Expression Profiles of Long Non-Coding RNA GAS5 and MicroRNA-222 in Younger AML Patients

Acute myeloid leukemia (AML) is a heterogeneous malignant disease both on clinical and genetic levels. AML has poor prognosis and, therefore, there is a constant need to find new prognostic markers, as well as markers that can be used as targets for innovative therapeutics. Recently, the search for new biomarkers has turned researchers’ attention towards non-coding RNAs, especially long non-coding RNAs (lncRNAs) and micro RNAs (miRNAs). We investigated the expression level of growth arrest-specific transcript 5 (GAS5) lncRNA in 94 younger AML patients, and also the expression level of miR-222 in a cohort of 39 AML patients with normal karyotype (AML-NK), in order to examine their prognostic potential. Our results showed that GAS5 expression level in AML patients was lower compared to healthy controls. Lower GAS5 expression on diagnosis was related to an adverse prognosis. In the AML-NK group patients had higher expression of miR-222 compared to healthy controls. A synergistic effect of GAS5low/miR-222high status on disease prognosis was not established. This is the first study focused on examining the GAS5 and miR-222 expression pattern in AML patients. Its initial findings indicate the need for further investigation of these two non-coding RNAs, their potential roles in leukemogenesis, and the prognosis of AML patients.

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Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽

10.3390/ani11072006 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2006

Author(s):

Hongyu Liu ◽

Ibrar Muhammad Khan ◽

Huiqun Yin ◽

Xinqi Zhou ◽

Muhammad Rizwan ◽

...

Keyword(s):

Target Genes ◽

Expression Profiles ◽

Age Groups ◽

Adherens Junction ◽

Integrated Analysis ◽

Sequencing Data ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Rna Interaction ◽

Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

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NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants

Nucleic Acids Research ◽

10.1093/nar/gkaa1046 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D165-D171

Author(s):

Lianhe Zhao ◽

Jiajia Wang ◽

Yanyan Li ◽

Tingrui Song ◽

Yang Wu ◽

...

Keyword(s):

Transcriptome Sequencing ◽

Expression Profiles ◽

Noncoding Rnas ◽

Transcript Level ◽

Tissue Expression ◽

Non Coding Rna ◽

Non Coding Rnas ◽

The Relationship ◽

Long Non Coding Rna ◽

Predicted Function

Abstract NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.

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Long Non-Coding RNA in the Pathogenesis of Cancers

Cells ◽

10.3390/cells8091015 ◽

2019 ◽

Vol 8 (9) ◽

pp. 1015 ◽

Cited By ~ 72

Author(s):

Chi ◽

Wang ◽

Yu ◽

Yang

Keyword(s):

Early Stage ◽

Gene Expressions ◽

Rna Transcripts ◽

The Past ◽

Non Coding Rna ◽

Incidence And Mortality ◽

Non Coding Rnas ◽

Tumor Growth And Metastasis ◽

New Biomarkers ◽

Long Non Coding Rna

The incidence and mortality rate of cancer has been quickly increasing in the past decades. At present, cancer has become the leading cause of death worldwide. Most of the cancers cannot be effectively diagnosed at the early stage. Although there are multiple therapeutic treatments, including surgery, radiotherapy, chemotherapy, and targeted drugs, their effectiveness is still limited. The overall survival rate of malignant cancers is still low. It is necessary to further study the mechanisms for malignant cancers, and explore new biomarkers and targets that are more sensitive and effective for early diagnosis, treatment, and prognosis of cancers than traditional biomarkers and methods. Long non-coding RNAs (lncRNAs) are a class of RNA transcripts with a length greater than 200 nucleotides. Generally, lncRNAs are not capable of encoding proteins or peptides. LncRNAs exert diverse biological functions by regulating gene expressions and functions at transcriptional, translational, and post-translational levels. In the past decade, it has been demonstrated that the dysregulated lncRNA profile is widely involved in the pathogenesis of many diseases, including cancer, metabolic disorders, and cardiovascular diseases. In particular, lncRNAs have been revealed to play an important role in tumor growth and metastasis. Many lncRNAs have been shown to be potential biomarkers and targets for the diagnosis and treatment of cancers. This review aims to briefly discuss the latest findings regarding the roles and mechanisms of some important lncRNAs in the pathogenesis of certain malignant cancers, including lung, breast, liver, and colorectal cancers, as well as hematological malignancies and neuroblastoma.

