Shared Gene Expression Research Articles

The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector.

Aedes albopictus mosquitoes are important vectors for a number of human pathogens including the Zika, dengue, and chikungunya viruses. Capable of displacing Aedes aegypti populations, this mosquito adapts to cooler environments which increases its geographical range and transmission potential. There are limited control strategies for Aedes albopictus mosquitoes which is likely attributed to the lack of comprehensive biological studies on this emerging vector. To fill this void, here using RNAseq we characterized Aedes albopictus mRNA expression profiles at 34 distinct time points throughout development providing the first high-resolution comprehensive view of the developmental transcriptome of this worldwide human disease vector. This enabled us to identify several patterns of shared gene expression among tissues as well as sex-specific expression patterns. To illuminate the similarities and differences with Aedes aegypti, a related human disease vector, we also performed a comparative analysis between the two developmental transcriptomes, identifying life stages where the two species exhibit similar and distinct gene expression patterns. These findings provide insights into the similarities and differences between Aedes albopictus and Aedes aegypti mosquito biology. In summary, the results generated from this study should form the basis for future investigations on the biology of Aedes albopictus and provide a gold mine resource for the development of transgene-based vector control strategies.

Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells.

Innate lymphoid cells (ILCs) are the latest identified innate immune cell family. Given their similarity in transcription factor expression and cytokine secretion profiles, ILCs have been considered as the innate phenocopy of CD4 Th cells. Here, we explored the transcriptome of circulating human ILC subsets as opposed to CD4 Th cell subsets. We describe transcriptomic differences between total ILCs and total CD4 Th cells, as well as between paired innate and adaptive cell subsets (ILC1 vs. Th1; ILC2 vs. Th2; and ILC3 vs. Th17 cells). In particular, we observed differences in expression of genes involved in cell trafficking such as CCR1, CCR6 and CXCR3, innate activation and inhibitory functions, including CD119, 2B4, TIGIT, and CTLA‐4, and neuropeptide receptors, such as VIPR2. Moreover, we report for the first time on distinct expression of long noncoding RNAs (lncRNAs) in innate vs. adaptive cells, arguing for a potential role of lncRNA in shaping human ILC biology. Altogether, our results point for unique, rather than redundant gene organization in ILCs compared to CD4 Th cells, in regard to kinetics, fine‐tuning and spatial organization of the immune response.

