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1.
Nat Rev Genet ; 25(3): 211-232, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37968332

ABSTRACT

Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.


Subject(s)
MicroRNAs , Neoplasms , RNA, Long Noncoding , Humans , RNA, Long Noncoding/genetics , RNA, Circular , RNA, Untranslated/genetics , Neoplasms/genetics , Neoplasms/therapy
2.
Mol Cell ; 81(21): 4349-4351, 2021 11 04.
Article in English | MEDLINE | ID: mdl-34739825

ABSTRACT

Sun et al. (2021) identified a novel translation initiation mechanism mediated through a new type of regulator named APPLE, a small peptide produced from a non-coding RNA transcript in acute myeloid leukemia, providing unforeseen opportunities for targeting the translation machinery in cancer cells.


Subject(s)
Leukemia, Myeloid, Acute , Humans , RNA, Untranslated
3.
Nature ; 578(7795): 449-454, 2020 02.
Article in English | MEDLINE | ID: mdl-32051587

ABSTRACT

The solid tumour microenvironment includes nerve fibres that arise from the peripheral nervous system1,2. Recent work indicates that newly formed adrenergic nerve fibres promote tumour growth, but the origin of these nerves and the mechanism of their inception are unknown1,3. Here, by comparing the transcriptomes of cancer-associated trigeminal sensory neurons with those of endogenous neurons in mouse models of oral cancer, we identified an adrenergic differentiation signature. We show that loss of TP53 leads to adrenergic transdifferentiation of tumour-associated sensory nerves through loss of the microRNA miR-34a. Tumour growth was inhibited by sensory denervation or pharmacological blockade of adrenergic receptors, but not by chemical sympathectomy of pre-existing adrenergic nerves. A retrospective analysis of samples from oral cancer revealed that p53 status was associated with nerve density, which was in turn associated with poor clinical outcomes. This crosstalk between cancer cells and neurons represents mechanism by which tumour-associated neurons are reprogrammed towards an adrenergic phenotype that can stimulate tumour progression, and is a potential target for anticancer therapy.


Subject(s)
Adrenergic Neurons/pathology , Cell Transdifferentiation , Cellular Reprogramming , Mouth Neoplasms/pathology , Sensory Receptor Cells/pathology , Tumor Suppressor Protein p53/deficiency , Adrenergic Antagonists/pharmacology , Adrenergic Antagonists/therapeutic use , Animals , Cell Division , Disease Models, Animal , Disease Progression , Female , Humans , Male , Mice , Mice, Inbred BALB C , MicroRNAs/genetics , Mouth Neoplasms/drug therapy , Mouth Neoplasms/genetics , Mouth Neoplasms/metabolism , Nerve Fibers/pathology , Neurites/pathology , Receptors, Adrenergic/metabolism , Retrospective Studies , Tumor Microenvironment , Tumor Suppressor Protein p53/genetics , Xenograft Model Antitumor Assays
4.
Proc Natl Acad Sci U S A ; 120(23): e2122053120, 2023 06 06.
Article in English | MEDLINE | ID: mdl-37252969

ABSTRACT

The causes and consequences of abnormal biogenesis of extracellular vesicles (EVs) are not yet well understood in malignancies, including in breast cancers (BCs). Given the hormonal signaling dependence of estrogen receptor-positive (ER+) BC, we hypothesized that 17ß-estradiol (estrogen) might influence EV production and microRNA (miRNA) loading. We report that physiological doses of 17ß-estradiol promote EV secretion specifically from ER+ BC cells via inhibition of miR-149-5p, hindering its regulatory activity on SP1, a transcription factor that regulates the EV biogenesis factor nSMase2. Additionally, miR-149-5p downregulation promotes hnRNPA1 expression, responsible for the loading of let-7's miRNAs into EVs. In multiple patient cohorts, we observed increased levels of let-7a-5p and let-7d-5p in EVs derived from the blood of premenopausal ER+ BC patients, and elevated EV levels in patients with high BMI, both conditions associated with higher levels of 17ß-estradiol. In brief, we identified a unique estrogen-driven mechanism by which ER+ BC cells eliminate tumor suppressor miRNAs in EVs, with effects on modulating tumor-associated macrophages in the microenvironment.


