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Mishra R, Thunuguntla P, Perkin A, Duraiyan D, Bagwill K, Gonzales S, Brizuela V, Daly S, Chang YJ, Abebe M, Rajana Y, Wichmann K, Bolick C, King J, Fiala M, Fortier J, Jayasinghe R, Schroeder M, Ding L, Vij R, Silva-Fisher J. LINC01432 binds to CELF2 in newly diagnosed multiple myeloma promoting short progression-free survival to standard therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600975. [PMID: 38979159 PMCID: PMC11230414 DOI: 10.1101/2024.06.27.600975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Multiple Myeloma (MM) is a highly prevalent and incurable form of cancer that arises from malignant plasma cells, with over 35,000 new cases diagnosed annually in the United States. While there are a growing number of approved therapies, MM remains incurable and nearly all patients will relapse and exhaust all available treatment options. Mechanisms for disease progression are unclear and in particular, little is known regarding the role of long non-coding RNAs (lncRNA) in mediating disease progression and response to treatment. In this study, we used transcriptome sequencing to compare newly diagnosed MM patients who had short progression-free survival (PFS) to standard first-line treatment (PFS < 24 months) to patients who had prolonged PFS (PFS > 24 months). We identified 157 differentially upregulated lncRNAs with short PFS and focused our efforts on characterizing the most upregulated lncRNA, LINC01432. We investigated LINC01432 overexpression and CRISPR/Cas9 knockdown in MM cell lines to show that LINC01432 overexpression significantly increases cell viability and reduces apoptosis, while knockdown significantly reduces viability and increases apoptosis, supporting the clinical relevance of this lncRNA. Next, we used individual-nucleotide resolution cross-linking immunoprecipitation with RT-qPCR to show that LINC01432 directly interacts with the RNA binding protein, CELF2. Lastly, we showed that LINC01432-targeted locked nucleic acid antisense oligonucleotides reduce viability and increases apoptosis. In summary, this fundamental study identified lncRNAs associated with short PFS to standard NDMM treatment and further characterized LINC01432, which inhibits apoptosis.
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Zhou X, Pan J, Chen L, Zhang S, Chen Y. DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data. Biomolecules 2024; 14:766. [PMID: 39062480 PMCID: PMC11274664 DOI: 10.3390/biom14070766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Understanding the dynamics of gene regulatory networks (GRNs) across diverse cell types poses a challenge yet holds immense value in unraveling the molecular mechanisms governing cellular processes. Current computational methods, which rely solely on expression changes from bulk RNA-seq and/or scRNA-seq data, often result in high rates of false positives and low precision. Here, we introduce an advanced computational tool, DeepIMAGER, for inferring cell-specific GRNs through deep learning and data integration. DeepIMAGER employs a supervised approach that transforms the co-expression patterns of gene pairs into image-like representations and leverages transcription factor (TF) binding information for model training. It is trained using comprehensive datasets that encompass scRNA-seq profiles and ChIP-seq data, capturing TF-gene pair information across various cell types. Comprehensive validations on six cell lines show DeepIMAGER exhibits superior performance in ten popular GRN inference tools and has remarkable robustness against dropout-zero events. DeepIMAGER was applied to scRNA-seq datasets of multiple myeloma (MM) and detected potential GRNs for TFs of RORC, MITF, and FOXD2 in MM dendritic cells. This technical innovation, combined with its capability to accurately decode GRNs from scRNA-seq, establishes DeepIMAGER as a valuable tool for unraveling complex regulatory networks in various cell types.
