Genome Wide Transcriptomic Analysis Identifies Dysregulated Splicing Factor Profile with Molecular and Functional Role in Multiple Myeloma

Alternative splicing (AS) is a critical post-transcriptional event, which affects the number of cellular processes. Aberrant splicing of some genes has been reported in multiple myeloma (MM). However, to date, whole-transcriptome-wide AS study has not been performed. We used deep RNA-sequencing data from 16 normal plasma cells (NPC) and 360 newly-diagnosed MM patients to describe the landscape of the alternative splicing events and the molecular mechanisms driving aberrant AS in MM. Global splicing analysis showed that mutually exclusive exon (MXE) (n=510) and Skipped Exon (SE) (n=417) are the most frequent splicing events in MM compared to NPC. Among these events, ~54% were observed in genes which are not differentially expressed between MM and NPC and 46% of the AS events (SE, MXE, retained intron, alternative 3'/5' sites) were observed in differentially expressed genes targeting 203 unique genes. AS affected RNA transcription regulation genes such as IKZF1, IKZF3, and key regulatory elements in MM including, IRF3, IRF4, or key transcription factors such as MEF2C, XPB1, STAT2, and ILF3. In general, AS targetted DNA replication, cell cycle, and apoptosis pathways. MM subgroups showed a heterogeneity for AS events. Monosomy 14, t(4;14), del1p and del17p had the highest number of unique (not observed in other subgroups) AS events compared to NPC.To understanding the molecular mechanisms driving aberrant alternate splicing we next investigated115 splicing factors (SF) in MM and associated them with AS events. We observed that ~40% of SF were dysregulated (dysregulated expression and/or copy number alteration) in MM compared to NPC, including SRSF, PCBP and RBM families. To understand the key binding regions, we have performed SF binding motif enrichment analysis around AS events and found that SRFS1, SRSF9, and PCB1 motifs to be enriched among the splicing events. Importantly, SRSF1 expression was linked with survival in two independent MM datasets.We therefore explored functional role of SRSF1 in MM with perturbation studies. While upregulation of SRSF1 expression significantly increased the cell growth and survival, conversely downregulation of SRSF1 inhibited the both. To dissect the mechanisms of SRSF1-mediated MM growth induction, we utilized SRSF1 mutants lacking either of the 2 RNA-recognition motifs or the serine/argine-rich C-terminal domain involved in protein-protein interactions, and recruitment of spliceosome components. We also utilized a C-terminal fusion of SRSF1 with the nuclear-retention signal of SRSF2 (NRS1 mutant), to force SRSF1 retention in the nucleus and assess the role of its nuclear versus cytoplasmic functions. These studies suggested that SRSF1-regulated AS effects MM cell proliferation. We surprisingly also found that even NRS1 mutant failed to promote MM growth, suggesting an important role of cytoplasmic SRSF1 in promoting MM cells proliferation.We next investigated alternative splicing pattern changes induced by SRSF1 knock down.When analyzing cellular functions of SRSF1-regulated splicing events, we found that SRSF1 knock down affect's genes in the RNA processing pathway as well as genes involved in cancer-related functions such as mTOR, E2F and MYC-related pathways. Splicing analysis was corroborated with immunoprecipitation (IP) followed by mass spectrometry (MS) analysis of T7-tagged SRSF1 MM cells.Finally, using genome wide chromatin and transcription landscape mapping techniques, we have found SRSF1 to be under the transcriptional control of oncogenic E2F1 in MM cells. Consistent with these findings, we observed greater in vitro loss of viability in a large panel of MM cell lines compared with PBMCs from healthy volunteers, following exposure to the splicing modulator pladeniolide. In summary, this study for the first time reports a detailed splicing landscape in myeloma and highlights the biological and clinical importance of alternative splicing events. Moreover, these results indicate a functional role and clinical significance of a gene involved in regulation of alternate splicing in MM, highlighting the need to further understand the splicing pattern in myeloma initiation and progression. Disclosures Anderson: Takeda: Consultancy, Speakers Bureau; Celgene: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; Janssen: Consultancy, Speakers Bureau; Oncopep: Other: Scientific Founder; Sanofi-Aventis: Other: Advisory Board; Bristol-Myers Squibb: Other: Scientific Founder. Avet-Loiseau:takeda: Consultancy, Other: travel fees, lecture fees, Research Funding; celgene: Consultancy, Other: travel fees, lecture fees, Research Funding. Munshi:Adaptive: Consultancy; Abbvie: Consultancy; Takeda: Consultancy; Janssen: Consultancy; Oncopep: Consultancy; Amgen: Consultancy; Celgene: Consultancy.