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Long Non-Coding RNA Expression Profiling in Aging Rats with Erectile Dysfunction

Cellular Physiology and Biochemistry ◽

10.1159/000438519 ◽

2015 ◽

Vol 37 (4) ◽

pp. 1513-1526 ◽

Cited By ~ 10

Author(s):

Lianjun Pan ◽

Jiehua Ma ◽

Feng Pan ◽

Dan Zhao ◽

Jianping Gao

Keyword(s):

Erectile Dysfunction ◽

Expression Profiles ◽

Critical Role ◽

Altered Expression ◽

Aged People ◽

Age Related ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Rna Expression Profiling ◽

Long Non Coding Rna

Background/Aims: Erectile dysfunction (ED) in aged people remains a topic of interest to andrological physicians. Long non-coding RNAs (lncRNAs), which form the largest group of non-coding RNAs, have been shown to regulate various biological processes. The function of lncRNAs in age-related erectile dysfunction (A-ED) pathogenesis remains poorly understood. Methods: This study aims to assess the differential expression profiles of mRNAs and lncRNAs between A-ED and normal control (NC) samples. Using a second-generation lncRNA microarray, we detected a total of 8,744 lncRNAs and 13,585 coding transcripts. Results: We identified 608 up-regulated and 406 down-regulated lncRNAs in A-ED compared with NC samples, by setting a filter of fold-change >2.0. Gene Ontology and pathway analysis revealed that a muscle contraction disorder induced by abnormal ion channels might play a critical role in the pathogenesis of A-ED. Conclusion: Our results show significantly altered expression profiles of lncRNAs and mRNAs between A-ED and NC. This study may provide information for further research on A-ED and may be helpful for finding a new therapeutic target for A-ED.

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Potential Biomarkers for Therapeutic Monitoring and Clinical Outcome in Breast Cancer

10.5772/intechopen.100311 ◽

2021 ◽

Author(s):

Yuki Yamamoto ◽

Sabrina La Salvia ◽

Sahoo Susmita ◽

Hidetoshi Tahara

Keyword(s):

Expression Profiles ◽

Therapeutic Targets ◽

Transfer Rna ◽

Therapeutic Monitoring ◽

Transfer Rnas ◽

Non Coding Rna ◽

Tumor Tissues ◽

Non Coding Rnas ◽

Long Non Coding Rna ◽

Potential Biomarkers

Non-coding RNAs are a species of RNA that are not translated to proteins. These include transfer RNAs and ribosomal RNAs, microRNAs, transfer RNA-derived fragments, and long non-coding RNA. It is known that expression levels of some non-coding RNAs included microRNAs are altered in cancer cells or tumor tissues. Moreover, expression profiles of such non-coding RNAs correlate between tissues and body fluids. Therefore, several non-coding RNAs are being used as diagnostic/prognosis biomarkers or therapeutic targets in cancer. In this chapter, we review about representative non-coding RNAs and introduce especially microRNA as diagnosis/prognosis biomarkers and therapeutic targets.

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Expression of long non-coding RNAs ROR and MALAT1 in uterine fibroids

Voprosy ginekologii akušerstva i perinatologii ◽

10.20953/1726-1678-2021-4-17-21 ◽

2021 ◽

Vol 20 (4) ◽

pp. 17-21

Author(s):

S.A. Levakov ◽

◽

G.Ya. Azadova ◽

A.E. Mamedova ◽

Kh.R. Movtaeva ◽

...

