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1.
Circ Res ; 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38639096

ABSTRACT

BACKGROUND: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood. METHODS: Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in nearly 19 000 single cells isolated during atherosclerosis progression in Ldlr-/-Apob100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study. RESULTS: Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity (SYNTAX/Duke scores). The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM, in cultured human vascular SMCs. CONCLUSIONS: By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced-stage, symptomatic atherosclerosis.

2.
Nucleic Acids Res ; 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38554106

ABSTRACT

The use of androgen receptor (AR) inhibitors in prostate cancer gives rise to increased cellular lineage plasticity resulting in resistance to AR-targeted therapies. In this study, we examined the chromatin landscape of AR-positive prostate cancer cells post-exposure to the AR inhibitor enzalutamide. We identified a novel regulator of cell plasticity, the homeobox transcription factor SIX2, whose motif is enriched in accessible chromatin regions after treatment. Depletion of SIX2 in androgen-independent PC-3 prostate cancer cells induced a switch from a stem-like to an epithelial state, resulting in reduced cancer-related properties such as proliferation, colony formation, and metastasis both in vitro and in vivo. These effects were mediated through the downregulation of the Wnt/ß-catenin signalling pathway and subsequent reduction of nuclear ß-catenin. Collectively, our findings provide compelling evidence that the depletion of SIX2 may represent a promising strategy for overcoming the cell plasticity mechanisms driving antiandrogen resistance in prostate cancer.

3.
Expert Rev Cardiovasc Ther ; 22(1-3): 75-89, 2024.
Article in English | MEDLINE | ID: mdl-38494784

ABSTRACT

INTRODUCTION: After understanding the genetic basis of cardiovascular disorders, the discovery of prime editing (PE), has opened new horizons for finding their cures. PE strategy is the most versatile editing tool to change cardiac genetic background for therapeutic interventions. The optimization of elements, prediction of efficiency, and discovery of the involved genes regulating the process have not been completed. The large size of the cargo and multi-elementary structure makes the in vivo heart delivery challenging. AREAS COVERED: Updated from recent published studies, the fundamentals of the PEs, their application in cardiology, potentials, shortcomings, and the future perspectives for the treatment of cardiac-related genetic disorders will be discussed. EXPERT OPINION: The ideal PE for the heart should be tissue-specific, regulatable, less immunogenic, high transducing, and safe. However, low efficiency, sup-optimal PE architecture, the large size of required elements, the unclear role of transcriptomics on the process, unpredictable off-target effects, and its context-dependency are subjects that need to be considered. It is also of great importance to see how beneficial or detrimental cell cycle or epigenomic modifier is to bring changes into cardiac cells. The PE delivery is challenging due to the size, multi-component properties of the editors and liver sink.


Subject(s)
Cardiology , Cardiovascular Diseases , Cardiovascular System , Heart Diseases , Humans , Heart
4.
Clin Proteomics ; 21(1): 11, 2024 Feb 17.
Article in English | MEDLINE | ID: mdl-38368345

ABSTRACT

BACKGROUND: Small incision lenticule extraction (SMILE) and femtosecond laser-assisted in situ keratomileusis (LASIK) are widely used surgical methods to correct myopia with comparable efficacy, predictability, and safety. We examined and compared the early changes of tear protein profiles after SMILE and FS-LASIK surgery in order to find possible differences in the initial corneal healing process. METHODS: SMILE operations for 26 eyes were made with Visumax femtosecond laser. In FS-LASIK surgery for 30 eyes, the flaps were made with Ziemer FEMTO LDV Z6 femtosecond laser and stromal ablation with Wavelight EX500 excimer laser. Tear samples were collected preoperatively, and 1.5 h and 1 month postoperatively using glass microcapillary tubes. Tear protein identification and quantification were performed with sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS). RESULTS: Immediately (1.5 h) after we found differences in 89 proteins after SMILE and in 123 after FS-LASIK operation compared to preoperative protein levels. Of these differentially expressed proteins, 48 proteins were common for both surgery types. There were, however, quantitative differences between SMILE and FS-LASIK. Upregulated proteins were mostly connected to inflammatory response and migration of the cells connected to immune system. One month after the operation protein expressions levels were returned to baseline levels with both surgical methods. CONCLUSIONS: Our study showed that immediate changes in protein profiles after SMILE and FS-LASIK surgeries and differences between the methods are connected to inflammatory process, and the protein levels quickly return to the baseline within 1 month. The differences in protein profiles between the methods are probably associated with the different size of the epithelial wound induced.