Subject(s)
Breast Neoplasms , Extracellular Vesicles , MicroRNAs , Humans , Female , MicroRNAs/genetics , MicroRNAs/metabolism , Breast Neoplasms/pathology , Estrogen Receptor alpha/genetics , Estrogen Receptor alpha/metabolism , Estradiol/pharmacology , Estradiol/metabolism , Estrogens/metabolism , Extracellular Vesicles/genetics , Extracellular Vesicles/metabolism , Tumor Microenvironment
5.
Trends Genet ; 38(4): 379-394, 2022 04.
Article in English | MEDLINE | ID: mdl-34728089

ABSTRACT

Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.


Subject(s)
MicroRNAs , Neoplasms , Epigenesis, Genetic/genetics , Gene Expression , Humans , MicroRNAs/genetics , Neoplasms/genetics
6.
Cell ; 140(5): 652-65, 2010 Mar 05.
Article in English | MEDLINE | ID: mdl-20211135

ABSTRACT

MicroRNAs and heterogeneous ribonucleoproteins (hnRNPs) are posttranscriptional gene regulators that bind mRNA in a sequence-specific manner. Here, we report that loss of miR-328 occurs in blast crisis chronic myelogenous leukemia (CML-BC) in a BCR/ABL dose- and kinase-dependent manner through the MAPK-hnRNP E2 pathway. Restoration of miR-328 expression rescues differentiation and impairs survival of leukemic blasts by simultaneously interacting with the translational regulator poly(rC)-binding protein hnRNP E2 and with the mRNA encoding the survival factor PIM1, respectively. The interaction with hnRNP E2 is independent of the microRNA's seed sequence and it leads to release of CEBPA mRNA from hnRNP E2-mediated translational inhibition. Altogether, these data reveal the dual ability of a microRNA to control cell fate both through base pairing with mRNA targets and through a decoy activity that interferes with the function of regulatory proteins.


Subject(s)
Heterogeneous-Nuclear Ribonucleoproteins/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , MicroRNAs/metabolism , Animals , Blast Crisis , CCAAT-Enhancer-Binding Proteins/metabolism , Cell Line, Tumor , Heterogeneous-Nuclear Ribonucleoproteins/metabolism , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism , Mice , Proto-Oncogene Proteins c-pim-1/metabolism , RNA-Induced Silencing Complex/metabolism
7.
Cancer Immunol Immunother ; 73(5): 85, 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38554185

ABSTRACT

TGF-ß1 and TGF-ßR1 play important roles in immune and inflammatory responses. Genetic variants of TGF-ß1 rs1800470 and TGF-ßR1 rs334348 have emerged as potentially prognostic biomarkers for HPV-related head and neck cancer, while their prognostic effect on survival of smoking-related head and neck cancer remains unknown. This study included 1403 patients with smoking-related head and neck cancer, and all these patients were genotyped for TGF-ß1 rs1800470 and TGF-ßR1 rs334348. Both univariate and multivariate analyses were performed to evaluate associations between the two functional genetic variants in microRNA binding sites of TGF-ß1 and TGF-ßR1 and survivals. Patients with TGF-ß1 rs1800470 CT or CC genotype had 30-35% risk reductions for OS, DSS, and DFS compared to patients with TT genotype among overall patients, ever smokers, and patients administered chemoradiation. Furthermore, patients with TGF-ßR1 rs334348 GA or GG genotype had significant 50-60% risk reductions for OS, DSS, and DFS compared to patients with AA genotype among overall patients and patients administered chemoradiation; among ever smokers, the risk reductions even reached 60-70%. The TCGA dataset was used for validation. These findings suggest that TGF-ß1 rs1800470 and TGF-ßR1 rs334348 significantly affect survival outcomes in patients with smoking-related head and neck cancer, especially in the subgroups of ever smokers and patients treated with chemoradiation. These genetic variants may serve as prognostic indicators for patients with smoking-related head and neck cancer and could play a role in advancing the field of personalized chemoradiation, thereby improving patient survival and quality of life.