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Microrna Mir-21 Is Upregulated after Different Microenvironmental Stimuli and Controls Proliferation, Chemotaxis and Chemoresistance in Chronic Lymphocytic Leukemia

Blood ◽

10.1182/blood.v124.21.1971.1971 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1971-1971

Author(s):

Marta Crespo ◽

Júlia Carabia ◽

Noelia Purroy ◽

Cecilia Carpio ◽

Pau Abrisqueta ◽

...

Keyword(s):

Overall Survival ◽

Clinical Outcome ◽

Research Funding ◽

Functional Role ◽

Molecular Mechanisms ◽

Culture Media ◽

Lymphocytic Leukemia ◽

High Expression ◽

Aberrant Expression

Abstract Aberrant expression of diverse microRNAs (miRNAs) has been related to pathogenesis and clinical outcome in patients with CLL. miR-21 is overexpressed in a wide variety of neoplasms where it participates in oncogenic events such as proliferation, resistance to treatment and metastasis. In CLL, miR-21 expression has been associated to refractoriness to fludarabine and to shorter overall survival. In addition, high expression of ZAP-70 protein in CLL is related to shorter overall survival and higher probability of progression. Several biological mechanisms have been described explaining the adverse prognosis associated with high ZAP-70 expression. In this sense, ZAP-70 protein increases the capability of CLL cells to respond to different survival and migration signals provided by the microenvironment. In a previous work, we found that transfected B-cell lines with a ZAP-70 expressing vector (Calpe at al, Blood 2011) had an increased expression of several molecules, including miR-21. Against this background, we studied the relationship between ZAP-70 protein and miR-21. For this, we firstly analyzed the correlation of ZAP-70 with miR-21 in primary CLL cells from 32 patients. In this series we observed that miR-21 expression analyzed by QRT-PCR was significantly higher in patients with high expression of ZAP-70 compared to patients with low expression of ZAP-70 (mean miR-21 in high ZAP-70 (N=17) = 5.781 ± 1.517; mean miR-21 in low ZAP-70 (N=15) = 0.6783 ± 0.2730; p=0.0082). In order to further analyze the molecular mechanisms regulating the induction of miR-21 and the potential role of ZAP-70 protein in this process, we co-cultured primary CLL cells (N=16) in conditions mimicking the microenvironment in the proliferation centers (bone marrow stromal cells with concomitant stimulation of CD40 and TLR9). In these conditions, besides ZAP-70 activation, we observed a 3.6 ± 0.78 mean fold induction in miR-21 expression after 48 hours compared to cells in suspension. Interestingly, this increase was only significant in patients with high expression of ZAP-70 (N=8; p= 0.0379). To define the role of ZAP-70 in miR-21 regulation, we stably transfected Ramos B-cells with ZAP-70 protein and found that both MAPK and STAT3 participate in the induction of miR-21 expression after ZAP-70 activation upon BCR crosslinking. Moreover, using this system we observed downregulation of the tumor suppressors PTEN, PDCD4 and PIAS3, all of which have been found to be targeted by miR-21 in malignant cells. Next, we aimed to study the functional role of miR-21 in primary CLL cells co-cultured in conditions mimicking the microenvironment from the proliferation centers. For this, we analyzed survival, proliferation and response to fludarabine after inhibition of miR-21 expression by transfecting primary CLL cells with antisense miR-21 inhibitor. The co-culture of primary CLL cells significantly increased their survival after 48 hours regardless the inhibition of miR-21. However, the induction of proliferation (measured as percentage of Ki-67 positive cells) was significantly inhibited by the suppression of miR-21 (N=13; p=0.022). Next, the analysis of a small pilot cohort showed a consistent but not yet significant overcoming of the chemoresistance induced by the co-culture after the inhibition of miR-21 Interestingly, the sensitivity to fludarabine of primary CLL cells cultured in suspension was also increased by the inhibition of miR-21. Finally, we examined the ability of primary CLL cells to migrate towards CXCL12 and observed that inhibition of miR-21 resulted in a 2.62-fold reduction of the migration index (ratio of cells migrating towards culture media to cells migrating towards media with 200ng/mL CXCL12). In conclusion, we have showed the correlation and participation of ZAP-70 protein in the regulation of miR-21. We have also observed that miR-21 contributes to CLL proliferation, resistance to fludarabine, and chemotaxis towards CXCL12. Although further experiments are warranted in order to fully elucidate the regulation and functional role of miR-21 in CLL, these results help to enlighten the biology behind the adverse clinical outcome of patients with CLL and high expression of ZAP-70, and could potentially be exploited for the development of new treatments in a near future. Disclosures Bosch: Roche: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding.