5.
Redox Biol ; 69: 103031, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38184997

ABSTRACT

The Kelch-like ECH-associated protein 1 (KEAP1) - Nuclear factor erythroid 2 -related factor 2 (NRF2) pathway is the major transcriptional stress response system in cells against oxidative and electrophilic stress. NRF2 is frequently constitutively active in many cancers, rendering the cells resistant to chemo- and radiotherapy. Loss-of-function (LOF) mutations in the repressor protein KEAP1 are common in non-small cell lung cancer, particularly adenocarcinoma. While the mutations can occur throughout the gene, they are enriched in certain areas, indicating that these may have unique functional importance. In this study, we show that in the GSEA analysis of TCGA lung adenocarcinoma RNA-seq data, the KEAP1 mutations in R320 and R470 were associated with enhanced Tumor Necrosis Factor alpha (TNFα) - Nuclear Factor kappa subunit B (NFκB) signaling as well as MYC and MTORC1 pathways. To address the functional role of these hotspot mutations, affinity purification and mass spectrometry (AP-MS) analysis of wild type (wt) KEAP1 and its mutation forms, R320Q and R470C were employed to interrogate differences in the protein interactome. We identified TNF receptor associated factor 2 (TRAF2) as a putative protein interaction partner. Both mutant KEAP1 forms showed increased interaction with TRAF2 and other anti-apoptotic proteins, suggesting that apoptosis signalling could be affected by the protein interactions. A549 lung adenocarcinoma cells overexpressing mutant KEAP1 showed high TRAF2-mediated NFκB activity and increased protection against apoptosis, XIAP being one of the key proteins involved in anti-apoptotic signalling. To conclude, KEAP1 R320Q and R470C and its interaction with TRAF2 leads to activation of NFκB pathway, thereby protecting against apoptosis.


Subject(s)
Adenocarcinoma of Lung , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Lung Neoplasms/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , TNF Receptor-Associated Factor 2/genetics , TNF Receptor-Associated Factor 2/metabolism , Kelch-Like ECH-Associated Protein 1/genetics , Kelch-Like ECH-Associated Protein 1/metabolism , NF-E2-Related Factor 2/metabolism , Cell Line, Tumor , Intracellular Signaling Peptides and Proteins/metabolism , Adenocarcinoma of Lung/genetics , Apoptosis/genetics , NF-kappa B/genetics , NF-kappa B/metabolism , Mutation
6.
Commun Biol ; 7(1): 108, 2024 01 18.
Article in English | MEDLINE | ID: mdl-38238517

ABSTRACT

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal subtype of castration-resistant prostate cancer resistant to androgen receptor (AR) inhibitors. Our study unveils that AR suppresses the neuronal development protein dihydropyrimidinase-related protein 5 (DPYSL5), providing a mechanism for neuroendocrine transformation under androgen deprivation therapy. Our unique CRPC-NEPC cohort, comprising 135 patient tumor samples, including 55 t-NEPC patient samples, exhibits a high expression of DPYSL5 in t-NEPC patient tumors. DPYSL5 correlates with neuroendocrine-related markers and inversely with AR and PSA. DPYSL5 overexpression in prostate cancer cells induces a neuron-like phenotype, enhances invasion, proliferation, and upregulates stemness and neuroendocrine-related markers. Mechanistically, DPYSL5 promotes prostate cancer cell plasticity via EZH2-mediated PRC2 activation. Depletion of DPYSL5 decreases proliferation, induces G1 phase cell cycle arrest, reverses neuroendocrine phenotype, and upregulates luminal genes. In conclusion, DPYSL5 plays a critical role in regulating prostate cancer cell plasticity, and we propose the AR/DPYSL5/EZH2/PRC2 axis as a driver of t-NEPC progression.