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Affiliation(s)
- Xiguo Zhou
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Jingyi Pan
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Liang Chen
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Shaoqiang Zhang
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Yong Chen
- Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
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Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
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4
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Zabeti Touchaei A, Vahidi S, Samadani AA. Decoding the regulatory landscape of lncRNAs as potential diagnostic and prognostic biomarkers for gastric and colorectal cancers. Clin Exp Med 2024; 24:29. [PMID: 38294554 PMCID: PMC10830721 DOI: 10.1007/s10238-023-01260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Colorectal cancer (CRC) and gastric cancer (GC) are major contributors to cancer-related mortality worldwide. Despite advancements in understanding molecular mechanisms and improved drug treatments, the overall survival rate for patients remains unsatisfactory. Metastasis and drug resistance are major challenges contributing to the high mortality rate in both CRC and GC. Recent research has shed light on the role of long noncoding RNAs (lncRNAs) in the development and progression of these cancers. LncRNAs regulate gene expression through various mechanisms, including epigenetic modifications and interactions with microRNAs (miRNAs) and proteins. They can serve as miRNA precursors or pseudogenes, modulating gene expression at transcriptional and post-transcriptional levels. Additionally, circulating lncRNAs have emerged as non-invasive biomarkers for the diagnosis, prognosis, and prediction of drug therapy response in CRC and GC. This review explores the intricate relationship between lncRNAs and CRC/GC, encompassing their roles in cancer development, progression, and chemoresistance. Furthermore, it discusses the potential of lncRNAs as therapeutic targets in these malignancies. The interplay between lncRNAs, miRNAs, and tumor microenvironment is also highlighted, emphasizing their impact on the complexity of cancer biology. Understanding the regulatory landscape and molecular mechanisms governed by lncRNAs in CRC and GC is crucial for the development of effective diagnostic and prognostic biomarkers, as well as novel therapeutic strategies. This review provides a comprehensive overview of the current knowledge and paves the way for further exploration of lncRNAs as key players in the management of CRC and GC.
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Affiliation(s)
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran.
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Nylund P, Garrido-Zabala B, Kalushkova A, Wiklund HJ. The complex nature of lncRNA-mediated chromatin dynamics in multiple myeloma. Front Oncol 2023; 13:1303677. [PMID: 38148842 PMCID: PMC10750364 DOI: 10.3389/fonc.2023.1303677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Extensive genome-wide sequencing efforts have unveiled the intricate regulatory potential of long non-protein coding RNAs (lncRNAs) within the domain of haematological malignancies. Notably, lncRNAs have been found to directly modulate chromatin architecture, thereby impacting gene expression and disease progression by interacting with DNA, RNA, and proteins in a tissue- or condition-specific manner. Furthermore, recent studies have highlighted the intricate epigenetic control of lncRNAs in cancer. Consequently, this provides a rationale to explore the possibility of therapeutically targeting lncRNAs themselves or the epigenetic mechanisms that govern their activity. Within the scope of this review, we will assess the current state of knowledge regarding the epigenetic regulation of lncRNAs and how, in turn, lncRNAs contribute to chromatin remodelling in the context of multiple myeloma.
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Affiliation(s)
| | | | | | - Helena Jernberg Wiklund
- Science for Life Laboratory, Department of Immunology, Genetic and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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El Moukhtari SH, Garbayo E, Amundarain A, Pascual-Gil S, Carrasco-León A, Prosper F, Agirre X, Blanco-Prieto MJ. Lipid nanoparticles for siRNA delivery in cancer treatment. J Control Release 2023; 361:130-146. [PMID: 37532145 DOI: 10.1016/j.jconrel.2023.07.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/08/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
RNA-based therapies, and siRNAs in particular, have attractive therapeutic potential for cancer treatment due to their ability to silence genes that are imperative for tumor progression. To be effective and solve issues related to their poor half-life and poor pharmacokinetic properties, siRNAs require adequate drug delivery systems that protect them from degradation and allow intracellular delivery. Among the various delivery vehicles available, lipid nanoparticles have emerged as the leading choice. These nanoparticles consist of cholesterol, phospholipids, PEG-lipids and most importantly ionizable cationic lipids. These ionizable lipids enable the binding of negatively charged siRNA, resulting in the formation of stable and neutral lipid nanoparticles with exceptionally high encapsulation efficiency. Lipid nanoparticles have demonstrated their effectiveness and versatility in delivering not only siRNAs but also multiple RNA molecules, contributing to their remarkable success. Furthermore, the advancement of efficient manufacturing techniques such as microfluidics, enables the rapid mixing of two miscible solvents without the need for shear forces. This facilitates the reproducible production of lipid nanoparticles and holds enormous potential for scalability. This is shown by the increasing number of preclinical and clinical trials evaluating the potential use of siRNA-LNPs for the treatment of solid and hematological tumors as well as in cancer immunotherapy. In this review, we provide an overview of the progress made on siRNA-LNP development for cancer treatment and outline the current preclinical and clinical landscape in this area. Finally, the translational challenges required to bring siRNA-LNPs further into the clinic are also discussed.