Subject(s)
Head and Neck Neoplasms , MicroRNAs , Humans , MicroRNAs/genetics , Transforming Growth Factor beta1/genetics , Quality of Life , Head and Neck Neoplasms/genetics , Head and Neck Neoplasms/therapy , Smoking/adverse effects
8.
Mol Cell ; 61(4): 520-534, 2016 Feb 18.
Article in English | MEDLINE | ID: mdl-26853146

ABSTRACT

Altered energy metabolism is a cancer hallmark as malignant cells tailor their metabolic pathways to meet their energy requirements. Glucose and glutamine are the major nutrients that fuel cellular metabolism, and the pathways utilizing these nutrients are often altered in cancer. Here, we show that the long ncRNA CCAT2, located at the 8q24 amplicon on cancer risk-associated rs6983267 SNP, regulates cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I (CFIm) complex with distinct affinities for the two subunits (CFIm25 and CFIm68). The CCAT2 interaction with the CFIm complex fine-tunes the alternative splicing of Glutaminase (GLS) by selecting the poly(A) site in intron 14 of the precursor mRNA. These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolism orchestrated by the two alleles of a long ncRNA.


Subject(s)
Glutaminase/genetics , Neoplasms/metabolism , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism , Alleles , Alternative Splicing , Energy Metabolism , HCT116 Cells , Humans , Neoplasms/genetics , RNA Precursors/chemistry , RNA Precursors/metabolism , RNA, Messenger/metabolism
9.
J Pharmacol Exp Ther ; 384(1): 10-19, 2023 01.
Article in English | MEDLINE | ID: mdl-36167417

ABSTRACT

Chromosomal instability (CIN) is characterized by an increased frequency of changes in chromosome structure or number and is regarded as a hallmark of cancer. CIN plays a prevalent role in tumorigenesis and cancer progression by assisting the cancer cells' phenotypic adaptation to stress, which have been tightly linked to therapy resistance and metastasis. Both CIN-inducing and CIN-repressing agents are being clinically tested for the treatment of cancer to increase CIN levels to unsustainable levels leading to cell death or to decrease CIN levels to limit the development of drug resistance, respectively. Non-coding RNAs (ncRNAs) including microRNAs and long ncRNAs (lncRNAs) have been fundamentally implicated in CIN. The miR-22, miR-26a, miR-28, and miR-186 target important checkpoint proteins involved in mediating chromosomal stability and their expression modulation has been directly related to CIN occurrence. lncRNAs derived from telomeric, centrosomal, and enhancer regions play an important role in mediating genome stability, while specific lncRNA transcripts including genomic instability inducing RNA called Ginir, P53-responsive lncRNA termed as GUARDIN, colon cancer-associated transcript 2, PCAT2, and ncRNA activated by DNA damage called NORAD have been shown to act within CIN-associated pathways. In this review, we discuss how these ncRNAs either maintain or disrupt the stability of chromosomes and how these mechanisms could be exploited for novel therapeutic approaches targeting CIN in cancer patients. SIGNIFICANCE STATEMENT: Chromosomal instability increases tumor heterogeneity and thereby assists the phenotypic adaptation of cancer cells, causing therapy resistance and metastasis. Several microRNAs and long non-coding RNAs that have been causally linked to chromosomal instability could represent novel therapeutic targets. Understanding the role of non-coding RNAs in regulating different genes involved in driving chromosomal instability will give insights into how non-coding RNAs can be utilized toward modifying chemotherapeutic regimens in different cancers.


Subject(s)
Colonic Neoplasms , MicroRNAs , RNA, Long Noncoding , Humans , RNA, Long Noncoding/genetics , Chromosomal Instability/genetics , MicroRNAs/genetics , MicroRNAs/metabolism
10.
Br J Cancer ; 126(6): 833-834, 2022 04.
Article in English | MEDLINE | ID: mdl-34912071

ABSTRACT

In this issue, Traversa et al. [1] reviewed our current knowledge about the role of circular and linear forms of PVT1 non-coding RNA in cancer and human diseases. They highlighted the technical challenges of these studies and raised a potential bias in the publications, which require more attention from researchers.