Subject(s)
Prostatic Neoplasms , Male , Humans , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Androgen Antagonists , Prostate/pathology , Hydrolases , Microtubule-Associated Proteins , Enhancer of Zeste Homolog 2 Protein/genetics
7.
Alzheimers Dement ; 20(2): 954-974, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37828821

ABSTRACT

INTRODUCTION: Alzheimer's disease (AD) is a neurodegenerative disease and the main cause of dementia in the elderly. AD pathology is characterized by accumulation of microglia around the beta-amyloid (Aß) plaques which assumes disease-specific transcriptional signatures, as for the disease-associated microglia (DAM). However, the regulators of microglial phagocytosis are still unknown. METHODS: We isolated Aß-laden microglia from the brain of 5xFAD mice for RNA sequencing to characterize the transcriptional signature in phagocytic microglia and to identify the key non-coding RNAs capable of regulating microglial phagocytosis. Through spatial sequencing, we show the transcriptional changes of microglia in the AD mouse brain in relation to Aß proximity. RESULTS: Finally, we show that phagocytic messenger RNAs are regulated by miR-7a-5p, miR-29a-3p and miR-146a-5p microRNAs and segregate the DAM population into phagocytic and non-phagocytic states. DISCUSSION: Our study pinpoints key regulators of microglial Aß clearing capacity suggesting new targets for future therapeutic approaches.


Subject(s)
Alzheimer Disease , MicroRNAs , Neurodegenerative Diseases , Humans , Mice , Animals , Aged , Alzheimer Disease/genetics , Alzheimer Disease/pathology , Microglia/pathology , Neurodegenerative Diseases/pathology , Amyloid beta-Peptides , MicroRNAs/genetics , Mice, Transgenic , Disease Models, Animal
8.
Vaccine ; 41(20): 3233-3246, 2023 05 11.
Article in English | MEDLINE | ID: mdl-37085458

ABSTRACT

The ongoing SARS-CoV-2 pandemic is controlled but not halted by public health measures and mass vaccination strategies which have exclusively relied on intramuscular vaccines. Intranasal vaccines can prime or recruit to the respiratory epithelium mucosal immune cells capable of preventing infection. Here we report a comprehensive series of studies on this concept using various mouse models, including HLA class II-humanized transgenic strains. We found that a single intranasal (i.n.) dose of serotype-5 adenoviral vectors expressing either the receptor binding domain (Ad5-RBD) or the complete ectodomain (Ad5-S) of the SARS-CoV-2 spike protein was effective in inducing i) serum and bronchoalveolar lavage (BAL) anti-spike IgA and IgG, ii) robust SARS-CoV-2-neutralizing activity in the serum and BAL, iii) rigorous spike-directed T helper 1 cell/cytotoxic T cell immunity, and iv) protection of mice from a challenge with the SARS-CoV-2 beta variant. Intramuscular (i.m.) Ad5-RBD or Ad5-S administration did not induce serum or BAL IgA, and resulted in lower neutralizing titers in the serum. Moreover, prior immunity induced by an intramuscular mRNA vaccine could be potently enhanced and modulated towards a mucosal IgA response by an i.n. Ad5-S booster. Notably, Ad5 DNA was found in the liver or spleen after i.m. but not i.n. administration, indicating a lack of systemic spread of the vaccine vector, which has been associated with a risk of thrombotic thrombocytopenia. Unlike in otherwise genetically identical HLA-DQ6 mice, in HLA-DQ8 mice Ad5-RBD vaccine was inferior to Ad5-S, suggesting that the RBD fragment does not contain a sufficient collection of helper-T cell epitopes to constitute an optimal vaccine antigen. Our data add to previous promising preclinical results on intranasal SARS-CoV-2 vaccination and support the potential of this approach to elicit mucosal immunity for preventing transmission of SARS-CoV-2.


Subject(s)
COVID-19 , Viral Vaccines , Humans , Animals , Mice , Spike Glycoprotein, Coronavirus/genetics , COVID-19 Vaccines , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/prevention & control , SARS-CoV-2 , Administration, Intranasal , Disease Models, Animal , Immunoglobulin A
9.
Neurobiol Dis ; 182: 106140, 2023 06 15.
Article in English | MEDLINE | ID: mdl-37120095