A Transcriptomic Continuum of Differentiation Arrest in Acute Leukemia

Introduction: Traditional classification of acute lymphoblastic and myeloid leukemias (ALLs and AMLs) remains heavily based on phenotypic resemblance to normal hematopoietic precursors of the respective lineages. This framework can provide diagnostic challenges for immunophenotypically heterogeneous immature leukemias, which often have poor responses to treatment. This system also takes little account of modern concepts of hematopoietic identity that are mainly based on transcriptional signature identification and functional assays. Recent advances in genome-wide analytical methods developed to reconstruct landscapes of normal differentiation now provide an opportunity to re-evaluate traditional binary approaches to myeloid and lymphoid lineage assignment in leukemia. Methods: We used novel computational tools, including the recently described Iterative Clustering and Guide Gene Selection (ICGS) method to perform transcriptional analyses of a series of 125 T-ALLs and AMLs, which comprised a high proportion of phenotypically immature cases (53.1% and 40.8% respectively). The leukemias were additionally characterized by targeted next generation sequencing (NGS). ICGS was also used to analyze independent adult and pediatric T-ALL cohorts. Results: There was significant overlap in gene expression between leukemias of different diagnostic categories. In contrast to traditional clustering methods, ICGS analysis permitted unbiased classification of acute leukemias along a continuum of hematopoietic differentiation, according to the expression of a limited number of lineage-discriminating guide genes that defined hematopoietic cell expression modules. While AMLs and T-ALLs at either end of the differentiation spectrum showed specific enrichment for transcriptional signatures of the corresponding lineage precursors, leukemias that were arrested at the myeloid/ T-lymphoid interface either showed no clear evidence of mature T-lymphoid or mature myeloid identity, or had incomplete Hematopoietic Stem and Progenitor Cell (HSPC) and mature myeloid cell profiles. NGS analysis revealed that the spectrum of differentiation arrest defined by ICGS is only partially paralleled by underlying mutational genotype. Notably, interface leukemias originally diagnosed as T-ALL were significantly more likely to have PTEN mutations than the rest of the T-ALL cohort (60% v 6.7%, p=0.0151), while RUNX1-mutated AMLs were restricted to interface clusters. We found that interface leukemias shared gene expression programs with a series of multi- or oligopotent hematopoietic progenitor populations, including the most immature CD34+CD1a-CD7- subset of early thymic precursors (ETPs). Within interface leukemias, enrichment for lymphoid progenitor population signatures including multi-lymphoid progenitors (MLPs), lymphoid-mono-dendritic progenitors (LMDPs), T-oriented CD127- and B-oriented CD127+ early lymphoid progenitors (ELPs) from an umbilical cord blood humanized mouse model and early B-cell progenitors, was more likely in cases that were originally diagnosed as AML, rather than T-ALL. In addition, transcriptional resemblance to both B/myeloid and T/myeloid mixed phenotype acute leukemias (MPALs) was primarily driven by AMLs within these interface clusters, suggesting that these cases demonstrate significant lymphoid transcriptional orientation. Conclusion: Our results suggest that traditional binary approaches to leukemia categorization are reductive, and that leukemias arrested at the T-lymphoid/ myeloid interface exhibit significant transcriptional heterogeneity. These data also provide evidence that a subset of leukemias originally diagnosed as AML may be more likely to arise from lymphoid-oriented progenitors and/or be arrested at an early stage of lymphoid orientation than is currently recognized. We believe that better identification of interface acute leukemias will allow improved evaluation of appropriate therapeutic options for these cases. Disclosures Boissel: NOVARTIS: Consultancy. Laurenti:GSK: Research Funding.

GENE-45. DISSECTING THE DRIVERS OF ADULT H3K27M-GLIOMAS AT THE SINGLE-CELL LEVEL

Abstract Diffuse midline gliomas are characterized by a lysine27-to-methionine mutation in histone H3 (H3K27M-glioma) and represent a highly aggressive molecular entity of high-grade gliomas. These mutations have primarily been described in children, but are also increasingly recognized in adults. In pediatric H3K27M-gliomas, the transcriptional architecture and cellular composition have been studied at the single-cell level. Data suggest that these tumors arise through malignant transformation of a glial progenitor during a specific neurodevelopmental time window. On the other hand, little is known about the architecture and cellular context of adult H3K27M-gliomas, and it remains to be elucidated whether they are driven by the same or by distinct oncogenic programs as their pediatric counterparts. Here, we utilize single-cell transcriptomics to characterize the transcriptional landscape of five H3K27M-gliomas from adult patients aged 22 to 56 years (median 33 years). We describe the specific cellular and microenvironmental architecture of the adult tumors, which comprises distinct populations of cancer and normal cells. We contrast our findings to 12 location-matched pediatric H3K27M-tumors from patients aged 2.5 to 15 years (median 8 years) to identify features related to tumorigenesis and developmental context in light of the shared hallmark H3K27M mutation. Our preliminary data indicate shared gene expression programs between adult and pediatric tumors. However, we find significant differences in the composition of the immune compartment as well as less pronounced differentiation programs in the adult tumors. Our findings provide an unprecedented insight into the composition of adult H3K27M-gliomas and advance our understanding of this molecular tumor class.

Copy number variations in individuals with conotruncal heart defects reveal some shared developmental pathways irrespective of 22q11.2 deletion status.

