Functional Peptides Encoded by Long Non-Coding RNAs in Gastrointestinal Cancer

Gastrointestinal cancer is by far the most common malignancy and the most common cause of cancer-related deaths worldwide. Recent studies have shown that long non-coding RNAs (lncRNAs) play an important role in the epigenetic regulation of cancer cells and regulate tumor progression by affecting chromatin modifications, gene transcription, translation, and sponge to miRNAs. In particular, lncRNA has recently been found to possess open reading frame (ORF), which can encode functional small peptides or proteins. These peptides interact with its targets to regulate transcription or the signal axis, thus promoting or inhibiting the occurrence and development of tumors. In this review, we summarize the involvement of lncRNAs and the function of lncRNAs encoded small peptides in gastrointestinal cancer.

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FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs

Non-Coding RNA ◽

10.3390/ncrna6040041 ◽

2020 ◽

Vol 6 (4) ◽

pp. 41

Author(s):

Mihnea P. Dragomir ◽

Ganiraju C. Manyam ◽

Leonie Florence Ott ◽

Léa Berland ◽

Erik Knutsen ◽

...

Keyword(s):

Open Reading Frames ◽

Start Codon ◽

Small Peptides ◽

Reading Frame ◽

Cellular Processes ◽

New Class ◽

Web Resource ◽

Non Coding Rnas ◽

Functional Peptides ◽

Small Open Reading Frames

Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs. The link for FuncPEP database can be found at the end of the Introduction Section.

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Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.703583 ◽

2021 ◽

Vol 9 ◽

Author(s):

Tristan Cardon ◽

Isabelle Fournier ◽

Michel Salzet

Keyword(s):

Signaling Pathways ◽

Protein Interaction ◽

Brain Cancer ◽

Transfer Rna ◽

Open Reading Frame ◽

Total Resection ◽

Rna Regulation ◽

Reading Frame ◽

Protein Protein Interaction ◽

Non Coding Rnas

Glioblastoma is the most common brain cancer in adults. Nevertheless, the median survival time is 15 months, if treated with at least a near total resection and followed by radiotherapy in association with temozolomide. In glioblastoma (GBM), variations of non-coding ribonucleic acid (ncRNA) expression have been demonstrated in tumor processes, especially in the regulation of major signaling pathways. Moreover, many ncRNAs present in their sequences an Open Reading Frame (ORF) allowing their translations into proteins, so-called alternative proteins (AltProt) and constituting the “ghost proteome.” This neglected world in GBM has been shown to be implicated in protein–protein interaction (PPI) with reference proteins (RefProt) reflecting involvement in signaling pathways linked to cellular mobility and transfer RNA regulation. More recently, clinical studies have revealed that AltProt is also involved in the patient’s survival and bad prognosis. We thus propose to review the ncRNAs involved in GBM and highlight their function in the disease.

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Mutations in the open reading frame of the β-site APP cleaving enzyme (BACE) locus are not a common cause of Alzheimer's disease

Neurogenetics ◽

10.1007/s100480100123 ◽

2001 ◽

Vol 3 (4) ◽

pp. 203-206 ◽

Cited By ~ 26

Author(s):

M. Nicolaou ◽

Y.-Q. Song ◽

C. Sato ◽

A. Orlacchio ◽

T. Kawarai ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Open Reading Frame ◽

Common Cause ◽

Reading Frame

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Non-coding RNAs: New therapeutic targets and opportunities for hepatocellular carcinoma

Advances in Modern Oncology Research ◽

10.18282/amor.v2.i1.91 ◽

2016 ◽

Vol 2 (1) ◽

pp. 5

Author(s):

Yu Cuiyun ◽

Qian Ning ◽

Zhi-Ping Li ◽

Wen Huang ◽

Jia Yu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Open Reading Frame ◽

Regulation Mechanism ◽

Biological Processes ◽

Biological Functions ◽

Protein Coding ◽

Reading Frame ◽

Rna Molecules ◽

Non Coding Rnas ◽

Diagnosis Therapy

<p align="left">Non-coding RNAs (ncRNA) are RNA molecules without protein coding functions owing to the lack of an open reading frame (ORF). Based on the length, ncRNAs can be divided into long and short ncRNAs; short ncRNAs include miRNAs and piRNAs. Hepatocellular carcinoma (HCC) is among the most frequent forms of cancer worldwide and its incidence is increasing rapidly. Studies have found that ncRNAs are likely to play a crucial role in a variety of biological processes including the pathogenesis and progression of HCC. In this review, we summarized the regulation mechanism and biological functions of ncRNAs in HCC with respect to its application in HCC diagnosis, therapy and prognosis.</p>

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