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Identification of Deubiquitinase OTUD1 As a Novel Player in Resistance of Multiple Myeloma to Bortezomib

Blood ◽

10.1182/blood-2019-127930 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 5526-5526

Author(s):

Alexander Vdovin ◽

Tomas Jelinek ◽

Matous Hrdinka ◽

Juli R. Bago ◽

Tereza Sevcikova ◽

...

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Multiple Myeloma ◽

Flow Cytometry ◽

Cell Death ◽

Research Funding ◽

Molecular Mechanisms ◽

Plasma Cells ◽

Hek293 Cells

Introduction Multiple myeloma (MM) being one of the most widely spread haematological malignancies remains an incurable disease. As malignant plasma cells produce abnormally large amounts of immunoglobulins they particularly rely on the ubiquitin-proteasome system (UPS) to avoid aberrant protein overload. This unique feature is targeted by proteasome inhibitors (PI) that induce MM cell death especially by increasing levels of reactive oxygen species (ROS). Despite the high efficacy of PI most of the MM patients eventually relapse and expansion of drug resistant clones makes the treatment ineffective. Therefore, uncovering new molecular mechanisms of drug resistance is a crucial task. UPS is a very complex system that involves hundreds of proteins. While the roles of the proteasome and E3 ligases in PI resistance are well established, the third UPS component, deubiquitinating enzymes (DUBs), is much less explored. In this work, we performed a comprehensive search for DUBs with impact on MM pathogenesis and PI resistance, and further investigated the underlying molecular mechanisms. Methods Gene expression and survival For analysis of DUB genes (n = 101) expression in blood cells, expression dataset Gds3997, DICE database and data from (Jourdan et al., J Immunol. 2011 Oct 15;187(8):3931-41., Jourdan et al., Blood. 2009 Dec 10;114(25):5173-81.) submitted to http://www.genomicscape.com were used. For survival analysis MM patients were divided into two groups by median of gene expression for each DUB (datasets GSE2658, GSE4581 and GSE9782). Cell line models RPMI8226 and HEK293 cells were used as model cell lines. Cells with OTUD1 knockdowns and overexpression were generated by lentiviral infection using vectors containing doxycycline-inducible shRNA's and different versions of OTUD1 gene, respectively. Proliferation and cell death MTT assay was used for the analysis of cell proliferation and viability. Cell death was also evaluated by flow cytometry by staining with Annexin V and 7-AAD. Cell migration Cells were labelled with calcein-AM and placed into the upper chamber of transwell insert with 8-µM pores. After 16 hours of migration towards SDF-1α gradient, cells were counted by fluorescence detection. ROS analysis ROS was detected by labelling cells with 2′,7′-dichlorodihydrofluorescein diacetate and measuring fluorescence intensity using flow cytometry. Immunoprecipitation HEK293 cells were co-transfected with HA-OTUD1 and FLAG-KEAP1, and reciprocal co-immunoprecipitation and western blot analyses were performed. Results We analysed the expression of all human DUBs in different blood cell types and identified OTUD1 as the most differentially expressed DUB between B-cell lineage and other haematopoietic cells. During B-cell maturation OTUD1 expression reaches the maximum in the bone marrow plasma cells. MM patients with low OTUD1 expression had significantly worse prognosis in OS based on three large datasets (p value= 0,035; 0,008; 2.4e−06. HR=0,55; 0,19; 0,41). Expression of shRNA targeting OTUD1 in MM cell line RPMI8226 did not affect cell proliferation and migration but dramatically increased survival under oxidative stress (high ROS) conditions induced by bortezomib. Treatment with bortezomib promoted expression of OTUD1 in the wild type MM cells in a ROS-dependent manner. Additionally, we identified oxidative stress regulator, the E3 ligase KEAP1 as a novel direct interaction partner of OTUD1 that regulates OTUD1 stability under high ROS conditions. Conclusion Based on the gene expression analysis, OTUD1 was identified as a novel, potentially important player in MM pathogenesis. Low levels of OTUD1 expression in MM patients correlate with significantly worse OS. Knocking down OTUD1 in MM cells causes resistance to bortezomib. Mechanistically, bortezomib-induced ROS promotes transcription of OTUD1 mRNA and further induces stabilization of OTUD1 on protein level via disruption of OTUD1-KEAP1 complex. Our collective data suggest on a crucial role of OTUD1 in bortezomib-mediated MM cytotoxity. Further mechanistic studies delineating the role of OTUD1 in MM pathogenesis and PI resistance are ongoing. Disclosures Hajek: Janssen: Honoraria, Other: Consultant or advisory relationship, Research Funding; Amgen: Honoraria, Other: Consultant or advisory relationship, Research Funding; Celgene: Honoraria, Other: Consultant or advisory relationship, Research Funding; AbbVie: Other: Consultant or advisory relationship; Bristol-Myers Squibb: Honoraria, Other: Consultant or advisory relationship, Research Funding; Novartis: Other: Consultant or advisory relationship, Research Funding; PharmaMar: Honoraria, Other: Consultant or advisory relationship; Takeda: Honoraria, Other: Consultant or advisory relationship, Research Funding.

