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1.
Adv Healthc Mater ; : e2400622, 2024 May 31.
Article in English | MEDLINE | ID: mdl-38820600

ABSTRACT

Virion-mediated outbreaks are imminent and despite rapid responses, continue to cause adverse symptoms and death. Therefore, tunable, sensitive, high-throughput assays are needed to help diagnose future virion-mediated outbreaks. Herein, we developed a tunable in situ assay to selectively enrich virions and extracellular vesicles (EVs) and simultaneously detect antigens and nucleic acids at a single-particle resolution. The Biochip Antigen and RNA Assay (BARA) enhanced sensitivities compared to quantitative reverse-transcription polymerase chain reaction (qRT-PCR), enabling the detection of virions in asymptomatic patients, genetic mutations in single virions, and enabling the continued long-term expression of viral RNA in the EV-enriched subpopulation in the plasma of patients with post-acute sequelae of COVID-19. BARA revealed highly accurate diagnoses of COVID-19 by simultaneously detecting the spike glycoprotein and nucleocapsid-encoding RNA in saliva and nasopharyngeal swab samples. Altogether, the single-particle detection of antigens and viral RNA provides a tunable framework for the diagnosis, monitoring, and mutation screening of current and future outbreaks. This article is protected by copyright. All rights reserved.

2.
J Biomed Sci ; 31(1): 30, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38500170

ABSTRACT

BACKGROUND: Acute lung injury (ALI) is a life-threatening respiratory condition characterized by severe inflammation and lung tissue damage, frequently causing rapid respiratory failure and long-term complications. The microRNA let-7a-5p is involved in the progression of lung injury, inflammation, and fibrosis by regulating immune cell activation and cytokine production. This study aims to use an innovative cellular electroporation platform to generate extracellular vesicles (EVs) carring let-7a-5p (EV-let-7a-5p) derived from transfected Wharton's jelly-mesenchymal stem cells (WJ-MSCs) as a potential gene therapy for ALI. METHODS: A cellular nanoporation (CNP) method was used to induce the production and release of EV-let-7a-5p from WJ-MSCs transfected with the relevant plasmid DNA. EV-let-7a-5p in the conditioned medium were isolated using a tangential flow filtration (TFF) system. EV characterization followed the minimal consensus guidelines outlined by the International Society for Extracellular Vesicles. We conducted a thorough set of therapeutic assessments, including the antifibrotic effects using a transforming growth factor beta (TGF-ß)-induced cell model, the modulation effects on macrophage polarization, and the influence of EV-let-7a-5p in a rat model of hyperoxia-induced ALI. RESULTS: The CNP platform significantly increased EV secretion from transfected WJ-MSCs, and the encapsulated let-7a-5p in engineered EVs was markedly higher than that in untreated WJ-MSCs. These EV-let-7a-5p did not influence cell proliferation and effectively mitigated the TGF-ß-induced fibrotic phenotype by downregulating SMAD2/3 phosphorylation in LL29 cells. Furthermore, EV-let-7a-5p regulated M2-like macrophage activation in an inflammatory microenvironment and significantly induced interleukin (IL)-10 secretion, demonstrating their modulatory effect on inflammation. Administering EVs from untreated WJ-MSCs slightly improved lung function and increased let-7a-5p expression in plasma in the hyperoxia-induced ALI rat model. In comparison, EV-let-7a-5p significantly reduced macrophage infiltration and collagen deposition while increasing IL-10 expression, causing a substantial improvement in lung function. CONCLUSION: This study reveals that the use of the CNP platform to stimulate and transfect WJ-MSCs could generate an abundance of let-7a-5p-enriched EVs, which underscores the therapeutic potential in countering inflammatory responses, fibrotic activation, and hyperoxia-induced lung injury. These results provide potential avenues for developing innovative therapeutic approaches for more effective interventions in ALI.