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Affiliation(s)
- Souhaila H El Moukhtari
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain
| | - Elisa Garbayo
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain
| | - Ane Amundarain
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pío XII 55, 31008 Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Simón Pascual-Gil
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain
| | - Arantxa Carrasco-León
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pío XII 55, 31008 Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Felipe Prosper
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pío XII 55, 31008 Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain; Departmento de Hematología and CCUN, Clínica Universidad de Navarra, University of Navarra, Avenida Pío XII 36, 31008 Pamplona, Spain
| | - Xabier Agirre
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, Avenida Pío XII 55, 31008 Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029, Madrid, Spain
| | - María J Blanco-Prieto
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra, IdiSNA, C/Irunlarrea 3, 31008 Pamplona, Spain.
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Guo N, Song Y, Zi F, Zheng J, Cheng J. Abnormal expression pattern of lncRNA H19 participates in multiple myeloma bone disease by unbalancing osteogenesis and osteolysis. Int Immunopharmacol 2023; 119:110058. [PMID: 37058751 DOI: 10.1016/j.intimp.2023.110058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 04/16/2023]
Abstract
BACKGROUND Accumulating genetic and epigenetic alterations in multiple myeloma (MM) have been demonstrated to be closely associated with osteolytic bone disease, generally characterized as increased osteoclast formation and decreased osteoblast activity. Previously, serum long non-coding RNA (lncRNA) H19 has been proved to be a biomarker for the diagnosis of MM. Whereas, its role in MM-associated bone homeostasis remains largely elusive. METHODS A cohort of 42 MM patients and 40 healthy volunteers were enrolled for evaluating differential expressions of H19 and its downstream effectors. The proliferative capacity of MM cells was monitored by CCK-8 assay. Alkaline phosphatase (ALP) staining and activity detection, either with Alizarin red staining (ARS) were employed to assess osteoblast formation. Osteoblast- or osteoclast-associated gene were detected using qRT-PCR and western blot analysis. Bioinformatics analysis, RNA pull-down, RNA immunoprecipitation (RIP), and chromatin immunoprecipitation (ChIP) were subjected to verify H19/miR-532-3p/E2F7/EZH2 axis, which was accounted for epigenetic suppression of PTEN. The functional role of H19 on MM development through unbalancing osteolysis and osteogenesis was also confirmed in the murine MM model. RESULTS Upregulation of serum H19 was observed in MM patients, suggesting its positive correlation with the poor prognosis of MM patients. Loss of H19 dramatically weakened cell proliferation of MM cells, promoted osteoblastic differentiation, and impaired osteoclast activity. While reinforced H19 exhibited the opposite effects. Akt/mTOR signaling plays an indispensable role in H19-mediated osteoblast formation and osteoclastgenesis. Mechanistically, H19 served as a sponge for miR-532-3p to upregulate E2F7, a transcriptional activator of EZH2, thereby accounting for modulating epigenetic suppression of PTEN. The in vivo experiments further validated that H19 exerted important impacts on tumor growth through breaking the balance between osteogenesis and osteolysis via Akt/mTOR signaling. CONCLUSION Collectively, increased enrichment of H19 in MM cells exhibits an essential role in MM development by disturbing bone homeostasis.
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Affiliation(s)
- Ninghong Guo
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Yuan Song
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Fuming Zi
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Jifu Zheng
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Jing Cheng
- Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China.