Keyword(s):

Molecular Mechanisms ◽

Uterine Fibroids ◽

Reproductive Age ◽

Expression Level ◽

Control Group ◽

Tissue Samples ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Long Non Coding Rna

Objective. To study the expression level of long non-coding RNAs ROR and MALAT1 in tissue samples of uterine fibroids. Patients and methods. Samples of myomatous nodes and tissues of normal myometrium in 28 women of reproductive age were examined. The analysis of the expression of long non-coding RNAs was carried out using a real-time reverse-transcription polymerase chain reaction (RT-PCR) with specific primers. Results. There was a significant decrease in the expression level of long non-coding RNA ROR and an increase in the MALAT1 expression in tissue samples of uterine fibroids relative to the control group. Conclusion. The results obtained demonstrate a possible role of long non-coding RNAs in the development of uterine fibroids and correlate with the data which we obtained for patients with endometriosis. Detecting the expression level of long non-coding RNAs can improve the existing methods for diagnosing this disease. However, further research is required to determine the clinical significance of MALAT1 and ROR, and the molecular mechanisms underlying the action of these RNAs in uterine fibroid cells. Key words: long non-coding RNAs, uterine fibroids, myomectomy, lncROR, MALAT1

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Advances in biomarkers for HCC

Thai Journal of Hepatology ◽

10.30856/th.jhep2018vol1iss2_07 ◽

2018 ◽

Vol 1 (2) ◽

pp. 29-32 ◽

Cited By ~ 1

Author(s):

Taya Kitiyakara

Keyword(s):

Hepatocellular Carcinoma ◽

Treatment Outcomes ◽

Alpha Fetoprotein ◽

Blood Tests ◽

Common Cancer ◽

Non Coding Rna ◽

Non Coding Rnas ◽

New Biomarkers ◽

Long Non Coding Rna ◽

Late Stages

Hepatocellular carcinoma is a common cancer worldwide and has a high mortality. Many patientspresent in the late stages and the outcome of treatment for these patients is poor. Biomarkerscould theoretically help to detect the disease at an earlier stage before symptoms occurand improve the treatment outcomes. The first biomarker found was alpha-fetoprotein (AFP) and it iscurrently used as part of the HCC surveillance recommended in many countries. However AFP isnot very accurate and 30-40% of HCCs may be missed. Currently there are other biomarkers underinvestigation. Most of the more common biomarkers studied are serum/blood tests and include AFP-L3,PIVKA-II, Glypican-2, VEGF and the non-coding RNAs, such as long non-coding RNA and microRNA,and metabolomics tests. Tests involving urine or patient breaths are still relatively uncommonbut are being investigated. The limitation on the use of these new biomarkers is from the availabilityand costs of the tests. Only AFP-L3 and PIVKA-II are currently commercially available. Keywords: Biomarker, hepatocellular carcinoma, alpha-fetoprotein, microRNA, screening

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Long non-coding RNA expression profiles in neutrophils revealed potential biomarker for prediction of renal involvement in SLE patients

Rheumatology ◽

10.1093/rheumatology/keaa575 ◽

2020 ◽

Author(s):

Bin Cai ◽

Jingyi Cai ◽

Zhihua Yin ◽

Xiaoyue Jiang ◽

Chao Yao ◽

...

Keyword(s):

Disease Activity ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Renal Involvement ◽

Differentially Expressed ◽

Healthy Controls ◽

Lncrna Expression ◽

Non Coding Rna ◽

Potential Biomarker ◽

Long Non Coding Rna

Abstract Objective The long non-coding RNA plays an important role in inflammation and autoimmune diseases. The aim of this study is to screen and identify abnormally expressed lncRNAs in peripheral blood neutrophils of SLE patients as novel biomarkers and to explore the relationship between lncRNAs levels and clinical features, disease activity and organ damage. Methods RNA-seq technology was used to screen differentially expressed lncRNAs in neutrophils from SLE patients and healthy donors. Based on the results of screening, candidate lncRNA levels in neutrophils of 88 SLE patients, 35 other connective disease controls, and 78 healthy controls were qualified by real-time quantitative polymerase chain reaction. Results LncRNA expression profiling revealed 360 up-regulated lncRNAs and 224 down-regulated lncRNAs in neutrophils of SLE patients when compared with healthy controls. qPCR assay validated that the expression of Lnc-FOSB-1:1 was significantly decreased in neutrophils of SLE patients when compared with other CTD patients or healthy controls. It correlated negatively with SLE Disease Activity Index 2000 (SLEDAI-2K) score (r = −0.541, P < 0.001) and IFN scores (r = −0.337, P = 0.001). More importantly, decreased Lnc-FOSB-1:1 expression was associated with lupus nephritis. Lower baseline Lnc-FOSB-1:1 level was associated with higher risk of future renal involvement (within an average of 2.6 years) in patients without renal disease at baseline (P = 0.019). Conclusion LncRNA expression profile in neutrophils of SLE patients revealed differentially expressed lncRNAs. Validation study on Lnc-FOSB-1:1 suggest that it is a potential biomarker for prediction of near future renal involvement.