Over 50% of patients with 22q11.2 deletion syndrome (DS) have a conotruncal or related cardiac defect (CTRD). We hypothesized that similar genetic variants, developmental pathways and biological functions, contribute to disease risk for CTRD in patients without a 22q11.2 deletion (ND-CTRD) and with a 22q11.2 deletion (DS-CTRD). To test this hypothesis, we performed rare CNV (rCNV)-based analyses on 630 ND-CTRD cases and 602 DS-CTRD cases with comparable cardiac lesions separately and jointly. First, we detected a collection of heart development related pathways from Gene Ontology and Mammalian Phenotype Ontology analysis. We then constructed gene regulation networks using unique genes collected from the rCNVs found in the ND-CTRD and DS-CTRD cohorts. These gene networks were clustered and their predicted functions were examined. We further investigated expression patterns of those unique genes using publicly available mouse embryo microarray expression data from single-cell embryos to fully developed hearts. By these bioinformatics approaches, we identified a commonly shared gene expression pattern in both the ND-CTRD and DS-CTRD cohorts. Computational analysis of gene functions characterized with this expression pattern revealed a collection of significantly enriched terms related to cardiovascular development. By our combined analysis of rCNVs in the ND-CTRD and DS-CTRD cohorts, a group of statistically significant shared pathways, biological functions, and gene expression patterns were identified that can be tested in future studies for their biological relevance.

Keratinocytes Share Gene Expression Fingerprint with Epidermal Langerhans Cells via mRNA Transfer

The immune functions of epithelia-resident dendritic cells are influenced by epithelial-derived cytokines. Here we identified a communication form between tissue-resident dendritic cells and niche cells that allows direct intracellular material exchange between the parties. We show that many keratinocyte (KC)-specific molecules such as keratins and adhesion molecules could be detected in the epidermal-resident Langerhans cells (LCs) as mRNA and protein. Furthermore, KC-derived Cre led to genetic recombination in the LCs. We also found that LCs containing KC-derived material were more prone to migration. The KC-specific signatures were transferred from KCs to LCs through an exosome-independent mechanism that likely involved nanotubes/dendrites. The transfer of material between epithelial cells and epithelia-associated dendritic cells was not limited to mice or to KC-to-LC transfer. Taken together, these data suggest that the epithelial environment might have a long-term effect on dendritic cell biology and that genetic tools that specifically target epithelial cells also affect tissue-resident immune cells.

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

BackgroundEpidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and biological processes between both diseases has also been reported.MethodsHere, for the first time, we compared the gene expression profiles of ASD frontal cortex tissues and 22 cancer types obtained by differential expression meta-analysis and report gene, pathway, and drug set-based overlaps between them.ResultsFour cancer types (brain, thyroid, kidney, and pancreatic cancers) presented a significant overlap in gene expression deregulations in the same direction as ASD whereas two cancer types (lung and prostate cancers) showed differential expression profiles significantly deregulated in the opposite direction from ASD. Functional enrichment and LINCS L1000 based drug set enrichment analyses revealed the implication of several biological processes and pathways that were affected jointly in both diseases, including impairments of the immune system, and impairments in oxidative phosphorylation and ATP synthesis among others. Our data also suggest that brain and kidney cancer have patterns of transcriptomic dysregulation in the PI3K/AKT/MTOR axis that are similar to those found in ASD.ConclusionsComparisons of ASD and cancer differential gene expression meta-analysis results suggest that brain, kidney, thyroid, and pancreatic cancers are candidates for direct comorbid associations with ASD. On the other hand, lung and prostate cancers are candidates for inverse comorbid associations with ASD. Joint perturbations in a set of specific biological processes underlie these associations which include several pathways previously implicated in both cancer and ASD encompassing immune system alterations, impairments of energy metabolism, cell cycle, and signaling through PI3K and G protein-coupled receptors among others. These findings could help to explain epidemiological observations pointing towards direct and inverse comorbid associations between ASD and specific cancer types and depict a complex scenario regarding the molecular patterns of association between ASD and cancer.