Subject(s)
MicroRNAs , Neoplasms , RNA, Long Noncoding , Cell Line, Tumor , Humans , Neoplasms/genetics , RNA, Long Noncoding/genetics
11.
Genome Res ; 29(9): 1377-1388, 2019 09.
Article in English | MEDLINE | ID: mdl-31434680

ABSTRACT

The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that ncRNAs, like many large proteins, have a multidomain architecture that organizes them spatially and functionally. As ncRNAs are beginning to be imprecisely classified into functional families, we review here how their structural properties might inform their functions with focus on structural architecture-function relationships. We will describe the properties of "interactor elements" (IEs) involved in direct physical interaction with nucleic acids, proteins, or lipids and of "structural elements" (SEs) directing their wiring within the "ncRNA interactor networks" through the emergence of secondary and/or tertiary structures. We suggest that spectrums of "letters" (ncRNA elements) are assembled into "words" (ncRNA domains) that are further organized into "phrases" (complete ncRNA structures) with functional meaning (signaling output) through complex "sentences" (the ncRNA interactor networks). This semiotic analogy can guide the exploitation of ncRNAs as new therapeutic targets through the development of IE-blockers and/or SE-lockers that will change the interactor partners' spectrum of proteins, RNAs, DNAs, or lipids and consequently influence disease phenotypes.


Subject(s)
RNA, Untranslated/chemistry , RNA, Untranslated/metabolism , DNA/chemistry , DNA/metabolism , Humans , Models, Molecular , Nucleic Acid Conformation , Proteins/chemistry , Proteins/metabolism
12.
Crit Care Med ; 50(2): 296-306, 2022 02 01.
Article in English | MEDLINE | ID: mdl-34259445

ABSTRACT

OBJECTIVES: To evaluate early activation of latent viruses in polytrauma patients and consider prognostic value of viral micro-RNAs in these patients. DESIGN: This was a subset analysis from a prospectively collected multicenter trauma database. Blood samples were obtained upon admission to the trauma bay (T0), and trauma metrics and recovery data were collected. SETTING: Two civilian Level 1 Trauma Centers and one Military Treatment Facility. PATIENTS: Adult polytrauma patients with Injury Severity Scores greater than or equal to 16 and available T0 plasma samples were included in this study. Patients with ICU admission greater than 14 days, mechanical ventilation greater than 7 days, or mortality within 28 days were considered to have a complicated recovery. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Polytrauma patients (n = 180) were identified, and complicated recovery was noted in 33%. Plasma samples from T0 underwent reverse transcriptase-quantitative polymerase chain reaction analysis for Kaposi's sarcoma-associated herpesvirus micro-RNAs (miR-K12_10b and miRK-12-12) and Epstein-Barr virus-associated micro-RNA (miR-BHRF-1), as well as Luminex multiplex array analysis for established mediators of inflammation. Ninety-eight percent of polytrauma patients were found to have detectable Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus micro-RNAs at T0, whereas healthy controls demonstrated 0% and 100% detection rate for Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus, respectively. Univariate analysis revealed associations between viral micro-RNAs and polytrauma patients' age, race, and postinjury complications. Multivariate least absolute shrinkage and selection operator analysis of clinical variables and systemic biomarkers at T0 revealed that interleukin-10 was the strongest predictor of all viral micro-RNAs. Multivariate least absolute shrinkage and selection operator analysis of systemic biomarkers as predictors of complicated recovery at T0 demonstrated that miR-BHRF-1, miR-K12-12, monocyte chemoattractant protein-1, and hepatocyte growth factor were independent predictors of complicated recovery with a model complicated recovery prediction area under the curve of 0.81. CONCLUSIONS: Viral micro-RNAs were detected within hours of injury and correlated with poor outcomes in polytrauma patients. Our findings suggest that transcription of viral micro-RNAs occurs early in the response to trauma and may be associated with the biological processes involved in polytrauma-induced complicated recovery.


Subject(s)
MicroRNAs/analysis , Multiple Trauma/immunology , Multiple Trauma/virology , RNA, Viral/analysis , Adult , Female , Herpesvirus 4, Human/genetics , Herpesvirus 4, Human/isolation & purification , Herpesvirus 8, Human/genetics , Herpesvirus 8, Human/isolation & purification , Humans , Male , MicroRNAs/blood , MicroRNAs/genetics , Middle Aged , RNA, Viral/blood , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/statistics & numerical data
13.
EMBO Rep ; 21(3): e46734, 2020 03 04.
Article in English | MEDLINE | ID: mdl-32017402