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Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽

10.3390/biology10030232 ◽

2021 ◽

Vol 10 (3) ◽

pp. 232

Author(s):

Weiran Zheng ◽

Haichao Hu ◽

Qisen Lu ◽

Peng Jin ◽

Linna Cai ◽

...

Keyword(s):

Virus Infection ◽

Mosaic Virus ◽

Nicotiana Benthamiana ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Differentially Expressed ◽

Genome Wide ◽

Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

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Abstract 12192: MBNL1 Directly Regulates the Alternative Splicing of mRNAs That Promote Myofibroblast Differentiation

Circulation ◽

10.1161/circ.130.suppl_2.12192 ◽

2014 ◽

Vol 130 (suppl_2) ◽

Author(s):

Jennifer Davis ◽

Michelle Sargent ◽

Jianjian Shi ◽

Lei Wei ◽

Maurice S Swanson ◽

...

Keyword(s):

Alternative Splicing ◽

Molecular Mechanisms ◽

Rna Binding ◽

Transforming Growth Factor ◽

Ventricular Remodeling ◽

Cardiac Injury ◽

Myofibroblast Differentiation ◽

Genome Wide ◽

A Genome

Rationale: During the cardiac injury response fibroblasts differentiate into myofibroblasts, a cell type that enhances extracellular matrix production and facilitates ventricular remodeling. To better understand the molecular mechanisms whereby myofibroblasts are generated in the heart we performed a genome-wide screen with 18,000 cDNAs, which identified the RNA-binding protein muscleblind-like splicing regulator 1 (MBNL1), suggesting a novel association between mRNA alternative splicing and the regulation of myofibroblast differentiation. Objective: To determine the mechanism whereby MBNL1 regulates myofibroblast differentiation and the cardiac fibrotic response. Methods and Results: Confirming the results from our genome wide screen, adenoviral-mediated overexpression of MBNL1 promoted transformation of rat cardiac fibroblasts and mouse embryonic fibroblasts (MEFs) into myofibroblasts, similar to the level of conversion obtained by the profibrotic agonist transforming growth factor β (TGFβ). Antithetically, Mbnl1 -/- MEFs were refractory to TGFβ-induced myofibroblast differentiation. MBNL1 expression is induced in transforming fibroblasts in response to TGFβ and angiotensin II. These results were extended in vivo by analysis of dermal wound healing, a process dependent on myofibroblast differentiation and their proper activity. By day 6 control mice had achieved 82% skin wound closure compared with only 40% in Mbnl1 -/- mice. Moreover, Mbnl1 -/- mice had reduced survival following myocardial infarction injury due to defective fibrotic scar formation and healing. High throughput RNA sequencing (RNAseq) and RNA immunoprecipitation revealed that MBNL1 directly regulates the alternative splicing of transcripts for myofibroblast signaling factors and cytoskeletal-assembly elements. Functional analysis of these factors as mediators of MBNL1 activity is also described here. Conclusions: Collectively, our data suggest that MBNL1 coordinates myofibroblast transformation by directly mediating the alternative splicing of an array of mRNAs encoding differentiation-specific signaling transcripts, which then alter the fibroblast proteome for myofibroblast structure and function.