Subject(s)
Acute Lung Injury , Extracellular Vesicles , Hyperoxia , MicroRNAs , Rats , Animals , Cells, Cultured , Hyperoxia/metabolism , Inflammation , MicroRNAs/genetics , MicroRNAs/metabolism , Transforming Growth Factor beta/genetics , Transforming Growth Factor beta/metabolism , Extracellular Vesicles/physiology , Fibrosis , Acute Lung Injury/therapy , Acute Lung Injury/metabolism
3.
Adv Sci (Weinh) ; 11(11): e2306373, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38204202

ABSTRACT

Detecting pancreatic duct adenocarcinoma (PDAC) in its early stages and predicting late-stage patient prognosis undergoing chemotherapy is challenging. This work shows that the activation of specific oncogenes leads to elevated expression of mRNAs and their corresponding proteins in extracellular vesicles (EVs) circulating in blood. Utilizing an immune lipoplex nanoparticle (ILN) biochip assay, these findings demonstrate that glypican 1 (GPC1) mRNA expression in the exosomes-rich (Exo) EV subpopulation and GPC1 membrane protein (mProtein) expression in the microvesicles-rich (MV) EV subpopulation, particularly the tumor associated microvesicles (tMV), served as a viable biomarker for PDAC. A combined analysis effectively discriminated early-stage PDAC patients from benign pancreatic diseases and healthy donors in sizable clinical from multiple hospitals. Furthermore, among late-stage PDAC patients undergoing chemotherapy, lower GPC1 tMV-mProtein and Exo-mRNA expression before treatment correlated significantly with prolonged overall survival. These findings underscore the potential of vesicular GPC1 expression for early PDAC screenings and chemotherapy prognosis.


Subject(s)
Carcinoma, Pancreatic Ductal , Extracellular Vesicles , Pancreatic Neoplasms , Humans , Biomarkers, Tumor/genetics , Carcinoma, Pancreatic Ductal/diagnosis , Carcinoma, Pancreatic Ductal/genetics , Extracellular Vesicles/metabolism , Glypicans/genetics , Glypicans/metabolism , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/genetics , Prognosis , RNA, Messenger/genetics , RNA, Messenger/metabolism
4.
Lab Chip ; 24(4): 819-831, 2024 02 13.
Article in English | MEDLINE | ID: mdl-38235543

ABSTRACT

Localized micro/nano-electroporation (MEP/NEP) shows tremendous potential in cell transfection with high cell viability, precise dose control, and good transfection efficacy. In MEP/NEP, micro or nanochannels are used to tailor the electric field distribution. Cells are positioned tightly by a micron or nanochannel, and the cargoes are delivered into the cell via the channel by electrophoresis (EP). Such confined geometries with micro and nanochannels are also widely used in sorting, isolation, and condensing of biomolecules and cells. Theoretical studies on the electrokinetic phenomena in these applications have been well established. However, for MEP/NEP applications, electrokinetic phenomena and their impact on the cell transfection efficiency and cell survival rate have not been studied comprehensively. In this work, we reveal the coupling between electric field, Joule heating, electroosmosis (EO), and EP in MEP/NEP at different channel sizes. A microfluidic biochip is used to investigate the electrokinetic phenomena in MEP/NEP on a single cell level. Bubble formation is observed at a threshold voltage due to Joule heating. The bubble is pushed to the cargo side due to EO and grows at the outlet of the nanochannel. As the voltage increases, the cargo transport efficiency decreases due to more intense EO, particularly for plasmid DNAs (3.5 kbp) with a low EP mobility. An 'electroporation zone' is defined for NEP/MEP systems with different channel sizes to avoid bubble formation and excessive EO velocity that may reduce the cargo delivery efficiency.


Subject(s)
Electroosmosis , Heating , Electroporation/methods , Transfection , Microfluidics
5.
Adv Sci (Weinh) ; 10(33): e2302622, 2023 11.
Article in English | MEDLINE | ID: mdl-37847907