ABSTRACT

The rare A673T variant was the first variant found within the amyloid precursor protein (APP) gene conferring protection against Alzheimer's disease (AD). Thereafter, different studies have discovered that the carriers of the APP A673T variant show reduced levels of amyloid beta (Aß) in the plasma and better cognitive performance at high age. Here, we analyzed cerebrospinal fluid (CSF) and plasma of APP A673T carriers and control individuals using a mass spectrometry-based proteomics approach to identify differentially regulated targets in an unbiased manner. Furthermore, the APP A673T variant was introduced into 2D and 3D neuronal cell culture models together with the pathogenic APP Swedish and London mutations. Consequently, we now report for the first time the protective effects of the APP A673T variant against AD-related alterations in the CSF, plasma, and brain biopsy samples from the frontal cortex. The CSF levels of soluble APPß (sAPPß) and Aß42 were significantly decreased on average 9-26% among three APP A673T carriers as compared to three well-matched controls not carrying the protective variant. Consistent with these CSF findings, immunohistochemical assessment of cortical biopsy samples from the same APP A673T carriers did not reveal Aß, phospho-tau, or p62 pathologies. We identified differentially regulated targets involved in protein phosphorylation, inflammation, and mitochondrial function in the CSF and plasma samples of APP A673T carriers. Some of the identified targets showed inverse levels in AD brain tissue with respect to increased AD-associated neurofibrillary pathology. In 2D and 3D neuronal cell culture models expressing APP with the Swedish and London mutations, the introduction of the APP A673T variant resulted in lower sAPPß levels. Concomitantly, the levels of sAPPα were increased, while decreased levels of CTFß and Aß42 were detected in some of these models. Our findings emphasize the important role of APP-derived peptides in the pathogenesis of AD and demonstrate the effectiveness of the protective APP A673T variant to shift APP processing towards the non-amyloidogenic pathway in vitro even in the presence of two pathogenic mutations.


Subject(s)
Alzheimer Disease , Amyloid beta-Protein Precursor , Humans , Amyloid beta-Protein Precursor/genetics , Amyloid beta-Protein Precursor/metabolism , Alzheimer Disease/cerebrospinal fluid , Amyloid beta-Peptides/metabolism , Heterozygote , Brain/metabolism
10.
Arterioscler Thromb Vasc Biol ; 43(1): e46-e61, 2023 01.
Article in English | MEDLINE | ID: mdl-36384268

ABSTRACT

BACKGROUND: Diabetes is a major risk factor for peripheral arterial disease. Clinical and preclinical studies suggest an impaired collateral remodeling and angiogenesis in response to atherosclerotic arterial occlusion in diabetic conditions, although the underlying mechanisms are poorly understood. OBJECTIVE: To clarify the cellular and molecular mechanisms underlying impaired postischemic adaptive vascular responses and to evaluate rHDL (reconstituted HDL)-ApoA-I nanotherapy to rescue the defect in type 2 diabetic mouse model of hindlimb ischemia. METHODS AND RESULTS: Hindlimb ischemia was induced by unilateral femoral artery ligation. Collateral and capillary parameters together with blood flow recovery were analyzed from normoxic adductor and ischemic gastrocnemius muscles, respectively, at day 3 and 7 post-ligation. In response to femoral artery ligation, collateral lumen area was significantly reduced in normoxic adductor muscles. Distally, ischemic gastrocnemius muscles displayed impaired perfusion recovery and angiogenesis paralleled with persistent inflammation. Muscle-specific mRNA sequencing revealed differential expression of genes critical for smooth muscle proliferation and sprouting angiogenesis in normoxic adductor and ischemic gastrocnemius, respectively, at day 7 post-ligation. Genes typical for macrophage (Mϕ) subsets were differentially expressed across both muscle types. Cell-specific gene expression, flow cytometry, and immunohistochemistry revealed persistent IFN-I response gene upregulation in arterial endothelial cells, ECs and Mϕs from T2DM mice associated with impaired collateral remodeling, angiogenesis and perfusion recovery. Furthermore, rHDL nanotherapy rescued impaired collateral remodeling and angiogenesis through dampening EC and Mϕ inflammation in T2DM mice. CONCLUSIONS: Our results suggest that an impaired collateral remodeling and sprouting angiogenesis in T2DM mice is associated with persistent IFN-I response in ECs and Mϕs. Dampening persistent inflammation and skewing ECs and Mϕ phenotype toward less inflammatory ones using rHDL nanotherapy may serve as a potential therapeutic target for T2DM peripheral arterial disease.


Subject(s)
Diabetes Mellitus, Experimental , Diabetes Mellitus, Type 2 , Peripheral Arterial Disease , Mice , Animals , Neovascularization, Physiologic , Endothelial Cells/metabolism , Apolipoprotein A-I/metabolism , Macrophages/metabolism , Ischemia , Muscle, Skeletal/blood supply , Femoral Artery/metabolism , Diabetes Mellitus, Type 2/genetics , Inflammation/metabolism , Peripheral Arterial Disease/metabolism , Phenotype , Hindlimb/blood supply , Mice, Inbred C57BL , Collateral Circulation
11.
PLoS One ; 17(3): e0265948, 2022.
Article in English | MEDLINE | ID: mdl-35358280