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

BackgroundMultiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants.MethodsWe performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance.ResultsThe known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies.ConclusionsOur integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.

Deconstructing pulmonary fibrosis at single‐cell resolution

RationaleDespite years of research, the fundamental mechanisms driving the pathogenesis of pulmonary fibrosis remain unclear. Numerous histopathologic patterns of pulmonary fibrosis have been identified in association with different patterns of risk factors, but to date it remains unclear as to what mechanisms are shared across different forms of pulmonary fibrosis and which drive distinct pathologies and outcomes. We hypothesize that using single‐cell transcriptomic approaches, we can decipher both the conserved and distinct mechanisms driving pulmonary fibrosis phenotypes.MethodsAt the time of lung transplantation, single‐cell suspensions were generated from the lung parenchyma of pulmonary fibrosis patients and from declined donor lungs (controls). Unsorted single‐cell suspensions and CD45 depleted fractions were used for scRNA‐seq. Single‐cell RNA‐sequencing library preparation was performed using the 10X Genomics 3′ or 5′ kit, and sequencing was performed on an Illumina hiSeq4000 or Novaseq. Following alignment, demultiplexing was performed using Cell Ranger. Graph‐based clustering and scRNA‐seq analysis was performed using the Seurat package in R. Developmental lineage reconstruction was performing using Monocle and p‐Creode. Diagnoses were assigned based on clinical interpretation of explant pathology.ResultsJoint graph‐based clustering and canonical correlation analysis of scRNA‐seq profiles from >30,000 cells from control (n=7), IPF (n=7), chronic hypersensitivity pneumonitis (cHP, n=4), and nonspecific interstitial pneumonia (NSIP, n=3) identified 21 distinct clusters, representing the major known subtypes in the lung, as well as numerous intermediate/transitional cell types and/or states. Strikingly, across pulmonary fibrosis phenotypes, collagen and ECM gene expression was highly enriched in ACTA2low, PDGFRa+ fibroblasts, while collagen and ECM gene expression were lower in ACTA2hi myofibroblasts; few collagen‐expressing inflammatory or epithelial cells were identified. A series of cell types co‐expressing AT1 and AT2 markers were identified in both fibrotic and control lungs. Compared to NSIP and cHP, IPF epithelial cells demonstrated increased senescence markers.ConclusionsAcross different histopathologic forms of pulmonary fibrosis, both shared and divergent pathologic gene expression programs can be identified. Further study is needed to more comprehensively define the common gene expression programs that drive progressive pulmonary fibrosis.Support or Funding InformationThis work was supported by NIH/NHLBI, the Doris Duke Charitable Foundation, and Boehringer Ingleheim.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke.

Patients with multiple sclerosis (MS) appear to have an increased risk of ischemic stroke (IS). Although MS and IS have very different phenotypes, gene-based and pathway-based analyses of large-scale genome-wide association studies (GWAS) have increasingly enhanced our understanding of these two diseases. Whether there are common molecular mechanisms connecting MS and IS is still unclear. Here, we describe the outcome of gene-based test and pathway-based analysis of GWAS datasets that explored potential gene expression links between MS and IS. After identifying significant gene sets individually of MS and IS, we performed pathway-based analysis in four biological pathway databases (KEGG, PANTHER, REACTOME, and WikiPathways) and GO categories. We discovered that there were 9 shared pathways between MS and IS in KEGG, 2 in PANTHER, 14 in REACTOME, 1 in WikiPathways, and 194 in GO annotations (p < 0.05). These results provide an improved understanding about possible shared mechanisms and treatments strategies for MS and IS. They also provide some basis for further studies of how these two diseases are linked at the molecular level.