ABSTRACT

Regenerative medicine in tissue engineering often relies on stem cells and specific growth factors at a supraphysiological dose. These approaches are costly and may cause severe side effects. Herein, therapeutic small extracellular vesicles (t-sEVs) endogenously loaded with a cocktail of human vascular endothelial growth factor A (VEGF-A) and human bone morphogenetic protein 2 (BMP-2) mRNAs within a customized injectable PEGylated poly (glycerol sebacate) acrylate (PEGS-A) hydrogel for bone regeneration in rats with challenging femur critical-size defects are introduced. Abundant t-sEVs are produced by a facile cellular nanoelectroporation system based on a commercially available track-etched membrane (TM-nanoEP) to deliver plasmid DNAs to human adipose-derived mesenchymal stem cells (hAdMSCs). Upregulated microRNAs associated with the therapeutic mRNAs are enriched in t-sEVs for enhanced angiogenic-osteogenic regeneration. Localized and controlled release of t-sEVs within the PEGS-A hydrogel leads to the retention of therapeutics in the defect site for highly efficient bone regeneration with minimal low accumulation in other organs.


Subject(s)
Osteogenesis , Vascular Endothelial Growth Factor A , Rats , Humans , Animals , RNA, Messenger/genetics , Bone Regeneration/genetics , Hydrogels/pharmacology
6.
Nat Commun ; 14(1): 6692, 2023 10 23.
Article in English | MEDLINE | ID: mdl-37872156

ABSTRACT

Pancreatic ductal adenocarcinoma (PDAC) tumours carry multiple gene mutations and respond poorly to treatments. There is currently an unmet need for drug carriers that can deliver multiple gene cargoes to target high solid tumour burden like PDAC. Here, we report a dual targeted extracellular vesicle (dtEV) carrying high loads of therapeutic RNA that effectively suppresses large PDAC tumours in mice. The EV surface contains a CD64 protein that has a tissue targeting peptide and a humanized monoclonal antibody. Cells sequentially transfected with plasmid DNAs encoding for the RNA and protein of interest by Transwell®-based asymmetric cell electroporation release abundant targeted EVs with high RNA loading. Together with a low dose chemotherapy drug, Gemcitabine, dtEVs suppress large orthotopic PANC-1 and patient derived xenograft tumours and metastasis in mice and extended animal survival. Our work presents a clinically accessible and scalable way to produce abundant EVs for delivering multiple gene cargoes to large solid tumours.


Subject(s)
Carcinoma, Pancreatic Ductal , Extracellular Vesicles , Pancreatic Neoplasms , Humans , Animals , Mice , Deoxycytidine/therapeutic use , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/therapy , Pancreatic Neoplasms/metabolism , Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/therapy , Carcinoma, Pancreatic Ductal/metabolism , RNA , Extracellular Vesicles/metabolism , Cell Line, Tumor , Pancreatic Neoplasms
7.
Nanoscale ; 15(8): 4080-4089, 2023 Feb 23.
Article in English | MEDLINE | ID: mdl-36744418

ABSTRACT

Nanochannel electroporation (NEP) is a new technology for cell transfection, which provides superior gene delivery and cell viability to conventional bulk electroporation (BEP). In NEP, the cells laid on a porous substrate are subjected to an asymmetric electric field which induces asymmetric membrane poration. The cell membrane near the channel outlet ('transfection membrane') is porated intensely, allowing direct delivery of genetic materials, while the rest of the cell membrane ('non-transfection membrane') remains much less perturbed for low cellular damage. In this work, the transfection window of NEP for the delivery of different sized molecules is systematically investigated. The results show that small molecules (∼0.6 kDa) can be delivered into cells at a relatively lower voltage without significantly impacting the non-transfection membrane. To deliver larger molecules (∼6 kDa), a higher working voltage is required at the cost of cell viability due to more severe damage of the non-transfection membrane. Through numerical analysis of both transient transmembrane potential (t-TMP) and dynamic transmembrane potential (d-TMP), here we show that the membrane damage on both transfection and non-transfection sides of the cell membrane can be predicted. The agreement between experimental results and numerical analysis provides a comprehensive understanding of cell membrane damage and cargo delivery in NEP.