ABSTRACT

The mechanisms that regulate the switch between epidermal progenitor state and differentiation are not fully understood. Recent findings indicate that the chromatin remodelling BAF complex (Brg1-associated factor complex or SWI/SNF complex) and the transcription factor p63 mutually recruit one another to open chromatin during epidermal differentiation. Here, we identify a long non-coding transcript that includes an ultraconserved element, uc.291, which physically interacts with ACTL6A and modulates chromatin remodelling to allow differentiation. Loss of uc.291 expression, both in primary keratinocytes and in three-dimensional skin equivalents, inhibits differentiation as indicated by epidermal differentiation complex genes down-regulation. ChIP experiments reveal that upon uc.291 depletion, ACTL6A is bound to the differentiation gene promoters and inhibits BAF complex targeting to induce terminal differentiation genes. In the presence of uc.291, the ACTL6A inhibitory effect is released, allowing chromatin changes to promote the expression of differentiation genes. Thus, uc.291 interacts with ACTL6A to modulate chromatin remodelling activity, allowing the transcription of late differentiation genes.


Subject(s)
Actins/genetics , Chromosomal Proteins, Non-Histone/genetics , DNA-Binding Proteins/genetics , RNA, Long Noncoding , Cells, Cultured , Chromatin/genetics , Chromatin Assembly and Disassembly , Chromosomal Proteins, Non-Histone/metabolism , Humans , RNA, Long Noncoding/genetics , Transcription Factors/genetics , Transcription Factors/metabolism
14.
Pharm Res ; 39(3): 511-528, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35294699

ABSTRACT

PURPOSE: Downregulation of miRNA-22 in triple-negative breast cancer (TNBC) is associated with upregulation of eukaryotic elongation 2 factor kinase (eEF2K) protein, which regulates tumor growth, chemoresistance, and tumor immunosurveillance. Moreover, exogenous administration of miRNA-22, loaded in nanoparticles to prevent degradation and improve tumor delivery (termed miRNA-22 nanotherapy), to suppress eEF2K production has shown potential as an investigational therapeutic agent in vivo. METHODS: To evaluate the translational potential of miRNA-22 nanotherapy, we developed a multiscale mechanistic model, calibrated to published in vivo data and extrapolated to the human scale, to describe and quantify the pharmacokinetics and pharmacodynamics of miRNA-22 in virtual patient populations. RESULTS: Our analysis revealed the dose-response relationship, suggested optimal treatment frequency for miRNA-22 nanotherapy, and highlighted key determinants of therapy response, from which combination with immune checkpoint inhibitors was identified as a candidate strategy for improving treatment outcomes. More importantly, drug synergy was identified between miRNA-22 and standard-of-care drugs against TNBC, providing a basis for rational therapeutic combinations for improved response CONCLUSIONS: The present study highlights the translational potential of miRNA-22 nanotherapy for TNBC in combination with standard-of-care drugs.


Subject(s)
MicroRNAs , Nanoparticles , Triple Negative Breast Neoplasms , Cell Line, Tumor , Drug Synergism , Humans , MicroRNAs/administration & dosage , MicroRNAs/genetics , Nanoparticles/administration & dosage , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/genetics
15.
Mol Cell ; 55(1): 138-47, 2014 Jul 03.
Article in English | MEDLINE | ID: mdl-24910097

ABSTRACT

Noncoding RNAs (ncRNAs) control cellular programs by affecting protein-coding genes, but evidence increasingly points to their involvement in a network of ncRNA-ncRNA interactions. Here, we show that a long ncRNA, Uc.283+A, controls pri-miRNA processing. Regulation requires complementarity between the lower stem region of the pri-miR-195 transcript and an ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In addition to identifying a case of RNA-directed regulation of miRNA biogenesis, our study reveals regulatory networks involving different ncRNA classes of importance in cancer.