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Galindo-Camacho RM, Blanco-Llamero C, da Ana R, Fuertes MA, Señoráns FJ, Silva AM, García ML, Souto EB. Therapeutic Approaches for Age-Related Macular Degeneration. Int J Mol Sci 2022; 23:11769. [PMID: 36233066 PMCID: PMC9570118 DOI: 10.3390/ijms231911769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
Damage to the retinal pigment epithelium, Bruch's membrane and/or tissues underlying macula is known to increase the risk of age-related macular degeneration (AMD). AMD is commonly categorized in two distinct types, namely, the nonexudative (dry form) and the exudative (wet form). Currently, there is no ideal treatment available for AMD. Recommended standard treatments are based on the use of vascular endothelial growth factor (VEGF), with the disadvantage of requiring repeated intravitreal injections which hinder patient's compliance to the therapy. In recent years, several synthetic and natural active compounds have been proposed as innovative therapeutic strategies against this disease. There is a growing interest in the development of formulations based on nanotechnology because of its important role in the management of posterior eye segment disorders, without the use of intravitreal injections, and furthermore, with the potential to prolong drug release and thus reduce adverse effects. In the same way, 3D bioprinting constitutes an alternative to regeneration therapies for the human retina to restore its functions. The application of 3D bioprinting may change the current and future perspectives of the treatment of patients with AMD, especially those who do not respond to conventional treatment. To monitor the progress of AMD treatment and disease, retinal images are used. In this work, we revised the recent challenges encountered in the treatment of different forms of AMD, innovative nanoformulations, 3D bioprinting, and techniques to monitor the progress.
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Affiliation(s)
- Ruth M. Galindo-Camacho
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Department of Pharmacy and Pharmaceutical Technology, and Physical Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
- Unit of Synthesis and Biomedical Applications of Peptides, IQAC-CSIC, 08034 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, 08028 Barcelona, Spain
| | - Cristina Blanco-Llamero
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Healthy Lipids Group, Departmental Section of Food Sciences, Faculty of Sciences, Autonomous University of Madrid, 28049 Madrid, Spain
| | - Raquel da Ana
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Mayra A. Fuertes
- Department of Pharmacy and Pharmaceutical Technology, and Physical Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Francisco J. Señoráns
- Healthy Lipids Group, Departmental Section of Food Sciences, Faculty of Sciences, Autonomous University of Madrid, 28049 Madrid, Spain
| | - Amélia M. Silva
- Department of Biology and Environment, University of Trás-os-Montes e Alto Douro, UTAD, Quinta de Prados, 5001-801 Vila Real, Portugal
- Centre for Research and Technology of Agro-Environmental and Biological Sciences, CITAB, UTAD, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - María L. García
- Department of Pharmacy and Pharmaceutical Technology, and Physical Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, 08028 Barcelona, Spain
| | - Eliana B. Souto
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- REQUIMTE/UCIBIO, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
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Zhang L, Zhou S, Zhou T, Li X, Tang J. Targeting the lncRNA DUXAP8/miR-29a/ PIK3CA Network Restores Doxorubicin Chemosensitivity via PI3K-AKT-mTOR Signaling and Synergizes With Inotuzumab Ozogamicin in Chemotherapy-Resistant B-Cell Acute Lymphoblastic Leukemia. Front Oncol 2022; 12:773601. [PMID: 35311115 PMCID: PMC8924619 DOI: 10.3389/fonc.2022.773601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/28/2022] [Indexed: 12/25/2022] Open
Abstract
Purpose This study aimed to determine the expression profiles of long non-coding RNA (lncRNA), microRNA (miRNA), and mRNA in chemotherapy-resistant B-cell acute lymphoblastic leukemia (B-ALL). Methods LncRNA, miRNA, and mRNA profiles were assessed by RNA-seq in diagnostic bone marrow samples from 6 chemotherapy-resistant and 6 chemotherapy-sensitive B-ALL patients. The lncRNA DUXAP8/miR-29a/PIK3CA signaling network was identified as the most dysregulated in chemoresistant patient samples, and its effect on cellular phenotypes, PI3K-AKT-mTOR signaling, and chemosensitivity of doxorubicin (Dox)-resistant Nalm-6 (N6/ADR), and Dox-resistant 697 (697/ADR) cells were assessed. Furthermore, its synergy with inotuzumab ozogamicin treatment was investigated. Results 1,338 lncRNAs, 75 miRNAs, and 1620 mRNAs were found to be dysregulated in chemotherapy-resistant