Subject(s)
Electroporation Therapies , Electroporation , Electroporation/methods , Transfection , Cell Membrane , Gene Transfer Techniques
8.
Nat Biomed Eng ; 7(7): 887-900, 2023 07.
Article in English | MEDLINE | ID: mdl-36635419

ABSTRACT

The success of messenger RNA therapeutics largely depends on the availability of delivery systems that enable the safe, effective and stable translation of genetic material into functional proteins. Here we show that extracellular vesicles (EVs) produced via cellular nanoporation from human dermal fibroblasts, and encapsulating mRNA encoding for extracellular-matrix α1 type-I collagen (COL1A1) induced the formation of collagen-protein grafts and reduced wrinkle formation in the collagen-depleted dermal tissue of mice with photoaged skin. We also show that the intradermal delivery of the mRNA-loaded EVs via a microneedle array led to the prolonged and more uniform synthesis and replacement of collagen in the dermis of the animals. The intradermal delivery of EV-based COL1A1 mRNA may make for an effective protein-replacement therapy for the treatment of photoaged skin.


Subject(s)
Dermis , Extracellular Vesicles , Humans , Mice , Animals , Dermis/metabolism , RNA, Messenger/metabolism , Collagen/metabolism , Skin/metabolism , Extracellular Vesicles/metabolism
9.
J Extracell Vesicles ; 11(9): e12258, 2022 09.
Article in English | MEDLINE | ID: mdl-36093740

ABSTRACT

Conventional PD-L1 immunohistochemical tissue biopsies only predict 20%-40% of non-small cell lung cancer (NSCLC) patients that will respond positively to anti-PD-1/PD-L1 immunotherapy. Herein, we present an immunogold biochip to quantify single extracellular vesicular RNA and protein (Au SERP) as a non-invasive alternative. With only 20 µl of purified serum, PD-1/PD-L1 proteins on the surface of extracellular vesicles (EVs) and EV PD-1/PD-L1 messenger RNA (mRNA) cargo were detected at a single-vesicle resolution and exceeded the sensitivities of their bulk-analysis conventional counterparts, ELISA and qRT-PCR, by 1000 times. By testing a cohort of 27 non-responding and 27 responding NSCLC patients, Au SERP indicated that the single-EV mRNA biomarkers surpass the single-EV protein biomarkers in predicting patient responses to immunotherapy. Dual single-EV PD-1/PD-L1 mRNA detection differentiated responders from non-responders with an accuracy of 72.2% and achieved an NSCLC diagnosis accuracy of 93.2%, suggesting the potential for Au SERP to provide enhanced immunotherapy predictions and cancer diagnoses within the clinical setting.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Extracellular Vesicles , Lung Neoplasms , B7-H1 Antigen/genetics , Biomarkers , Carcinoma, Non-Small-Cell Lung/genetics , Extracellular Vesicles/metabolism , Humans , Immunologic Factors/therapeutic use , Immunotherapy , Lung Neoplasms/genetics , RNA/therapeutic use , RNA, Messenger/metabolism
10.
Cell Rep ; 40(3): 111115, 2022 07 19.
Article in English | MEDLINE | ID: mdl-35858552

ABSTRACT

The existence of "leukemia-initiating cells" (LICs) in chronic lymphocytic leukemia (CLL) remains controversial due to the difficulty in isolating and identifying the tumor-initiating cells. Here, we demonstrate a microchannel electroporation (MEP) microarray that injects RNA-detecting probes into single live cells, allowing the imaging and characterization of heterogeneous LICs by intracellular RNA expression. Using limited-cell FACS sequencing (LC-FACSeq), we can detect and monitor rare live LICs during leukemogenesis and characterize their differential drug sensitivity. Disease-associated mutation accumulation in developing B lymphoid but not myeloid lineage in CLL patient hematopoietic stem cells (CLL-HSCs), and development of independent clonal CLL-like cells in murine patient-derived xenograft models, suggests the existence of CLL LICs. Furthermore, we identify differential protein ubiquitination and unfolding response signatures in GATA2high CLL-HSCs that exhibit increased sensitivity to lenalidomide and resistance to fludarabine compared to GATA2lowCLL-HSCs. These results highlight the existence of therapeutically targetable disease precursors in CLL.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Animals , Cells, Cultured , Hematopoietic Stem Cells/metabolism , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/metabolism , Mice , Neoplastic Stem Cells/metabolism , RNA/metabolism
12.
Lab Chip ; 22(13): 2502-2518, 2022 06 28.
Article in English | MEDLINE | ID: mdl-35579189