ABSTRACT

MicroRNAs are well characterized in their role in silencing gene expression by targeting 3´-UTR of mRNAs in cytoplasm. However, recent studies have shown that miRNAs have a role in the regulation of genes in the nucleus, where they are abundantly located. We show here that in mouse endothelial cell line (C166), nuclear microRNA miR-466c participates in the regulation of vascular endothelial growth factor a (Vegfa) gene expression in hypoxia. Upregulation of Vegfa expression in response to hypoxia was significantly compromised after removal of miR-466c with CRISPR-Cas9 genomic deletion. We identified a promoter-associated long non-coding RNA on mouse Vegfa promoter and show that miR-466c directly binds to this transcript to modulate Vegfa expression. Collectively, these observations suggest that miR-466c regulates Vegfa gene transcription in the nucleus by targeting the promoter, and expands on our understanding of the role of miRNAs well beyond their canonical role.


Subject(s)
MicroRNAs , RNA, Long Noncoding , Vascular Endothelial Growth Factor A , Animals , Hypoxia/genetics , Mice , MicroRNAs/genetics , RNA, Long Noncoding/genetics , RNA, Messenger , Vascular Endothelial Growth Factor A/metabolism
12.
Hum Gene Ther ; 32(19-20): 1295-1307, 2021 10.
Article in English | MEDLINE | ID: mdl-34494459

ABSTRACT

Based on recent success in using modified RNA in clinical applications, we tested the safety, feasibility, and efficacy of direct delivery of citrate-saline-formulated mRNA into an hibernating ischemic heart muscle using an electromechanical mapping and injection catheter system (NOGA/Myostar) in a porcine chronic myocardial ischemia model. Chronic ischemia was induced in domestic pigs (n = 24) using a bottleneck stent placed in the left anterior descending coronary artery. Low (1 mg) and high (7.5 mg) doses of citrate-saline-formulated vascular endothelial growth factor (VEGF)-A165 mRNA were administered in the study. LacZ mRNA and citrate-saline buffer were used as controls. Ten intramyocardial injections (200 µL each) of the mRNAs or citrate-saline buffer were given endovascularly into the hibernating ischemic myocardium using the NOGA catheter. Positron emission tomography 15O-radiowater imaging was performed 7 days after the induction of ischemia and 28 days after the mRNA delivery to measure quantitative myocardial blood perfusion. Coronary angiography, left ventricular function measurements, and clinical chemistry were obtained at each time point. Thirty-five days after the mRNA transfers, pigs were sacrificed, and infarct size and general histology were analyzed. LacZ mRNA pigs were sacrificed 24 h after the transduction. Citrate-saline-formulated mRNA delivery into the ischemic myocardium with endovascular injection catheter did not lead to meaningful transduction with the translation of VEGF-A165, nor therapeutic effects in the heart. VEGF-A165 mRNA showed no statistically significant improvements in left ventricular ejection fraction (LVEF), cardiac output, myocardial perfusion, infarct size, collateral growth, or capillary area in the study groups. However, there was a trend in the high-dose group toward an improved LVEF and cardiac output at rest. No significant adverse effects were observed. In conclusion, the NOGA/Myostar injection catheter system is ineffective in delivering citrate-saline-formulated mRNAs into the heart muscle with the doses and methods used in a porcine chronic myocardial ischemia model.


Subject(s)
Myocardial Ischemia , Vascular Endothelial Growth Factor A , Animals , Catheters , Citric Acid , Myocardial Ischemia/genetics , Myocardial Ischemia/therapy , Myocardium , RNA, Messenger/genetics , Stroke Volume , Swine , Ventricular Function, Left
13.
Curr Atheroscler Rep ; 23(8): 45, 2021 06 19.
Article in English | MEDLINE | ID: mdl-34146172

ABSTRACT

PURPOSE OF REVIEW: Atherosclerosis, defined by inflammation and accumulation of cholesterol, extracellular matrix, and cell debris into the arteries is a common factor behind cardiovascular diseases (CVD), such as coronary artery disease, peripheral artery disease, and stroke. In this review, we discuss and describe novel RNA interference (RNAi)-based therapies in clinical trials and on the market. RECENT FINDINGS: The first RNAi-based therapies have entered clinical use for the control of atherosclerosis risk factors, i.e., blood cholesterol levels. The most advanced treatment is silencing of proprotein convertase subtilisin/kexin type 9 (PCSK9) with a drug called inclisiran, which has been approved for the treatment of hypercholesterolemia in late 2020, and results in a robust decrease in plasma cholesterol levels. As the new RNAi therapies for atherosclerosis are now entering markets, the usefulness of these therapies will be further evaluated in larger patient cohorts. Thus, it remains to be seen how fast, effectively and eminently these new drugs consolidate their niche within the cardiovascular disease drug palette.