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Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

10.1101/2020.05.25.115154 ◽

2020 ◽

Author(s):

Kashyap Chhatbar ◽

Justyna Cholewa-Waclaw ◽

Ruth Shah ◽

Adrian Bird ◽

Guido Sanguinetti

Keyword(s):

Alternative Splicing ◽

Dna Sequences ◽

Molecular Mechanisms ◽

Data Sets ◽

Learning Approaches ◽

Global Regulator ◽

Major Function ◽

Quantitative Analyses ◽

Different Levels

AbstractMeCP2 is an abundant protein in mature nerve cells, where it binds to DNA sequences containing methylated cytosine. Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome (RTT), provoking intensive study of the underlying molecular mechanisms. Multiple functions have been proposed, one of which involves a regulatory role in splicing. Here we leverage the recent availability of high-quality transcriptomic data sets to probe quantitatively the potential influence of MeCP2 on alternative splicing. Using a variety of machine learning approaches that can capture both linear and non-linear associations, we show that widely different levels of MeCP2 have a minimal effect on alternative splicing in three different systems. Alternative splicing was also apparently indifferent to developmental changes in DNA methylation levels. Our results suggest that regulation of splicing is not a major function of MeCP2. They also highlight the importance of multi-variate quantitative analyses in the formulation of biological hypotheses.

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DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral modelAiptasia

10.1101/213066 ◽

2017 ◽

Cited By ~ 3

Author(s):

Yong Li ◽

Yi Jin Liew ◽

Guoxin Cui ◽

Maha J Cziesielski ◽

Noura Zahran ◽

...

Keyword(s):

Dna Methylation ◽

Molecular Mechanisms ◽

Model System ◽

Epigenetic Mechanism ◽

Symbiotic Relationship ◽

Epigenetic Mechanisms ◽

Genome Wide ◽

Spurious Transcription ◽

Coral Reef Ecosystems

The symbiotic relationship between cnidarians and dinoflagellates is the cornerstone of coral reef ecosystems. Although research is focusing on the molecular mechanisms underlying this symbiosis, the role of epigenetic mechanisms, which have been implicated in transcriptional regulation and acclimation to environmental change, is unknown. To assess the role of DNA methylation in the cnidarian-dinoflagellate symbiosis, we analyzed genome-wide CpG methylation, histone associations, and transcriptomic states of symbiotic and aposymbiotic anemones in the model systemAiptasia. We find methylated genes are marked by histone H3K36me3 and show significant reduction of spurious transcription and transcriptional noise, revealing a role of DNA methylation in the maintenance of transcriptional homeostasis. Changes in DNA methylation and expression show enrichment for symbiosis-related processes such as immunity, apoptosis, phagocytosis recognition and phagosome formation, and unveil intricate interactions between the underlying pathways. Our results demonstrate that DNA methylation provides an epigenetic mechanism of transcriptional homeostasis during symbiosis.

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Alternative Splicing During the Chlamydomonasreinhardtii Cell Cycle

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401622 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3797-3810

Author(s):

Manishi Pandey ◽

Gary D. Stormo ◽

Susan K. Dutcher

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Alternative Splicing ◽

Chlamydomonas Reinhardtii ◽

Intron Retention ◽

Exon Skipping ◽

Dark Phase ◽

Periodic Patterns ◽

Genome Wide ◽

Splicing Pattern

Genome-wide analysis of transcriptome data in Chlamydomonas reinhardtii shows periodic patterns in gene expression levels when cultures are grown under alternating light and dark cycles so that G1 of the cell cycle occurs in the light phase and S/M/G0 occurs during the dark phase. However, alternative splicing, a process that enables a greater protein diversity from a limited set of genes, remains largely unexplored by previous transcriptome based studies in C. reinhardtii. In this study, we used existing longitudinal RNA-seq data obtained during the light-dark cycle to investigate the changes in the alternative splicing pattern and found that 3277 genes (19.75% of 17,746 genes) undergo alternative splicing. These splicing events include Alternative 5′ (Alt 5′), Alternative 3′ (Alt 3′) and Exon skipping (ES) events that are referred as alternative site selection (ASS) events and Intron retention (IR) events. By clustering analysis, we identified a subset of events (26 ASS events and 10 IR events) that show periodic changes in the splicing pattern during the cell cycle. About two-thirds of these 36 genes either introduce a pre-termination codon (PTC) or introduce insertions or deletions into functional domains of the proteins, which implicate splicing in altering gene function. These findings suggest that alternative splicing is also regulated during the Chlamydomonas cell cycle, although not as extensively as changes in gene expression. The longitudinal changes in the alternative splicing pattern during the cell cycle captured by this study provides an important resource to investigate alternative splicing in genes of interest during the cell cycle in Chlamydomonas reinhardtii and other eukaryotes.