ABSTRACT

Investigating cellular and vesicular heterogeneity in breast cancer remains a challenge, which encourages the development of controllable in vitro systems that mimic the tumor microenvironment. Although three-dimensional cell culture better recapitulates the heterogeneity observed in tumor growth and extracellular vesicle (EV) biogenesis, the physiological relevance is often contrasted with the control offered by two-dimensional cell culture. Therefore, to challenge this misconception we developed a novel microfluidic system harboring highly tunable three-dimensional EV microbioreactors (EVµBRs) to model micrometastatic EV release in breast cancer while capitalizing on the convenient, low-volume, and sterile interface provided by microfluidics. The diameter and cellular occupancy of the EVµBRs could be precisely tailored to various configurations, supporting the formation of breast cancer tumor spheroids. To immobilize the EVµBRs within a microchannel and facilitate EV extraction, oxygen inhibition in free-radical polymerization was repurposed to rapidly generate two-layer hydrodynamic traps in situ using a digital-micromirror device (DMD)-based ultraviolet (UV) projection system. Breast cancer tumor spheroid-derived EVs were harvested with as little as 20 µL from the microfluidic system and quantified by single-EV immunofluorescence for CD63 and CD81. Despite the low-volume extraction, differences in biomarker expression and coexpression of the tetraspanins on single EVs were observed. Furthermore, the EVµBRs were capable of recapitulating heterogeneity at a cellular and vesicular degree, indicating the utility and robustness of the microfluidic system to investigate physiologically relevant EVs in breast cancer and other disease models.


Subject(s)
Breast Neoplasms , Extracellular Vesicles , Microgels , Breast Neoplasms/pathology , Cell Culture Techniques , Extracellular Vesicles/metabolism , Female , Humans , Microfluidics , Tumor Microenvironment
13.
Blood ; 139(9): 1340-1358, 2022 03 03.
Article in English | MEDLINE | ID: mdl-34788382

ABSTRACT

Dysregulated cellular differentiation is a hallmark of acute leukemogenesis. Phosphatases are widely suppressed in cancers but have not been traditionally associated with differentiation. In this study, we found that the silencing of protein phosphatase 2A (PP2A) directly blocks differentiation in acute myeloid leukemia (AML). Gene expression and mass cytometric profiling revealed that PP2A activation modulates cell cycle and transcriptional regulators that program terminal myeloid differentiation. Using a novel pharmacological agent, OSU-2S, in parallel with genetic approaches, we discovered that PP2A enforced c-Myc and p21 dependent terminal differentiation, proliferation arrest, and apoptosis in AML. Finally, we demonstrated that PP2A activation decreased leukemia-initiating stem cells, increased leukemic blast maturation, and improved overall survival in murine Tet2-/-Flt3ITD/WT and human cell-line derived xenograft AML models in vivo. Our findings identify the PP2A/c-Myc/p21 axis as a critical regulator of the differentiation/proliferation switch in AML that can be therapeutically targeted in malignancies with dysregulated maturation fate.


Subject(s)
Cyclin-Dependent Kinase Inhibitor p21/metabolism , Leukemia, Myeloid, Acute/metabolism , Protein Phosphatase 2/metabolism , Proto-Oncogene Proteins c-myc/metabolism , Animals , Cell Line, Tumor , Cyclin-Dependent Kinase Inhibitor p21/genetics , Humans , Leukemia, Myeloid, Acute/genetics , Mice , Mice, Knockout , Protein Phosphatase 2/genetics , Proto-Oncogene Proteins c-myc/genetics
14.
Blood Adv ; 5(16): 3152-3162, 2021 08 24.
Article in English | MEDLINE | ID: mdl-34424320