Subject(s)
Atherosclerosis , Hypercholesterolemia , Atherosclerosis/genetics , Atherosclerosis/therapy , Humans , Proprotein Convertase 9/genetics , RNAi Therapeutics
14.
Genome Med ; 12(1): 99, 2020 11 20.
Article in English | MEDLINE | ID: mdl-33218352

ABSTRACT

BACKGROUND: Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. METHODS: We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. RESULTS: We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment resistance, we show that inhibition of ETS-transcription factors reduced cell viability and resolved pathways contributing to this using scRNA-seq. CONCLUSIONS: Our data provide a detailed picture of the transcription factor activities characterizing both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia.


Subject(s)
Cell Differentiation/genetics , Cell Proliferation , Core Binding Factor Alpha 2 Subunit/genetics , Leukemia/genetics , Lymphocytes/physiology , Proto-Oncogene Proteins c-ets/genetics , Repressor Proteins/genetics , Bone Marrow , Cell Line, Tumor , Child , Core Binding Factor Alpha 2 Subunit/metabolism , Drug Delivery Systems , Gene Expression Regulation, Neoplastic , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Leukemia/drug therapy , Proto-Oncogene Proteins c-ets/metabolism , Repressor Proteins/metabolism , Transcription Factors , Transcriptome , Translocation, Genetic , ETS Translocation Variant 6 Protein
15.
Clin Proteomics ; 17: 36, 2020.
Article in English | MEDLINE | ID: mdl-33088244

ABSTRACT

BACKGROUND: Femtosecond laser-assisted in situ keratomileusis (LASIK) has proven to be an efficacious, predictable, and safe procedure for the correction of refractive errors. We examined the early tear protein changes of patients undergoing LASIK surgery in order to better understand the mechanisms and proteins related to laser corneal surgery and initial recovery. METHODS: Corneal flaps were created with Ziemer FEMTO LDV Z6 I femtosecond laser and stroma was ablated using Wavelight EX500 excimer laser. Tear samples were collected preoperatively as well as 1.5 h and 1 month after LASIK treatment using glass microcapillary tubes. Relative quantification of tear proteins was performed with sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS). RESULTS: SWATH-MS revealed that 158 proteins had altered expression levels 1.5 h after the operation. Two-thirds of these proteins, mostly connected to migration and inflammation response, returned to preoperative levels within the first postoperative month. The other proteins, which did not return to baseline levels, included proteins connected to for example epithelial barrier function. We also identified several proteins, which correlated with surgical variables, such as the amount of correction, flap thickness and flap diameter. CONCLUSIONS: The present study showed that an uneventful femtosecond LASIK refractive surgery induced a significant immune cell migration and inflammation-associated changes in tear proteomics profile quickly after the operation, but the expression of most proteins recovered almost completely to the preoperative levels within the first month. The individual proteins identified in our study are potential targets for the follow-up and modification of LASIK-induced biochemical processes.

16.
Mol Ther ; 28(7): 1731-1740, 2020 07 08.
Article in English | MEDLINE | ID: mdl-32243833

ABSTRACT

VEGF-B gene therapy is a promising proangiogenic treatment for ischemic heart disease, but, unexpectedly, we found that high doses of VEGF-B promote ventricular arrhythmias (VAs). VEGF-B knockout, alpha myosin heavy-chain promoter (αMHC)-VEGF-B transgenic mice, and pigs transduced intramyocardially with adenoviral (Ad)VEGF- B186 were studied. Immunostaining showed a 2-fold increase in the number of nerves per field (76 vs. 39 in controls, p < 0.001) and an abnormal nerve distribution in the hypertrophic hearts of 11- to 20-month-old αMHC-VEGF-B mice. AdVEGF-B186 gene transfer (GT) led to local sprouting of nerve endings in pig myocardium (141 vs. 78 nerves per field in controls, p < 0.05). During dobutamine stress, 60% of the αMHC-VEGF-B hypertrophic mice had arrhythmias as compared to 7% in controls, and 20% of the AdVEGF-B186-transduced pigs and 100% of the combination of AdVEGF-B186- and AdsVEGFR-1-transduced pigs displayed VAs and even ventricular fibrillation. AdVEGF-B186 GT significantly increased the risk of sudden cardiac death in pigs when compared to any other GT with different VEGFs (hazard ratio, 500.5; 95% confidence interval [CI] 46.4-5,396.7; p < 0.0001). In gene expression analysis, VEGF-B induced the upregulation of Nr4a2, ATF6, and MANF in cardiomyocytes, molecules previously linked to nerve growth and differentiation. Thus, high AdVEGF-B186 overexpression induced nerve growth in the adult heart via a VEGFR-1 signaling-independent mechanism, leading to an increased risk of VA and sudden cardiac death.