B-ALL in comparison to chemotherapy-sensitive B-ALL patient samples. Through bioinformatics analyses and RT-qPCR validation, the lncRNA DUXAP8/miR-29a/PIK3CA network and PI3K-AKT-mTOR signaling were identified as significantly associated with B-ALL chemotherapy resistance. In N6/ADR and 697/ADR cells, LncRNA DUXAP8 overexpression and PIK3CA overexpression induced proliferation and inhibited apoptosis, and their respective knockdowns inhibited proliferation, facilitated apoptosis, and restored Dox chemosensitivity. MiR-29a was shown to affect the lncRNA DUXAP8/PIK3CA network, and luciferase reporter gene assay showed direct binding between lncRNA DUXAP8 and miR-29a, as well as between miR-29a and PIK3CA. Targeting lncRNA DUXAP8/miR-29a/PIK3CA network synergized with inotuzumab ozogamicin's effect on N6/ADR and 697/ADR cells. Conclusion Targeting the lncRNA DUXAP8/miR-29a/PIK3CA network not only induced an apoptotic effect on Dox-resistant B-ALL and restored Dox chemosensitivity via PI3K-AKT-mTOR signaling but also showed synergism with inotuzumab ozogamicin treatment.
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Affiliation(s)
- Li Zhang
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, China.,Orofacial Reconstruction and Regeneration Laboratory, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, China.,Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shixia Zhou
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Stem Cell Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tiejun Zhou
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaoming Li
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Stem Cell Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Junling Tang
- Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Stem Cell Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Luo YH, Yang YP, Chien CS, Yarmishyn AA, Adekunle Ishola A, Chien Y, Chen YM, Tsai PH, Lin TW, Wang ML, Chiou SH. Circular RNA hsa_circ_0000190 Facilitates the Tumorigenesis and Immune Evasion by Upregulating the Expression of Soluble PD-L1 in Non-Small-Cell Lung Cancer. Int J Mol Sci 2021; 23:64. [PMID: 35008490 PMCID: PMC8744551 DOI: 10.3390/ijms23010064] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of death from cancer in Taiwan and throughout the world. Immunotherapy has revealed promising and significant efficacy in NSCLC, through immune checkpoint inhibition by blocking programmed cell death protein (PD)-1/PD-1 ligand (PD-L1) signaling pathway to restore patients' T-cell immunity. One novel type of long, non-coding RNAs, circular RNAs (circRNAs), are endogenous, stable, and widely expressed in tissues, saliva, blood, urine, and exosomes. Our previous results revealed that the plasma level of hsa_circ_0000190 can be monitored by liquid-biopsy-based droplet digital PCR and may serve as a valuable blood-based biomarker to monitor the disease progression and the efficacy of immunotherapy. In this study, hsa_circ_0000190 was shown to increase the PD-L1 mRNA-mediated soluble PD-L1 (sPD-L1) expression, consequently interfering with the efficacy of anti-PD-L1 antibody and T-cell activation, which may result in immunotherapy resistance and poor outcome. Our results unraveled that hsa_circ_0000190 facilitated the tumorigenesis and immune evasion of NSCLC by upregulating sPD-L1 expression, potentially developing a different aspect in elucidating the molecular immunopathogenesis of NSCLC. Hsa_circ_0000190 upregulation can be an effective indicator for the progression of NSCLC, and hsa_circ_0000190 downregulation may possess a potential therapeutic value for the treatment of NSCLC in combination with immunotherapy.
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Affiliation(s)
- Yung-Hung Luo
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (Y.-M.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-P.Y.); (M.-L.W.)
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Yi-Ping Yang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-P.Y.); (M.-L.W.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
- School of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chian-Shiu Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Aliaksandr A. Yarmishyn
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
| | - Afeez Adekunle Ishola
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan
| | - Yueh Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (Y.-M.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-P.Y.); (M.-L.W.)
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
| | - Tzu-Wei Lin
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
| | - Mong-Lien Wang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-P.Y.); (M.-L.W.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-S.C.); (A.A.Y.); (A.A.I.); (Y.C.); (P.-H.T.); (T.-W.L.)
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
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