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Alternative splicing of leptin receptor overlapping transcript in osteosarcoma

Experimental Biology and Medicine ◽

10.1177/1535370220949139 ◽

2020 ◽

Vol 245 (16) ◽

pp. 1437-1443

Author(s):

Emel Rothzerg ◽

Xuan D Ho ◽

Jiake Xu ◽

David Wood ◽

Aare Märtson ◽

...

Keyword(s):

Alternative Splicing ◽

Molecular Mechanisms ◽

Leptin Receptor ◽

Osteogenic Sarcoma ◽

Differentially Expressed ◽

Primary Malignancy ◽

Transcript Variants ◽

Potential Biomarker ◽

Whole Transcriptome Analysis ◽

Tumor Biopsies

Alternative splicing of RNA is an essential mechanism that increases proteomic diversity in eukaryotic cells. Aberrant alternative splicing is often associated with various human diseases, including cancer. We conducted whole-transcriptome analysis of 18 osteosarcoma bone samples (paired normal—tumor biopsies). Using RNA-seq, we identified statistically significant (FDR <0.05) 26 differentially expressed transcript variants of leptin receptor overlapping transcript ( LEPROT) gene. Some of the transcripts were overexpressed in normal cells, whereas others were overexpressed in tumor cells. The function of LEPROT is not completely understood. Herein, we highlight a possible association between OS and aberrant alternative splicing events and its interaction with the expression of LEPROT. We also discuss the role of LEPROT in regulating growth hormone and its receptor, and the relationship with initiation and progression of OS. This research study may help to understand the association of alternative splicing mechanism in OS and in tumorigenesis more generally. Further, LEPROT gene can also be considered as a potential biomarker of osteosarcoma. Impact statement Osteosarcoma (OS, also known as osteogenic sarcoma) is the most common primary malignancy of bone in children and adolescents. The molecular mechanisms of OS are extremely complicated and its molecular mediators remain to be elucidated. We sequenced total RNA from 18 OS bone samples (paired normal—tumor biopsies). We found statistically significant (FDR <0.05) 26 differentially expressed transcript variants of LEPROT gene with different expressions in normal and tumor samples. These findings contribute to the understanding of molecular mechanisms of OS development and provide encouragement to pursue further research.

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Identification of Long Noncoding RNA Associated ceRNA Networks in Rosacea

BioMed Research International ◽

10.1155/2020/9705950 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Lian Wang ◽

Ruifeng Lu ◽

Yujia Wang ◽

Xiaoyun Wang ◽

Dan Hao ◽

...

Keyword(s):

Noncoding Rna ◽

Molecular Mechanisms ◽

Functional Enrichment ◽

Differentially Expressed ◽

Control Group ◽

Group 13 ◽

Regulatory Processes ◽

Coexpression Networks

Rosacea is a chronic and relapsing inflammatory cutaneous disorder with highly variable prevalence worldwide that adversely affects the health of patients and their quality of life. However, the molecular characterization of each rosacea subtype is still unclear. Furthermore, little is known about the role of long noncoding RNAs (lncRNAs) in the pathogenesis or regulatory processes of this disorder. In the current study, we established lncRNA-mRNA coexpression networks for three rosacea subtypes (erythematotelangiectatic, papulopustular, and phymatous) and performed their functional enrichment analyses using Gene Onotology, KEGG, GSEA, and WGCNA. Compared to the control group, 13 differentially expressed lncRNAs and 525 differentially expressed mRNAs were identified in the three rosacea subtypes. The differentially expressed genes identified were enriched in four signaling pathways and the GO terms found were associated with leukocyte migration. In addition, we found nine differentially expressed lncRNAs in all three rosacea subtype-related networks, including NEAT1 and HOTAIR, which may play important roles in the pathology of rosacea. Our study provided novel insights into lncRNA-mRNA coexpression networks to discover the molecular mechanisms involved in rosacea development that can be used as future targets of rosacea diagnosis, prevention, and treatment.

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