Long noncoding RNAs: from genomic junk to rising stars in the early detection of cancer

Miranda‐Castro, Rebeca; de‐los‐Santos‐Álvarez, Noemí; Lobo-Castañón, Marı́a Jesús

doi:10.1007/s00216-019-01607-6

Cited by 34 publications

(27 citation statements)

References 42 publications

(41 reference statements)

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“…Unlike ctDNA the mRNA copy number is larger than two, up to thousands copies, so their concentration in fluids is higher (Siravegna et al, 2017). Non-coding RNAs, formerly known as dark matter, are now regarded as crucial molecules in cancer biology (Miranda-Castro et al, 2019). The shorter RNAs (mi-RNA) have been studied more intensively than the longer counterparts (lncRNA) but both are promising markers in spite of the presence of ribonucleases because they used to be encapsulated in EV or linked to other macromolecules (Wang et al, 2019a).…”

Section: Targets In Liquid Biopsiesmentioning

confidence: 99%

The Translational Potential of Electrochemical DNA-Based Liquid Biopsy

Miranda‐Castro

Palchetti

de‐los‐Santos‐Álvarez

2020

Front. Chem.

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Latest technological advancement has tremendously expanded the knowledge on the composition of body fluids and the cancer-associated changes, which has fueled the replacement of invasive biopsies with liquid biopsies by using appropriate specific receptors. DNA emerges as a versatile analytical reagent in electrochemical devices for hybridization-based or aptamer-based recognition of all kind of biomarkers. In this mini review, we briefly introduce the current affordable targets (tumor-derived nucleic acids, circulating tumor cells and exosomes) in body fluids, and then we provide an overview of selected electrochemical methods already applied in clinical samples by dividing them into three large categories according to sample type: red (blood), yellow (urine), and white (saliva and sweat) diagnostics. This review focuses on the hurdles of the complex matrices rather than a comprehensive and detailed revision of the format schemes of DNA-based electrochemical sensing. This diverse perspective compiles some challenges that are often forgotten and critically underlines real sample analysis or clinical validation assays. Finally, the needs and trends to reach the market are briefly outlined.

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Section: Targets In Liquid Biopsiesmentioning

confidence: 99%

The Translational Potential of Electrochemical DNA-Based Liquid Biopsy

Miranda‐Castro

Palchetti

de‐los‐Santos‐Álvarez

2020

Front. Chem.

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“…They may function as oncogenes or tumour suppressors [34]. Apart from their low concentration (~femtomolar level) in body fluids of early-stage cancer patients, the strong intramolecular secondary structure of ncRNAs due to their large size is also a challenge for the determination of lncRNAs [35].…”

Section: Long Non-coding Rnasmentioning

confidence: 99%

Advances in Electrochemical (Bio)Sensing Targeting Epigenetic Modifications of Nucleic Acids

et al. 2019

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Nucleic acids epigenetic modifications including DNA and RNA methylation and post transcriptional gene regulation by noncoding RNAs (ncRNAs) such as microRNAs and long ncRNAs (lncRNAs), are of great relevance due to their role in mammalian development and the initiation and progression of various diseases like cancer. Over the past decades, a great research effort was made for determining nucleic acid methylation, electrochemical biosensors rapidly developing as efficient analytical tools for the determination of epigenetic modification of nucleic acids. In this review article, a critical overview of recently reported advances in their development and use for the determination of epigenetic modifications of nucleic acids, including the presence of methylated bases in DNA and RNA and the aberrant expression of microRNAs and lncRNAs, is provided. Special emphasis is made on methodologies successfully applied to real clinical samples, unmet challenges or key points toward future research.

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“…To date, multiple lncRNAs have been identified in CRC [ 29 ] and several studies have shown their involvement in key biological processes, from transcriptional regulation [ 30 , 31 , 32 , 33 ], to cellular mechanisms [ 34 , 35 , 36 , 37 , 38 ], and tumor progression [ 39 ]. Some reports have shown that cancer cells secrete lncRNAs into biological fluids [ 40 , 41 ]. This mechanism suggests that oncogenic signals can be spread to other cells, and it opens interesting perspectives for biomarker discovery [ 42 , 43 ].…”

Section: Introductionmentioning

confidence: 99%

Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples

Iraola-Guzmán

Brunet-Vega

Pegueroles

et al. 2020

Cancers

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Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.

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Long noncoding RNAs: from genomic junk to rising stars in the early detection of cancer

Cited by 34 publications

References 42 publications

The Translational Potential of Electrochemical DNA-Based Liquid Biopsy

The Translational Potential of Electrochemical DNA-Based Liquid Biopsy

Advances in Electrochemical (Bio)Sensing Targeting Epigenetic Modifications of Nucleic Acids

Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples

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