNBC. Our findings also raise concerns regarding gene expression based TNBC subtyping. Future studies are warranted to elucidate the role of regional heterogeneity in TNBC as a driver of treatment resistance