ABSTRACT

Antibody-drug conjugates directed against tumor-specific targets have allowed targeted delivery of highly potent chemotherapy to malignant cells while sparing normal cells. Receptor tyrosine kinase-like orphan receptor 1 (ROR1) is an oncofetal protein with limited expression on normal adult tissues and is overexpressed on the surface of malignant cells in mantle cell lymphoma, acute lymphocytic leukemia with t(1;19)(q23;p13) translocation, and chronic lymphocytic leukemia. This differential expression makes ROR1 an attractive target for antibody-drug conjugate therapy, especially in malignancies such as mantle cell lymphoma and acute lymphocytic leukemia, in which systemic chemotherapy remains the gold standard. Several preclinical and phase 1 clinical studies have established the safety and effectiveness of anti-ROR1 monoclonal antibody-based therapies. Herein we describe a humanized, first-in-class anti-ROR1 antibody-drug conjugate, huXBR1-402-G5-PNU, which links a novel anti-ROR1 antibody (huXBR1-402) to a highly potent anthracycline derivative (PNU). We found that huXBR1-402-G5-PNU is cytotoxic to proliferating ROR1+ malignant cells in vitro and suppressed leukemia proliferation and extended survival in multiple models of mice engrafted with human ROR1+ leukemia. Lastly, we show that the B-cell lymphoma 2 (BCL2)-dependent cytotoxicity of huXBR1-402-G5-PNU can be leveraged by combined treatment strategies with the BCL2 inhibitor venetoclax. Together, our data present compelling preclinical evidence for the efficacy of huXBR1-402-G5-PNU in treating ROR1+ hematologic malignancies.


Subject(s)
Hematologic Neoplasms , Immunoconjugates , Leukemia, Lymphocytic, Chronic, B-Cell , Lymphoma, Mantle-Cell , Animals , Antibodies, Monoclonal , Lymphoma, Mantle-Cell/drug therapy , Lymphoma, Mantle-Cell/genetics , Mice
15.
Nanomaterials (Basel) ; 11(7)2021 Jun 30.
Article in English | MEDLINE | ID: mdl-34209111

ABSTRACT

Anticancer nanomedicines have been studied over 30 years, but fewer than 10 formulations have been approved for clinical therapy today. Despite abundant options of anticancer drugs, it remains challenging to have agents specifically target cancer cells while reducing collateral toxicity to healthy tissue. Nanocompartments that can be selective toward points deeply within malignant tissues are a promising concept, but the heterogeneity of tumor tissue, inefficiency of cargo loading and releasing, and low uniformity of manufacture required from preclinical to commercialization are major obstacles. Technological advances have been made in this field, creating engineered nanomaterials with improved uniformity, flexibility of cargo loading, diversity of surface modification, and less inducible immune responses. This review highlights the developmental process of approved nanomedicines and the opportunities for novel materials that combine insights of tumors and nanotechnology to develop a more effective nanomedicine for cancer patients.

16.
JCI Insight ; 5(12)2020 06 18.
Article in English | MEDLINE | ID: mdl-32554930

ABSTRACT

Detecting, characterizing, and monitoring rare populations of cells can increase testing sensitivity, give insight into disease mechanism, and inform clinical decision making. One area that can benefit from increased resolution is management of cancers in clinical remission but with measurable residual disease (MRD) by multicolor FACS. Detecting and monitoring genomic clonal resistance to treatment in the setting of MRD is technically difficult and resource intensive due to the limited amounts of disease cells. Here, we describe limited-cell FACS sequencing (LC-FACSeq), a reproducible, highly sensitive method of characterizing clonal evolution in rare cells relevant to different types of acute and chronic leukemias. We demonstrate the utility of LC-FACSeq for broad multigene gene panels and its application for monitoring sequential acquisition of mutations conferring therapy resistance and clonal evolution in long-term ibrutinib treatment of patients with chronic lymphocytic leukemia. This technique is generalizable for monitoring of other blood and marrow infiltrating cancers.