Subject(s)
MicroRNAs/metabolism , RNA, Long Noncoding/physiology , Conserved Sequence , HCT116 Cells , Humans , MicroRNAs/genetics , RNA Processing, Post-Transcriptional , RNA, Long Noncoding/metabolism
16.
Int J Mol Sci ; 23(7)2022 Mar 23.
Article in English | MEDLINE | ID: mdl-35408829

ABSTRACT

Leukemias are a group of malignancies of the blood and bone marrow. Multiple types of leukemia are known, however reliable treatments have not been developed for most leukemia types. Furthermore, even relatively reliable treatments can result in relapses. MicroRNAs (miRNAs) are a class of short, noncoding RNAs responsible for epigenetic regulation of gene expression and have been proposed as a source of potential novel therapeutic targets for leukemias. In order to identify central miRNAs for leukemia, we conducted data synthesis using two databases: miRTarBase and DISNOR. A total of 137 unique miRNAs associated with 16 types of leukemia were retrieved from miRTarBase and 86 protein-coding genes associated with leukemia were retrieved from the DISNOR database. Based on these data, we formed a visual network of 248 miRNA-target interactions (MTI) between leukemia-associated genes and miRNAs associated with ≥4 leukemia types. We then manually reviewed the literature describing these 248 MTIs for interactions identified in leukemia studies. This manually curated data was then used to visualize a network of 64 MTIs identified in leukemia patients, cell lines and animal models. We also formed a visual network of miRNA-leukemia associations. Finally, we compiled leukemia clinical trials from the ClinicalTrials database. miRNAs with the highest number of MTIs were miR-125b-5p, miR-155-5p, miR-181a-5p and miR-19a-3p, while target genes with the highest number of MTIs were TP53, BCL2, KIT, ATM, RUNX1 and ABL1. The analysis of 248 MTIs revealed a large, highly interconnected network. Additionally, a large MTI subnetwork was present in the network visualized from manually reviewed data. The interconnectedness of the MTI subnetwork suggests that certain miRNAs represent central disease molecules for multiple leukemia types. Additional studies on miRNAs, their target genes and associated biological pathways are required to elucidate the therapeutic potential of miRNAs in leukemia.


Subject(s)
Leukemia , MicroRNAs , Animals , Epigenesis, Genetic , Gene Expression Profiling , Humans , Leukemia/genetics , MicroRNAs/genetics , MicroRNAs/metabolism
17.
Mol Cancer ; 20(1): 24, 2021 02 01.
Article in English | MEDLINE | ID: mdl-33522932

ABSTRACT

Noncoding RNA (ncRNA) transcripts that did not code proteins but regulate their functions were extensively studied for the last two decades and the plethora of discoveries have instigated scientists to investigate their dynamic roles in several diseases especially in cancer. However, there is much more to learn about the role of ncRNAs as drivers of malignant cell evolution in relation to macrophage polarization in the tumor microenvironment. At the initial stage of tumor development, macrophages have an important role in directing Go/No-go decisions to the promotion of tumor growth, immunosuppression, and angiogenesis. Tumor-associated macrophages behave differently as they are predominantly induced to be polarized into M2, a pro-tumorigenic type when recruited with the tumor tissue and thereby favoring the tumorigenesis. Polarization of macrophages into M1 or M2 subtypes plays a vital role in regulating tumor progression, metastasis, and clinical outcome, highlighting the importance of studying the factors driving this process. A substantial number of studies have demonstrated that ncRNAs are involved in the macrophage polarization based on their ability to drive M1 or M2 polarization and in this review we have described their functions and categorized them into oncogenes, tumor suppressors, Juggling tumor suppressors, and Juggling oncogenes.


Subject(s)
Biomarkers, Tumor , Macrophage Activation/genetics , Macrophages/metabolism , Neoplasms/etiology , Neoplasms/metabolism , RNA, Untranslated/genetics , Animals , Cell Plasticity/genetics , Cell Plasticity/immunology , Disease Susceptibility , Gene Expression Regulation, Neoplastic , Humans , Macrophage Activation/immunology , Macrophages/immunology , MicroRNAs/genetics , Molecular Targeted Therapy , Neoplasms/pathology , Neoplasms/therapy , RNA, Long Noncoding , Tumor Microenvironment
18.
Gastroenterology ; 159(6): 2146-2162.e33, 2020 12.
Article in English | MEDLINE | ID: mdl-32805281

ABSTRACT

BACKGROUND & AIMS: Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic. METHODS: We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, γ-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 2'-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients. RESULTS: High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in microsatellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients. CONCLUSIONS: We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.