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Circulating Long Non-Coding RNA GAS5 Is Overexpressed in Serum from Osteoporotic Patients and Is Associated with Increased Risk of Bone Fragility

International Journal of Molecular Sciences ◽

10.3390/ijms21186930 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6930

Author(s):

Virginia Veronica Visconti ◽

Simona Fittipaldi ◽

Simone Ciuffi ◽

Francesca Marini ◽

Giancarlo Isaia ◽

...

Keyword(s):

Direct Sequencing ◽

Fragility Fractures ◽

Bone Fragility ◽

Expression Level ◽

Pcr Analysis ◽

Diagnosis And Prognosis ◽

Non Coding Rna ◽

Increased Risk ◽

Non Coding Rnas ◽

Long Non Coding Rna

Osteoporosis (OP) is a multifactorial disorder in which environmental factors along with genetic variants and epigenetic mechanisms have been implicated. Long non-coding RNAs (lncRNAs) have recently emerged as important regulators of bone metabolism and OP aetiology. In this study, we analyzed the expression level and the genetic association of lncRNA GAS5 in OP patients compared to controls. Quantitative RT-PCR analysis of GAS5 was performed on the serum of 56 OP patients and 28 healthy individuals. OP subjects were divided into three groups of analysis: 29 with fragility fractures of lumbar spine (OP_VF), 14 with fragility fractures of femoral neck (OP_FF) and 13 without fractures (OP_WF). Genotyping of the rs145204276 insertion/deletion polymorphism has also been performed by Restriction fragment length polymorphism (RFLP) and direct sequencing analyses. Expression of circulating GAS5 is significantly increased in OP patients compared to controls (p < 0.01), with a statistically higher significance in fractured OP individuals vs. healthy subjects (p < 0.001). No statistically significant change was found in female OP patients; conversely, GAS5 is upregulated in the subgroup of fractured OP women sera (p < 0.01) and in all OP males (p < 0.05). Furthermore, a direct correlation between GAS5 expression level and parathyroid hormone (PTH) concentration was found in OP patients (r = 0.2930; p = 0.0389). Genetic analysis of rs145204276 revealed that the deletion allele was correlated with a higher expression of GAS5 in OP patients (0.22 ± 0.02 vs. 0.15 ± 0.01, ** p < 0.01). Our results suggest circulating GAS5 as a putative biomarker for the diagnosis and prognosis of OP and OP-related fractures.

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Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles

Genes ◽

10.3390/genes10030205 ◽

2019 ◽

Vol 10 (3) ◽

pp. 205 ◽

Cited By ~ 1

Author(s):

Olga A. Postnikova ◽

Igor B. Rogozin ◽

William Samuel ◽

German Nudelman ◽

Vladimir N. Babenko ◽

...

Keyword(s):

Retinal Pigment Epithelium ◽

Expression Profiles ◽

Pigment Epithelium ◽

Retinal Pigment ◽

Non Coding Rna ◽

Small Set ◽

Flexible Adaptation ◽

Non Coding Rnas ◽

Whole Genome Alignment ◽

Long Non Coding Rna

Currently, several long non-coding RNAs (lncRNAs) (TUG1, MALAT1, MEG3 and others) have been discovered to regulate normal visual function and may potentially contribute to dysfunction of the retina. We decided to extend these analyses of lncRNA genes to the retinal pigment epithelium (RPE) to determine whether there is conservation of RPE-expressed lncRNA between human and bovine genomes. We reconstructed bovine RPE lncRNAs based on genome-guided assembly. Next, we predicted homologous human transcripts based on whole genome alignment. We found a small set of conserved lncRNAs that could be involved in signature RPE functions that are conserved across mammals. However, the fraction of conserved lncRNAs in the overall pool of lncRNA found in RPE appeared to be very small (less than 5%), perhaps reflecting a fast and flexible adaptation of the mammalian eye to various environmental conditions.

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