Potential Biomarkers for Therapeutic Monitoring and Clinical Outcome in Breast Cancer

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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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 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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Genome-wide analysis of long non-coding RNA expression and function in colorectal cancer

Tumor Biology ◽

10.1177/1010428317703650 ◽

2017 ◽

Vol 39 (5) ◽

pp. 101042831770365 ◽

Cited By ~ 10

Author(s):

Fangyuan Jing ◽

Huicheng Jin ◽

Yingying Mao ◽

Yingjun Li ◽

Ye Ding ◽

...

Keyword(s):

Colorectal Cancer ◽

Expression Profile ◽

Colorectal Carcinogenesis ◽

Rna Expression ◽

Rna Transcripts ◽

Non Coding Rna ◽

Tumor Tissues ◽

Non Coding Rnas ◽

Long Non Coding Rna

Long non-coding RNAs (lncRNAs) are widely transcribed in the genome, but their expression profile and roles in colorectal cancer are not well understood. The aim of this study was to investigate the long non-coding RNA expression profile in colorectal cancer and look for potential diagnostic biomarkers of colorectal cancer. Long non-coding RNA microarray was applied to investigate the global long non-coding RNA expression profile in colorectal cancer. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed using standard enrichment computational methods. The expression levels of selected long non-coding RNAs were validated by quantitative reverse transcription polymerase chain reaction. The relationship between long non-coding RNA expression levels and clinicopathological characteristics of colorectal cancer patients was assessed. Coexpression analyses were carried out to find the coexpressed genes of differentially expressed long non-coding RNAs, followed by gene ontology analysis to predict the possible role of the selected long non-coding RNAs in colorectal carcinogenesis. In this study, a total of 1596 long non-coding RNA transcripts and 1866 messenger RNA transcripts were dysregulated in tumor tissues compared with paired normal tissues. The top upregulated long non-coding RNAs in tumor tissues were CCAT1, UCA1, RP5-881L22.5, NOS2P3, and BC005081 and the top downregulated long non-coding RNAs were AK055386, AC078941.1, RP4-800J21.3, RP11-628E19.3, and RP11-384P7.7. Long non-coding RNA UCA1 was significantly upregulated in colon cancer, and AK055386 was significantly downregulated in tumor with dimension <5 cm. Functional prediction analyses showed that both the long non-coding RNAs coexpress with cell cycle related messenger RNAs. The current long non-coding RNA study provided novel insights into expression profile in colorectal cancer and predicted the potential roles of long non-coding RNAs in colorectal carcinogenesis. Among the dysregulated long non-coding RNAs, UCA1 was found to be associated with anatomic site, and AK055386 was found associated with tumor size. Further functional investigations into the molecular mechanisms are warranted to clarify the role of long non-coding RNA in colorectal carcinogenesis.

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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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Altered Long Non-coding RNA Expression in Cancer: Potential Biomarkers and Therapeutic Targets?

Topics in Medicinal Chemistry - Chemical Epigenetics ◽

10.1007/7355_2019_83 ◽

2019 ◽

pp. 401-428 ◽

Cited By ~ 1

Author(s):

David Hanly ◽

Manel Esteller ◽

María Berdasco

Keyword(s):

Therapeutic Targets ◽

Rna Expression ◽

Non Coding Rna ◽

Long Non Coding Rna ◽

Potential Biomarkers

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

Diagnostics ◽

10.3390/diagnostics12010086 ◽

2021 ◽

Vol 12 (1) ◽

pp. 86

Author(s):

Djordje Pavlovic ◽

Natasa Tosic ◽

Branka Zukic ◽

Zlatko Pravdic ◽

Nada Suvajdzic Vukovic ◽

...

Keyword(s):

Malignant Disease ◽

Expression Profiles ◽

Normal Karyotype ◽

Expression Level ◽

Healthy Controls ◽

Non Coding Rna ◽

Micro Rnas ◽

Non Coding Rnas ◽

New Biomarkers ◽

Long Non Coding Rna

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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