Subject(s)
Arrhythmias, Cardiac/pathology , Myosin Heavy Chains/genetics , Sympathetic Nervous System/pathology , Up-Regulation , Vascular Endothelial Growth Factor B/genetics , Animals , Animals, Genetically Modified , Arrhythmias, Cardiac/genetics , Arrhythmias, Cardiac/metabolism , Dependovirus/genetics , Disease Notification , Female , Gene Knockout Techniques , Genetic Therapy , Genetic Vectors/administration & dosage , Male , Mice , Promoter Regions, Genetic , Recombinant Proteins/metabolism , Swine , Sympathetic Nervous System/metabolism , Transduction, Genetic , Vascular Endothelial Growth Factor B/adverse effects , Vascular Endothelial Growth Factor B/metabolism
17.
Curr Atheroscler Rep ; 22(2): 10, 2020 02 07.
Article in English | MEDLINE | ID: mdl-32034521

ABSTRACT

PURPOSE OF REVIEW: Atherosclerosis is characterized by accumulation of lipids and chronic inflammation in medium size to large arteries. Recently, RNA-based antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) are being developed, along with small molecule-based drugs and monoclonal antibodies, for the treatment of risk factors associated with atherosclerosis.. The purpose of this review is to describe nucleic acid-based therapeutics and introduce novel RNAs that might become future tools for treatment of atherosclerosis. RECENT FINDINGS: RNA-based inhibitors for PCSK9, Lp(a), ApoCIII, and ANGPTL3 have been successfully tested in phase II-III clinical trials. Moreover, multiple microRNA and long non-coding RNAs have been found to reduce atherogenesis in preclinical animal models. Clinical trials especially with ASOs and siRNAs directed to liver, targeting cholesterol and lipoprotein metabolism, have shown promising results. Additional research in larger patient cohorts is needed to fully evaluate the therapeutic potential of these new drugs.


Subject(s)
Anticholesteremic Agents/therapeutic use , Atherosclerosis/drug therapy , MicroRNAs/therapeutic use , Oligonucleotides, Antisense/therapeutic use , RNA, Long Noncoding/therapeutic use , RNA, Small Interfering/therapeutic use , Angiopoietin-Like Protein 3 , Angiopoietin-like Proteins/antagonists & inhibitors , Animals , Apolipoprotein C-III/antagonists & inhibitors , Atherosclerosis/metabolism , Humans , Lipoprotein(a)/antagonists & inhibitors , Lipoprotein(a)/metabolism , Liver/metabolism , Oligonucleotides, Antisense/pharmacology , PCSK9 Inhibitors , RNA, Small Interfering/pharmacology
18.
Cell Mol Life Sci ; 77(20): 4093-4115, 2020 Oct.
Article in English | MEDLINE | ID: mdl-31820036

ABSTRACT

Intercellular communication is fundamental to the survival and maintenance of all multicellular systems, whereas dysregulation of communication pathways can drive cancer progression. Extracellular vesicles (EVs) are mediators of cell-to-cell communication that regulate a variety of cellular processes involved in tumor progression. Overexpression of a specific plasma membrane enzyme, hyaluronan synthase 3 (HAS3), is one of the factors that can induce EV shedding. HAS3, and particularly its product hyaluronan (HA), are carried by EVs and are known to be associated with the tumorigenic properties of cancer cells. To elucidate the specific effects of cancerous, HAS3-induced EVs on target cells, normal human keratinocytes and melanoma cells were treated with EVs derived from GFP-HAS3 expressing metastatic melanoma cells. We found that the HA receptor CD44 participated in the regulation of EV binding to target cells. Furthermore, GFP-HAS3-positive EVs induced HA secretion, proliferation and invasion of target cells. Our results suggest that HAS3-EVs contains increased quantities of IHH, which activates the target cell hedgehog signaling cascade and leads to the activation of c-Myc and regulation of claspin expression. This signaling of IHH in HAS3-EVs resulted in increased cell proliferation. Claspin immunostaining correlated with HA content in human cutaneous melanocytic lesions, supporting our in vitro findings and suggesting a reciprocal regulation between claspin expression and HA synthesis. This study shows for the first time that EVs originating from HAS3 overexpressing cells carry mitogenic signals that induce proliferation and epithelial-to-mesenchymal transition in target cells. The study also identifies a novel feedback regulation between the hedgehog signaling pathway and HA metabolism in melanoma, mediated by EVs carrying HA and IHH.