Subject(s)
Chromosomal Instability , Colorectal Neoplasms/genetics , Neoplasms, Experimental/genetics , RNA, Long Noncoding/metabolism , RNA-Binding Proteins/genetics , Animals , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Aurora Kinase B/metabolism , Azoxymethane/toxicity , Carcinogenesis/genetics , Cell Line, Tumor , Colon/cytology , Colon/pathology , Colorectal Neoplasms/chemically induced , Colorectal Neoplasms/pathology , Cytogenetic Analysis , Dextrans/toxicity , Drug Resistance, Neoplasm/genetics , Female , Gene Expression Regulation, Neoplastic , Gene Knockdown Techniques , Humans , Intestinal Mucosa/cytology , Intestinal Mucosa/pathology , Male , Mice , Mice, Transgenic , Neoplasms, Experimental/chemically induced , Neoplasms, Experimental/pathology , Organoids , Primary Cell Culture , Proto-Oncogene Proteins c-myc/metabolism , RNA, Long Noncoding/genetics , RNA-Binding Proteins/metabolism , Signal Transduction/genetics
19.
Genome Res ; 28(4): 432-447, 2018 04.
Article in English | MEDLINE | ID: mdl-29567676

ABSTRACT

The cancer-risk-associated rs6983267 single nucleotide polymorphism (SNP) and the accompanying long noncoding RNA CCAT2 in the highly amplified 8q24.21 region have been implicated in cancer predisposition, although causality has not been established. Here, using allele-specific CCAT2 transgenic mice, we demonstrate that CCAT2 overexpression leads to spontaneous myeloid malignancies. We further identified that CCAT2 is overexpressed in bone marrow and peripheral blood of myelodysplastic/myeloproliferative neoplasms (MDS/MPN) patients. CCAT2 induces global deregulation of gene expression by down-regulating EZH2 in vitro and in vivo in an allele-specific manner. We also identified a novel non-APOBEC, non-ADAR, RNA editing at the SNP locus in MDS/MPN patients and CCAT2-transgenic mice. The RNA transcribed from the SNP locus in malignant hematopoietic cells have different allelic composition from the corresponding genomic DNA, a phenomenon rarely observed in normal cells. Our findings provide fundamental insights into the functional role of rs6983267 SNP and CCAT2 in myeloid malignancies.


Subject(s)
Cell Proliferation/genetics , Myelodysplastic-Myeloproliferative Diseases/genetics , RNA, Long Noncoding/genetics , Adult , Aged , Aged, 80 and over , Animals , Cell Line, Tumor , Female , Gene Expression Regulation, Neoplastic , Humans , Male , Mice , Mice, Transgenic , Middle Aged , Myelodysplastic-Myeloproliferative Diseases/pathology , Polymorphism, Single Nucleotide/genetics , RNA Editing/genetics
20.
CA Cancer J Clin ; 64(5): 311-36, 2014.
Article in English | MEDLINE | ID: mdl-25104502

ABSTRACT

The interplay between abnormalities in genes coding for proteins and noncoding microRNAs (miRNAs) has been among the most exciting yet unexpected discoveries in oncology over the last decade. The complexity of this network has redefined cancer research as miRNAs, produced from what was once considered "genomic trash," have shown to be crucial for cancer initiation, progression, and dissemination. Naturally occurring miRNAs are very short transcripts that never produce a protein or amino acid chain, but act by regulating protein expression during cellular processes such as growth, development, and differentiation at the transcriptional, posttranscriptional, and/or translational level. In this review article, miRNAs are presented as ubiquitous players involved in all cancer hallmarks. The authors also describe the most used methods to detect their expression, which have revealed the identity of hundreds of miRNAs dysregulated in cancer cells or tumor microenvironment cells. Furthermore, the role of miRNAs as hormones and as reliable cancer biomarkers and predictors of treatment response is discussed. Along with this, the authors explore current strategies in designing miRNA-targeting therapeutics, as well as the associated challenges that research envisions to overcome. Finally, a new wave in molecular oncology translational research is introduced: the study of long noncoding RNAs.


Subject(s)
MicroRNAs/physiology , Neoplasms/diagnosis , Neoplasms/therapy , Biomarkers, Tumor/analysis , Biomarkers, Tumor/genetics , Gene Expression Regulation, Neoplastic , Genome , Humans , MicroRNAs/analysis , MicroRNAs/therapeutic use , Mutation , Neoplasms/genetics
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