Subject(s)
Adenine/analogs & derivatives , Clonal Evolution/immunology , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia/drug therapy , Neoplasm, Residual/drug therapy , Piperidines/therapeutic use , Adenine/therapeutic use , Clone Cells , Humans , Leukemia/immunology , Mutation/genetics , Neoplasm, Residual/diagnosis
17.
J Transl Med ; 18(1): 63, 2020 02 10.
Article in English | MEDLINE | ID: mdl-32039730

ABSTRACT

BACKGROUND: Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cell populations without the need for sample pooling or RNA extraction. We term the use of single-cell chemistries for sequencing low numbers of cells limiting-cell RNA-seq (lcRNA-seq). Currently, there is no customized algorithm to select robust/low-noise transcripts from lcRNA-seq data for between-group comparisons. METHODS: Herein, we present CLEAR, a workflow that identifies reliably quantifiable transcripts in lcRNA-seq data for differentially expressed genes (DEG) analysis. Total RNA obtained from primary chronic lymphocytic leukemia (CLL) CD5+ and CD5- cells were used to develop the CLEAR algorithm. Once established, the performance of CLEAR was evaluated with FACS-sorted cells enriched from mouse Dentate Gyrus (DG). RESULTS: When using CLEAR transcripts vs. using all transcripts in CLL samples, downstream analyses revealed a higher proportion of shared transcripts across three input amounts and improved principal component analysis (PCA) separation of the two cell types. In mouse DG samples, CLEAR identifies noisy transcripts and their removal improves PCA separation of the anticipated cell populations. In addition, CLEAR was applied to two publicly-available datasets to demonstrate its utility in lcRNA-seq data from other institutions. If imputation is applied to limit the effect of missing data points, CLEAR can also be used in large clinical trials and in single cell studies. CONCLUSIONS: lcRNA-seq coupled with CLEAR is widely used in our institution for profiling immune cells (circulating or tissue-infiltrating) for its transcript preservation characteristics. CLEAR fills an important niche in pre-processing lcRNA-seq data to facilitate transcriptome profiling and DEG analysis. We demonstrate the utility of CLEAR in analyzing rare cell populations in clinical samples and in murine neural DG region without sample pooling.


Subject(s)
Gene Expression Profiling , Transcriptome , Animals , Mice , RNA-Seq , Sequence Analysis, RNA , Transcriptome/genetics , Exome Sequencing
18.
Blood ; 134(5): 432-444, 2019 08 01.
Article in English | MEDLINE | ID: mdl-31151986

ABSTRACT

Chronic lymphocytic leukemia (CLL) occurs in 2 major forms: aggressive and indolent. Low miR-29b expression in aggressive CLL is associated with poor prognosis. Indiscriminate miR-29b overexpression in the B-lineage of mice causes aberrance, thus warranting the need for selective introduction of miR-29b into B-CLL cells for therapeutic benefit. The oncofetal antigen receptor tyrosine kinase orphan receptor 1 (ROR1) is expressed on malignant B-CLL cells, but not normal B cells, encouraging us with ROR1-targeted delivery for therapeutic miRs. Here, we describe targeted delivery of miR-29b to ROR1+ CLL cells leading to downregulation of DNMT1 and DNMT3A, modulation of global DNA methylation, decreased SP1, and increased p21 expression in cell lines and primary CLL cells in vitro. Furthermore, using an Eµ-TCL1 mouse model expressing human ROR1, we report the therapeutic benefit of enhanced survival via cellular reprograming by downregulation of DNMT1 and DNMT3A in vivo. Gene expression profiling of engrafted murine leukemia identified reprogramming of cell cycle regulators with decreased SP1 and increased p21 expression after targeted miR-29b treatment. This finding was confirmed by protein modulation, leading to cell cycle arrest and survival benefit in vivo. Importantly, SP1 knockdown results in p21-dependent compensation of the miR-29b effect on cell cycle arrest. These studies form a basis for leukemic cell-targeted delivery of miR-29b as a promising therapeutic approach for CLL and other ROR1+ B-cell malignancies.