SA89 - SHARED IMMUNE/INFLAMMATION RELATED CO-EXPRESSION NETWORK FROM FRONTAL CORTEX IN THE NORMAL AGED BRAIN AND IN SCHIZOPHRENIA

Background Schizophrenia is a common and devastating brain disease. However, the exact causes of the disease remain unknown. Previous studies identify shared gene expression profiles between schizophrenia and the normal aged brain and suggest that brain aging may be accelerated in those with schizophrenia. Methods We constructed co-expression networks using RNA-Seq data from frontal cortex of 114 normal individuals ranging in age from 29 to 106 years as well as RNA-Seq data from frontal cortex of 64 subjects with schizophrenia and 66 unaffected controls ranging in age from 19 to 70. We compared co-expression modules significantly associated with schizophrenia to those whose expression levels were significantly correlated with aging in normal individuals. Results We identified a significant overlap between nodes in the immune/inflammation module that were associated with schizophrenia and those in the immune/inflammation module correlated with aging in normal subjects (P Discussion The results show that an activated immune/inflammation related co-expression network is associated with the normal aging brain as well as with schizophrenia and supports the hypothesis that there may be accelerated brain aging in schizophrenia.

Perturbation of IIS/TOR signaling alters the landscape of sex-differential gene expression in Drosophila

BackgroundThe core functions of the insulin/insulin-like signaling and target of rapamycin (IIS/TOR) pathway are nutrient sensing, energy homeostasis, growth, and regulation of stress responses. This pathway is also known to interact directly and indirectly with the sex determination regulatory hierarchy. The IIS/TOR pathway plays a role in directing sexually dimorphic traits, including dimorphism of growth, metabolism, stress and behavior. Previous studies of sexually dimorphic gene expression in the adult head, which includes both nervous system and endocrine tissues, have revealed variation in sex-differential expression, depending in part on genotype and environment. To understand the degree to which the environmentally responsive insulin signaling pathway contributes to sexual dimorphism of gene expression, we examined the effect of perturbation of the pathway on gene expression in male and female Drosophila heads.ResultsOur data reveal a large effect of insulin signaling on gene expression, with greater than 50% of genes examined changing expression. Males and females have a shared gene expression response to knock-down of InR function, with significant enrichment for pathways involved in metabolism. Perturbation of insulin signaling has a greater impact on gene expression in males, with more genes changing expression and with gene expression differences of larger magnitude. Primarily as a consequence of the response in males, we find that reduced insulin signaling results in a striking increase in sex-differential expression. This includes sex-differences in expression of immune, defense and stress response genes, genes involved in modulating reproductive behavior, genes linking insulin signaling and ageing, and in the insulin signaling pathway itself.ConclusionsOur results demonstrate that perturbation of insulin signaling results in thousands of genes displaying sex differences in expression that are not differentially expressed in control conditions. Thus, insulin signaling may play a role in variability of somatic, sex-differential expression. The finding that perturbation of the IIS/TOR pathway results in an altered landscape of sex-differential expression suggests a role of insulin signaling in the physiological underpinnings of trade-offs, sexual conflict and sex differences in expression variability.

Relapse-Initiating Clones Preexisting at Diagnosis in B- Cell Acute Lymphoblastic Leukemia Help Predict Molecular Pathways of Relapse

