Serotonergic And Hypocretinergic Systems Modulate Ventilation And Hypercapnic Ventilatory Responses

Thesis (Ph.D.) University of Alaska Fairbanks, 2009Serotonergic (5-HT) cells of the medullary raphe are putative central chemoreceptors, one of multiple chemoreceptive sites in the brainstem that interact to produce the respiratory chemoreflex. This role is debated, and the importance of 5-HT neurons as chemoreceptors in relatively intact systems is unclear. The main focus of this dissertation is to provide further physiological evidence for the involvement and modulation of 5-HT neurons in CO2 chemosensitivity. This is of interest as a large number of Sudden Infant Death Syndrome (SIDS) cases report dysfunction in the 5-HT system, and CO2 may be an exogenous stressor leading to SIDS when in combination with this underlying vulnerability. Also, since SIDS occurs primarily during sleep, I also focus on the potential functional interaction between the 5-HT and hypocretinergic systems, as hypocretins play a role in arousal and also potentially in chemosensitivity. I confirm the hypothesis that the serotonergic and hypocretinergic systems modulate ventilation and hypercapnic ventilatory responses. Using the in situ preparation derived from juvenile rats and the in vitro medullary slice preparation from mice, I verify that 5-HT neurons are critical in generating a response to CO2, primarily via facilitation of the respiratory rhythm through 5-HT2 receptors. I also find evidence to support the hypothesis that hypocretins play a significant role in the neuroventilatory response to CO2 through activation of hypocretin receptors type 1. By comparing results from rhythmic medullary slice preparations from wildtype (normal 5-HT function) and Lmx1bf/f/p (lack central 5-HT neurons) neonatal mice, I attempt to identify whether changes in hypoglossal nerve output in response to acidosis are affected by hypocretin receptors, and whether this is dependent on the presence of 5-HT neurons. Frequency results from such studies are inconclusive; however, hypocretins do appear to mediate the burst duration response via serotonergic mechanisms. I also find that hypocretins facilitate baseline neural ventilatory output in part through 5-HT neurons. Thus, both the 5-HT and hypocretinergic systems are involved in modulating ventilation and hypercapnic ventilatory responses

Novel pyrrolobenzodiazepine benzofused hybrid molecules inhibit NF-κB activity and synergise with bortezomib and ibrutinib in hematological cancers

Chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) are incurable hematological malignancies that are pathologically linked with aberrant NF-κB activation. In this study, we identified a group of novel C8-linked benzofused Pyrrolo[2,1-c][1,4]benzodiazepines (PBD) monomeric hybrids capable of sequence-selective inhibition of NF-κB with low nanomolar LD50 values in CLL (n=46) and MM cell lines (n=5). The lead compound, DC-1-192, significantly inhibited NF-κB DNA binding after just 4h exposure and demonstrating inhibitory effects on both canonical and non-canonical NF-κB subunits. In primary CLL cells, sensitivity to DC-1-192 was inversely correlated with RelA subunit expression (r2=0.2) and samples with BIRC3 or NOTCH1 mutations showed increased sensitivity (P=0.001). RNA-sequencing and gene set enrichment analysis confirmed the over-representation of NF-κB regulated genes in the down-regulated gene list. Furthermore, In vivo efficacy studies in NOD/SCID mice, using a systemic RPMI 8226 human multiple myeloma xenograft model, showed that DC-1-192 significantly prolonged survival (P=0.017). In addition, DC1-192 showed synergy with bortezomib and ibrutinib; synergy with ibrutinib was enhanced when CLL cells were co-cultured on CD40L-expressing fibroblasts in order to mimic the cytoprotective lymph node microenvironment (P = 0.01). Given that NF-κB plays a role in both bortezomib and ibrutinib resistance mechanisms, these data provide a strong rationale for the use of DC-1-192 in the treatment of NF-κB-driven cancers, particularly in the context of relapsed/refractory disease

MFA15 (MFA 2015)

Catalogue of a culminating student exhibition held at the Mildred Lane Kemper Art Museum, May 1 - August 2, 2015 . Introduction / Heather Corcoran and Patricia Olynyk -- Diana Casanova / Emily J. Hanson -- Andrea M. Coates : in the operating theater / Stephanie Dering -- Margaux Crump -- Brandon Daniels -- Addoley Dzegede : do you prefer answers or truth? / Aaron Coleman -- Vita Eruhimovitz -- Carling Hale -- Amanda Helman -- Mike Helms / Ming Ying Hong -- Ming Ying Hong / Emily J. Hanson -- Sea A Joung / Ervin Malakaj -- Stephanie Kang / Jeremy Shipley -- Dayna Jean Kriz / Andrew Johnson -- Thomas Moore : you should move to the city / Nathaniel Rosenthalis -- Jacob Muldowney -- Laurel Panella / Garrett Clough -- Caitlin Penny -- On the bridge, between Juarez and El Paso / Eric Lyle Schultz -- Jeremy Shipley -- Emmeline Solomon -- Kellie Spano / Margaux Crump -- Michael Aaron Williams -- Austin R. Wolf : monumental labor / Adam Turl.https://openscholarship.wustl.edu/books/1015/thumbnail.jp

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Impact of Host Genes and Strand Selection on miRNA and miRNA* Expression

Dysregulation of miRNAs expression plays a critical role in the pathogenesis of genetic, multifactorial disorders and in human cancers. We exploited sequence, genomic and expression information to investigate two main aspects of post-transcriptional regulation in miRNA biogenesis, namely strand selection regulation and expression relationships between intragenic miRNAs and host genes. We considered miRNAs expression profiles, measured in five sizeable microarray datasets, including samples from different normal cell types and tissues, as well as different tumours and disease states. First, the study of expression profiles of “sister” miRNA pairs (miRNA/miRNA*, 5′ and 3′ strands of the same hairpin precursor) showed that the strand selection is highly regulated since it shows tissue-/cell-/condition-specific modulation. We used information about the direction and the strength of the strand selection bias to perform an unsupervised cluster analysis for the sample classification evidencing that is able to distinguish among different tissues, and sometimes between normal and malignant cells. Then, considering a minimum expression threshold, in few miRNA pairs only one mature miRNA is always present in all considered cell types, whereas the majority of pairs were concurrently expressed in some cell types and alternatively in others. In a significant fraction of concurrently expressed pairs, the major and the minor forms found at comparable levels may contribute to post-transcriptional gene silencing, possibly in a coordinate way. In the second part of the study, the behaved tendency to co-expression of intragenic miRNAs and their “host” mRNA genes was confuted by expression profiles examination, suggesting that the expression profile of a given host gene can hardly be a good estimator of co-transcribed miRNA(s) for post-transcriptional regulatory networks inference. Our results point out the regulatory importance of post-transcriptional phases of miRNAs biogenesis, reinforcing the role of such layer of miRNA biogenesis in miRNA-based regulation of cell activities