Subject(s)
Cell Cycle Checkpoints/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , MicroRNAs/genetics , Receptor Tyrosine Kinase-like Orphan Receptors/antagonists & inhibitors , Animals , Biomarkers, Tumor , Cell Line, Tumor , Cell Survival/drug effects , Cell Survival/genetics , DNA Methylation , Disease Models, Animal , Epigenesis, Genetic , Humans , Immunoconjugates/administration & dosage , Immunoconjugates/chemistry , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/mortality , Leukemia, Lymphocytic, Chronic, B-Cell/pathology , Mice , MicroRNAs/administration & dosage , MicroRNAs/chemistry , Nanoparticles/administration & dosage , Nanoparticles/chemistry , Survival Rate , Theranostic Nanomedicine , Treatment Outcome , Xenograft Model Antitumor Assays
19.
Small ; 12(43): 5971-5980, 2016 Nov.
Article in English | MEDLINE | ID: mdl-27648733

ABSTRACT

While electroporation has been widely used as a physical method for gene transfection in vitro and in vivo, its application in gene therapy of cardiovascular cells remains challenging. Due to the high concentration of ion-transport proteins in the sarcolemma, conventional electroporation of primary cardiomyocytes tends to cause ion-channel activation and abnormal ion flux, resulting in low transfection efficiency and high mortality. In this work, a high-throughput nanoelectroporation technique based on a nanochannel array platform is reported, which enables massively parallel delivery of genetic cargo (microRNA, plasmids) into mouse primary cardiomyocytes in a controllable, highly efficient, and benign manner. A simple "dipping-trap" approach was implemented to precisely position a large number of cells on the nanoelectroporation platform. With dosage control, our device precisely titrates the level of miR-29, a potential therapeutic agent for cardiac fibrosis, and determines the minimum concentration of miR-29 causing side effects in mouse primary cardiomyocytes. Moreover, the dose-dependent effect of miR-29 on mitochondrial potential and homeostasis is monitored. Altogether, our nanochannel array platform provides efficient trapping and transfection of primary mouse cardiomyocyte, which can improve the quality control for future microRNA therapy in heart diseases.


Subject(s)
Myocytes, Cardiac/metabolism , Nanoparticles/chemistry , Nanotechnology/methods , Transfection/methods , Animals , Cells, Cultured , Computer Simulation , Electroporation , Mice , MicroRNAs/metabolism
20.
Oncotarget ; 7(37): 59273-59286, 2016 Sep 13.
Article in English | MEDLINE | ID: mdl-27517749

ABSTRACT

Deregulation of microRNAs' expression frequently occurs in acute myeloid leukemia (AML). Lower miR-181a expression is associated with worse outcomes, but the exact mechanisms by which miR-181a mediates this effect remain elusive. Aberrant activation of the RAS pathway contributes to myeloid leukemogenesis. Here, we report that miR-181a directly binds to 3'-untranslated regions (UTRs); downregulates KRAS, NRAS and MAPK1; and decreases AML growth. The delivery of miR-181a mimics to target AML cells using transferrin-targeting lipopolyplex nanoparticles (NP) increased mature miR-181a; downregulated KRAS, NRAS and MAPK1; and resulted in decreased phosphorylation of the downstream RAS effectors. NP-mediated upregulation of miR-181a led to reduced proliferation, impaired colony formation and increased sensitivity to chemotherapy. Ectopic expression of KRAS, NRAS and MAPK1 attenuated the anti-leukemic activity of miR-181a mimics, thereby validating the relevance of the deregulated miR-181a-RAS network in AML. Finally, treatment with miR-181a-NP in a murine AML model resulted in longer survival compared to mice treated with scramble-NP control. These data support that targeting the RAS-MAPK-pathway by miR-181a mimics represents a novel promising therapeutic approach for AML and possibly for other RAS-driven cancers.


Subject(s)
GTP Phosphohydrolases/genetics , Leukemia, Myeloid, Acute/therapy , Membrane Proteins/genetics , MicroRNAs/genetics , Proto-Oncogene Proteins p21(ras)/genetics , 3' Untranslated Regions/genetics , Animals , Cell Line, Tumor , Disease Models, Animal , Female , GTP Phosphohydrolases/metabolism , Gene Expression Regulation, Neoplastic , Humans , Leukemia, Myeloid, Acute/genetics , Membrane Proteins/metabolism , Mice , Mice, SCID , Mitogen-Activated Protein Kinase 1/metabolism , Nanoparticles , Proto-Oncogene Proteins p21(ras)/metabolism , Signal Transduction
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