Disease recurrence remains a significant cause of mortality in B-cell acute lymphoblastic leukemia (B-ALL). Genomic analysis of matched diagnosis and relapse samples have demonstrated that relapse arises from a minor subclone already present at diagnosis and not the dominant clone in the majority of patients. However, the reasons why only some clones survive therapy and generate relapse are obscure and elucidation of the mechanisms that underlie these differing fates may be revealed by functional analysis of isolated subclones. Previous work has shown that the subclonal diversity in B-ALL exists at the level of the leukemia-initiating cells capable of generating patient derived xenografts (Notta et al., Nature, 2011). In order to investigate the functional consequences of genetic clonal evolution during disease progression, we performed in-depth genomic and functional analysis of 14 paired diagnosis/relapse samples from adult and pediatric B-ALL patients with varying cytogenetic abnormalities. Diagnosis-specific, relapse-specific, and shared clonal and subclonal variants were identified by whole exome sequencing of the patient samples. Targeted sequencing of these variants in 372 xenografts generated by transplantation of CD19+ cells in a limiting cell dilution assay uncovered clonal variation. This analysis provided for the unequivocal identification of minor subclones ancestral to the relapse, termed diagnosis Relapse-Initiating (dRI) clones, in the diagnostic sample. Our xenografting approach enabled the physical isolation of dRI clones providing a unique opportunity to interrogate their epigenetic and transcriptional landscapes in order to unravel their relapse initiating capacity. To this end, representative diagnosis, dRI and relapse clones from 5 of the 14 patients were subjected to RNAseq and ATACseq (assay for transposase-accessible chromatin using sequencing) analysis. Despite the differences in transcriptional and chromatin openness between patients, principal component analysis of subclones from individual patients positioned the dRI clones as evolutionary intermediates between the diagnosis and relapse clones. Hierarchical clustering of the most significantly differentially expressed genes and open chromatin regions demonstrated that dRI clones shared gene expression and chromatin accessibility signatures with both the dominant diagnosis clone as well as the dominant relapse clone. To gain mechanistic insight into the data we used gene set enrichment analysis (GSEA) and identified common molecular pathways present in all patients that were enriched in dRI clones and persisted at the time of relapse in comparison to the dominant diagnosis clone. dRI and relapse clones converged in the activation of genes involved in cellular functions such as endocytosis, autophagy and innate immune response. In addition, cell surface proteins like ABC transporters and ephrins were also upregulated in dRI and relapse clones. Remarkably, functional interrogation of dRI clones in secondary xenografts, in comparison to more representative diagnosis clones, displayed increased tolerance to standard chemotherapeutic agents (dexamethasone, L-asparaginase and vincristine). Investigation of the molecular pathways and cellular receptors/transporters identified by gene expression analysis are being assessed in vitro and in vivo as potential targets for novel therapeutic approaches and disease monitoring.Overall, we have shown evidence that minor subclones at diagnosis, ancestral to the relapse clone, possess functional advantages and unique properties over other diagnostic subclones prior to treatment exposure. In depth analysis of pathways identified in these dRI subclones will shed light on potential new therapeutic approaches for abrogating and reducing disease recurrence in B-ALL. DisclosuresMullighan:Amgen: Honoraria, Speakers Bureau; Cancer Prevention and Research Institute of Texas: Consultancy; Abbvie: Research Funding; Pfizer: Honoraria, Research Funding, Speakers Bureau; Loxo Oncology: Research Funding.

Gene expression data analysis for characterizing shared and type specific mechanisms of HCC and B-CLL

Abstract Background Comparing gene expression profiles using gene expression datasets of different types of tumors is frequently used to identify molecular mechanisms of cancer. This study aimed to find shared and type specific gene expression profiles of hepatocellular carcinoma (HCC) and B-cell chronic lymphocytic leukemia (B-CLL). Material and methods Gene expression microarrays for HCC and B-CLL and RNA-sequencing expression data for liver HCC and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) were analyzed and differentially expressed probe sets or genes for each cancer type were detected. Probe sets and genes that were shared or specifically expressed in both cancer types were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) terms for Biological Process (BP) annotations were performed. Results According to our analysis shared upregulated genes were mainly annotated in cell cycle processes. Some of the genes that changed only in HCC were annotated in cell cycle and metabolic processes, and some of the genes, altered only in B-CLL, were annotated in immune response and hemopoiesis. Conclusion These results contribute to cancer research that aim to find the conserved gene expression profiles in different cancer types and widen the knowledge of HCC and B-CLL specific mechanisms.

Tp53 deficiency causes a wide tumor spectrum and increases embryonal rhabdomyosarcoma metastasis in zebrafish.