Subject(s)
Extracellular Vesicles/genetics , Hedgehog Proteins/genetics , Hyaluronan Synthases/genetics , Melanoma/genetics , Proto-Oncogene Proteins c-myc/genetics , Up-Regulation/genetics , Cell Line , Cell Line, Tumor , Cell Proliferation/genetics , Epithelial-Mesenchymal Transition/genetics , Humans , Hyaluronan Receptors/genetics , Signal Transduction/genetics
19.
J Mater Chem B ; 8(2): 282-289, 2020 01 14.
Article in English | MEDLINE | ID: mdl-31803886

ABSTRACT

In this paper we describe a straightforward supramolecular strategy to encapsulate silicon phthalocyanine (SiPc) photosensitizers (PS) in polymeric micelles made of poly(ε-caprolactone)-b-methoxypoly(ethylene glycol) (PCL-PEG) block copolymers. While PCL-PEG micelles are promising nanocarriers based on their biocompatibility and biodegradability, the design of our new PS favors their encapsulation. In particular, they combine two axial benzoyl substituents, each of them carrying either three hydrophilic methoxy(triethylenoxy) chains (1), three hydrophobic dodecyloxy chains (3), or both kinds of chains (2). The SiPc derivatives 1 and 2 are therefore amphiphilic, with the SiPc unit contributing to the hydrophobic core, while lipophilicity increases along the series, making it possible to correlate the loading efficacy in PCL-PEG micelles with the hydrophobic/hydrophilic balance of the PS structure. This has led to a new kind of third-generation nano-PS that efficiently photogenerates 1O2, while preliminary in vitro experiments demonstrate an excellent cellular uptake and a promising PDT activity.


Subject(s)
Indoles/chemistry , Organosilicon Compounds/chemistry , Photosensitizing Agents/chemistry , Drug Carriers/chemistry , Micelles , Polyesters/chemistry , Polyethylene Glycols/chemistry
20.
Clin Ophthalmol ; 13: 741-754, 2019.
Article in English | MEDLINE | ID: mdl-31114152

ABSTRACT

PURPOSE: To study self-reported patient satisfaction and dry eye symptoms in hyperopic correction with femtosecond laser-assisted in situ keratomileusis (FS-LASIK). PATIENTS AND METHODS: Ninety-eight eyes (53 patients) were treated with FS-LASIK for hyperopia. Patients' self-reported dry eye symptoms and satisfaction with near and far vision were graded on the visual analog scale (VAS) preoperatively and 1 month postoperatively. RESULTS: Ninety-one percent of the eyes with the plano target (54 eyes) achieved an uncorrected distance visual acuity of 20/20 or better. Predictability, defined as spherical equivalent refraction within ±0.5 D of target, was 88% of all eyes. None of the eyes lost two or more Snellen lines of corrected distance visual acuity. There was no significant change in the self-reported dry eye sensation (VAS score from 2.7±2.0 to 2.8±2.0; P=0.66). In 44 monovision patients, satisfaction with both far vision (from 71.2±19.8 to 89.2±8.7; P<0.0001) and near vision (from 51.7±26.2 to 89.3±13.2; P<0.0001) increased significantly. In nine emmetropic patients, satisfaction with neither far vision nor near vision was significantly improved, although there was a clear tendency (from 73.7±23.7 to 86.9±15.3; P=0.22, and from 58.9±29.1 to 81.6±17.4; P=0.11, respectively). In the monovision patient group, far vision satisfaction decreased when dry eye symptoms increased. Monovision patients, as predicted, were more satisfied with their near vision, when postoperative spherical equivalent from target was on the myopic side. CONCLUSION: FS-LASIK correction of hyperopia significantly improved patient satisfaction with both near and far vision in monovision patients. Hyperopic patients had no significant changes in postoperative dry eye symptoms compared to preoperative values.

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