Preethi H. Gunaratne
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View article: Identification of immunogenic KIF5B-RET fusion neopeptides driving immune stimulation in tumor specific CD8+ T cells
Identification of immunogenic KIF5B-RET fusion neopeptides driving immune stimulation in tumor specific CD8+ T cells Open
Introduction Non-classical neoantigens at the fusion junctions of chimeric RNAs are tumor- specific with a low risk of autoimmunity and therefore represent ideal targets for personalized vaccines. We present a platform to discover immunoge…
View article: Identifying bio-behavioural signatures of persistent opioid use risk in trauma injury patients: a protocol for a prospective cohort study
Identifying bio-behavioural signatures of persistent opioid use risk in trauma injury patients: a protocol for a prospective cohort study Open
Introduction Exposure to prescription opioids following traumatic injury can increase the risk of developing tolerance, persistent opioid use and opioid use disorder. The mechanisms underlying opioid tolerance or dependence are not well un…
View article: Interactions between ADGRF1 (GPR110) and extracellular matrix proteins govern its effects on tumorigenesis in HER2‐positive breast cancer
Interactions between ADGRF1 (GPR110) and extracellular matrix proteins govern its effects on tumorigenesis in HER2‐positive breast cancer Open
Background and Purpose We and others have previously shown that ADGRF1, an adhesion G protein‐coupled receptor, is overexpressed and associated with poor survival in many cancers, including human epidermal growth factor receptor‐2 (HER2) b…
View article: Plasma microRNAs to Select Optimal Patients for Antibody Production from Anti-Addiction Vaccines
Plasma microRNAs to Select Optimal Patients for Antibody Production from Anti-Addiction Vaccines Open
Background: Cocaine and illicit amphetamines (disguised as “Adderall”) are being laced with fentanyl and producing accidental and intentional fatal overdoses. Vaccines can prevent these overdoses, but 33% of humans generate insufficient an…
View article: Spatial Transcriptomics Reveals Inflammation and Trans-differentiation States of Acute Myeloid Leukemia in Extramedullary and Medullary Tissues
Spatial Transcriptomics Reveals Inflammation and Trans-differentiation States of Acute Myeloid Leukemia in Extramedullary and Medullary Tissues Open
Acute myeloid leukemia (AML) is a heterogeneous disease of the bone marrow (medullary) but can also involve extramedullary tissues. While single cell dynamics of AML in suspension are previously explored, a comprehensive spatial transcript…
View article: Multimodal Spatial Transcriptomic Profiling Elucidates Niche-Specific Dynamics in Medullary and Extramedullary Acute Myeloid Leukemia
Multimodal Spatial Transcriptomic Profiling Elucidates Niche-Specific Dynamics in Medullary and Extramedullary Acute Myeloid Leukemia Open
Background: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by variable leukemic states that primarily originate in the bone marrow (medullary) and can also occur in extramedullary (EM) tissues, indicating its adaptab…
View article: Single-nucleus transcriptomic analysis reveals the regulatory circuitry of myofiber XBP1 during regenerative myogenesis
Single-nucleus transcriptomic analysis reveals the regulatory circuitry of myofiber XBP1 during regenerative myogenesis Open
SUMMARY Endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) are activated in skeletal muscle in multiple conditions. However, the role of the UPR in the regulation of muscle regeneration remains less understood. We de…
View article: β1 integrins regulate cellular behaviour and cardiomyocyte organization during ventricular wall formation
β1 integrins regulate cellular behaviour and cardiomyocyte organization during ventricular wall formation Open
Aims The mechanisms regulating the cellular behaviour and cardiomyocyte organization during ventricular wall morphogenesis are poorly understood. Cardiomyocytes are surrounded by extracellular matrix (ECM) and interact with ECM via integri…
View article: Laminin Alpha 2 Enhances the Protective Effect of Exosomes on Human iPSC-Derived Cardiomyocytes in an In Vitro Ischemia-Reoxygenation Model
Laminin Alpha 2 Enhances the Protective Effect of Exosomes on Human iPSC-Derived Cardiomyocytes in an In Vitro Ischemia-Reoxygenation Model Open
Ischemic heart disease, a leading cause of death worldwide, manifests clinically as myocardial infarction. Contemporary therapies using mesenchymal stromal cells (MSCs) and their derivative (exosomes, EXOs) were developed to decrease the p…
View article: FIGURE 4 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 4 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
∆Np63 cooperates with the FOX family members to regulate cell motility genes. A, qRT-PCR for the indicated ΔNp63-specific target genes in epidermal cells of the indicated genotype. Data are mean ± SD, n = 3, * versus WT, P < 0.005, two-tai…
View article: FIGURE 6 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 6 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
TAp63 and NRF2 coordinately regulate the expression of TAp63-specific target genes. A, qRT-PCR for the indicated TAp63-specific target genes in epidermal cells of the indicated genotype. Data are mean ± SD, n = 3, * versus WT, P < 0.005, t…
View article: Table S3 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Table S3 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
List of biological pathways differentially enriched (FDR-adjusted P < 0.01) in TAp63-/- and/or ΔNp63-/- mouse epidermal cells versus the WT mouse epidermal cells. The pathways are grouped based on the biological processes and the different…
View article: Table S4 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Table S4 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
List of DNA oligonucleotides to assess the expression levels of the TAp63 and ∆Np63 target genes.
View article: Data from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Data from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
The p53 family member TP63 encodes two sets of N-terminal isoforms, TAp63 and ΔNp63 isoforms. They each regulate diverse biological functions in epidermal morphogenesis and in cancer. In the skin, where their activities have been extensive…
View article: Supplementary Figure S2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Supplementary Figure S2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
Identification of ∆Np63 and TAp63 regulated transcriptomes
View article: FIGURE 5 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 5 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
∆Np63 and TAp63 control the expression of their common target genes together with Stat proteins. A, qRT-PCR for the indicated ΔNp63 and TAp63 common target genes in epidermal cells of the indicated genotype. Data are mean ± SD, n = 3, * ve…
View article: FIGURE 3 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 3 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
∆Np63 and TAp63 control distinct biological processes by cooperating with different transcription factors. A, Venn diagrams of ΔNp63-specific, common, and TAp63-specific direct target genes, with p63 ChIP-seq peaks ± 10 kb from their genom…
View article: FIGURE 2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
Identification of ∆Np63 and TAp63 regulated transcriptomes. A, Unsupervised clustering of the transcriptional profiles in WT, ΔNp63−/−, and TAp63−/− epidermal cells using Pearson correlation coefficient (PCC). B, Heat map visualization of …
View article: Table S4 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Table S4 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
List of DNA oligonucleotides to assess the expression levels of the TAp63 and ∆Np63 target genes.
View article: Supplementary Figure S2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Supplementary Figure S2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
Identification of ∆Np63 and TAp63 regulated transcriptomes
View article: FIGURE 3 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 3 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
∆Np63 and TAp63 control distinct biological processes by cooperating with different transcription factors. A, Venn diagrams of ΔNp63-specific, common, and TAp63-specific direct target genes, with p63 ChIP-seq peaks ± 10 kb from their genom…
View article: FIGURE 7 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
FIGURE 7 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
TAp63 promotes the NRF2-dependent oxidative stress response. A, Venn diagram of the differentially regulated genes in the indicated ΔNp63-competent versus deleted murine primary epithelial cell types. Listed are the pathways enriched in ea…
View article: Table S1 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Table S1 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses Open
List of DNA oligonucleotides for the TAp63 and ∆Np63 ChIP assays