The TP53 tumor-suppressor gene is mutated in >50% of human tumors and Li-Fraumeni patients with germ line inactivation are predisposed to developing cancer. Here, we generated tp53 deleted zebrafish that spontaneously develop malignant peripheral nerve-sheath tumors, angiosarcomas, germ cell tumors, and an aggressive Natural Killer cell-like leukemia for which no animal model has been developed. Because the tp53 deletion was generated in syngeneic zebrafish, engraftment of fluorescent-labeled tumors could be dynamically visualized over time. Importantly, engrafted tumors shared gene expression signatures with predicted cells of origin in human tissue. Finally, we showed that tp53del/del enhanced invasion and metastasis in kRASG12D-induced embryonal rhabdomyosarcoma (ERMS), but did not alter the overall frequency of cancer stem cells, suggesting novel pro-metastatic roles for TP53 loss-of-function in human muscle tumors. In summary, we have developed a Li-Fraumeni zebrafish model that is amenable to large-scale transplantation and direct visualization of tumor growth in live animals.

Neuroinflammation and ER-stress are key mechanisms of acute bilirubin toxicity and hearing loss in a mouse model.

Hyperbilirubinemia (jaundice) is caused by raised levels of unconjugated bilirubin in the blood. When severe, susceptible brain regions including the cerebellum and auditory brainstem are damaged causing neurological sequelae such as ataxia, hearing loss and kernicterus. The mechanism(s) by which bilirubin exerts its toxic effect have not been completely understood to date. In this study we investigated the acute mechanisms by which bilirubin causes the neurotoxicity that contributes to hearing loss. We developed a novel mouse model that exhibits the neurological features seen in human Bilirubin-Induced Neurological Dysfunction (BIND) syndrome that we assessed with a behavioural score and auditory brainstem responses (ABR). Guided by initial experiments applying bilirubin to cultured cells in vitro, we performed whole genome gene expression measurements on mouse brain tissue (cerebellum and auditory brainstem) following bilirubin exposure to gain mechanistic insights into biochemical processes affected, and investigated further using immunoblotting. We then compared the gene changes induced by bilirubin to bacterial lipopolysaccharide (LPS), a well characterized inducer of neuroinflammation, to assess the degree of similarity between them. Finally, we examined the extent to which genetic perturbation of inflammation and both known and novel anti-inflammatory drugs could protect hearing from bilirubin-induced toxicity. The in vitro results indicated that bilirubin induces changes in gene expression consistent with endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR). These gene changes were similar to the gene expression signature of thapsigargin–a known ER stress inducer. It also induced gene expression changes associated with inflammation and NF-κB activation. The in vivo model showed behavioural impairment and a raised auditory threshold. Whole genome gene expression analysis confirmed inflammation as a key mechanism of bilirubin neurotoxicity in the auditory pathway and shared gene expression hallmarks induced by exposure to bacterial lipopolysaccharide (LPS) a well-characterized inducer of neuroinflammation. Interestingly, bilirubin caused more severe damage to the auditory system than LPS in this model, but consistent with our hypothesis of neuroinflammation being a primary part of bilirubin toxicity, the hearing loss was protected by perturbing the inflammatory response. This was carried out genetically using lipocalin-2 (LCN2)-null mice, which is an inflammatory cytokine highly upregulated in response to bilirubin. Finally, we tested known and novel anti-inflammatory compounds (interfering with NF-κB and TNFα signalling), and also demonstrated protection of the auditory system from bilirubin toxicity. We have developed a novel, reversible, model for jaundice that shows movement impairment and auditory loss consistent with human symptoms. We used this model to establish ER-stress and inflammation as major contributors to bilirubin toxicity. Because of the rapid and reversible onset of toxicity in this novel model it represents a system to screen therapeutic compounds. We have demonstrated this by targeting inflammation genetically and with anti-inflammatory small molecules that offered protection against bilirubin toxicity. This also suggests that anti-inflammatory drugs could be of therapeutic use in hyperbilirubinemia.

A monocyte gene expression signature in the early clinical course of Parkinson\u2019s disease

Microglia are the main immune cells of the brain and express a large genetic pattern of genes linked to Parkinson’s disease risk alleles. Monocytes like microglia are myeloid-lineage cells, raising the questions of the extent to which they share gene expression with microglia and whether they are already altered early in the clinical course of the disease. To decipher a monocytic gene expression signature in Parkinson’s disease, we performed RNA-seq and applied the two-sample Kolmogorov-Smirnov test to identify differentially expressed genes between controls and patients with Parkinson's disease and changes in gene expression variability and dysregulation. The gene expression profiles of normal human monocytes and microglia showed a plethora of differentially expressed genes. Additionally, we identified a distinct gene expression pattern of monocytes isolated from Parkinson’s disease patients at an early disease stage compared to controls using the Kolmogorov-Smirnov test. Differentially expressed genes included genes involved in immune activation such as HLA-DQB1, MYD88, REL, and TNF-α. Our data suggest that future studies of distinct leukocyte subsets are warranted to identify possible surrogate biomarkers and may lead to the identification of novel interventions early in the disease course.

Convergent evolution of gene expression in two high-toothed stickleback populations.

Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus). Are convergently evolved cis and/or trans changes in gene expression associated with convergently evolved morphological evolution? Do cis or trans regulatory changes contribute more to gene expression changes accompanying an evolved morphological gain trait? Transcriptome data from dental tissue of ancestral low-toothed and two independently derived high-toothed stickleback populations revealed significantly shared gene expression changes that have convergently evolved in the two high-toothed populations. Comparing cis and trans regulatory changes using phased gene expression data from F1 hybrids, we found that trans regulatory changes were predominant and more likely to be shared among both high-toothed populations. In contrast, while cis regulatory changes have evolved in both high-toothed populations, overall these changes were distinct and not shared among high-toothed populations. Together these data suggest that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar trans regulatory environments.

Shared effects of DISC1 disruption and elevated WNT signaling in human cerebral organoids

The development of three-dimensional culture methods has allowed for the study of developing cortical morphology in human cells. This provides a new tool to study the neurodevelopmental consequences of disease-associated mutations. Here, we study the effects of isogenic DISC1 mutation in cerebral organoids. DISC1 has been implicated in psychiatric disease based on genetic studies, including its interruption by a balanced translocation that increases the risk of major mental illness. Isogenic wild-type and DISC1-disrupted human-induced pluripotent stem cells were used to generate cerebral organoids, which were then examined for morphology and gene expression. We show that DISC1-mutant cerebral organoids display disorganized structural morphology and impaired proliferation, which is phenocopied by WNT agonism and rescued by WNT antagonism. Furthermore, there are many shared changes in gene expression with DISC1 disruption and WNT agonism, including in neural progenitor and cell fate markers, regulators of neuronal migration, and interneuron markers. These shared gene expression changes suggest mechanisms for the observed morphologic dysregulation with DISC1 disruption and points to new avenues for future studies. The shared changes in three-dimensional cerebral organoid morphology and gene expression with DISC1 interruption and WNT agonism further strengthens the link between DISC1 mutation, abnormalities in WNT signaling, and neuropsychiatric disease.

Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis

Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis unveiled six interaction networks/crosstalks through overlapping edges between commonly dysregulated pathways of EMS and MS. The PTPN1, ERBB3, and CDH1 were observed to be the highly ranked hub genes connected with disease-related genes of both EMS and MS. Androgen receptor (AR) and nuclear factor-kB p65 (RelA) were observed to be the most enriched transcription factor in the upstream of shared down-regulated and up-regulated genes, respectively. The two disease sample sets compared through crosstalk interactions between shared pathways revealed commonly up- and down-regulated expressions of 10 immunomodulatory proteins as probable linkers between EMS and MS. This study pinpoints the number of shared genes, pathways, protein kinases, and upstream regulators that may help in the development of biomarkers for diagnosis of MS and endometriosis at the same time through improved understanding of shared molecular signatures and crosstalk.