Plasma RNA Integrity Analysis

Wong, Bel; Lo, Y.M. Dennis

doi:10.1196/annals.1368.023

Cited by 11 publications

(5 citation statements)

References 13 publications

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“…We further evaluated the integrity of cfsRNA by quantifying the amounts of the 3 different regions of ACTB and DDX4 transcripts. Such an analysis has previously been done in studies of cfRNA integrity in serum and saliva (21,23,24 ). As is shown in Fig.…”

Section: Amplification and Integrity Analysis Of Cfsrnamentioning

confidence: 84%

Presence and Characterization of Cell-Free Seminal RNA in Healthy Individuals: Implications for Noninvasive Disease Diagnosis and Gene Expression Studies of the Male Reproductive System

Huang

Ding

et al. 2009

Clinical Chemistry

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Section: Amplification and Integrity Analysis Of Cfsrnamentioning

confidence: 84%

Presence and Characterization of Cell-Free Seminal RNA in Healthy Individuals: Implications for Noninvasive Disease Diagnosis and Gene Expression Studies of the Male Reproductive System

Huang

Ding

et al. 2009

Clinical Chemistry

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“…However, outside of miRNAs there has been little research on other cell-free (cf) RNA species in the circulating transcriptome. Part of the reason for this paucity of knowledge is the presence of high levels of RNase activity in blood, which typically results in fragmentation of longer RNA species such as mRNA [8,9]. This makes detection of these molecules particularly challenging.…”

Section: Introductionmentioning

confidence: 99%

The Circulating Transcriptome as a Source of Biomarkers for Melanoma

Solé

Tramonti

Schramm

et al. 2019

Cancers

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The circulating transcriptome is a valuable source of cancer biomarkers, which, with the exception of microRNAs (miRNAs), remains relatively unexplored. To elucidate which RNAs are present in plasma from melanoma patients and which could be used to distinguish cancer patients from healthy individuals, we used next generation sequencing (NGS), and validation was carried out by qPCR and/or ddPCR. We identified 442 different microRNAs in samples, eleven of which were differentially expressed (p < 0.05). Levels of miR-134-5p and miR-320a-3p were significantly down-regulated (p < 0.001) in melanoma samples (n = 96) compared to healthy controls (n = 28). Differentially expressed protein-encoding mRNA 5′-fragments were enriched for the angiopoietin, p21-activated kinase (PAK), and EIF2 pathways. Levels of ATM1, AMFR, SOS1, and CD109 gene fragments were up-regulated (p < 0.001) in melanoma samples (n = 144) compared to healthy controls (n = 41) (AUC = 0.825). Over 40% of mapped reads were YRNAs, a class of non-coding RNAs that to date has been little explored. Expression levels of RNY3P1, RNY4P1, and RNY4P25 were significantly higher in patients with stage 0 disease than either healthy controls or more advanced stage disease (p < 0.001). In conclusion, we have identified a number of novel RNA biomarkers, which, most importantly, we validated in multi-center retrospective and prospective cohorts, suggesting potential diagnostic use of these RNA species.

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“…The analysis of cell‐free RNA (cfRNA) offers the possibility to detect transcriptional gene expression with high sensitivity and detectability. 8 Due to high RNase activities in blood, the fragmentation of long RNA molecules, such as messenger RNA (mRNA), can occur 9 , 10 , 11 ; therefore, previous studies have mainly focused on optimizing technical implementation rather than identifying potential biomarkers due to associated challenges, such as low quality and quantity of RNA in samples. 12 , 13 , 14 Despite a few reports that demonstrated the use of cfRNA as a potential cancer biomarker, 15 , 16 currently, there are no universally applicable and reliable cfRNA biomarker candidates, and clinical application is still under investigation due to lack of standardization.…”

Section: Introductionmentioning

confidence: 99%

Circulating cell‐free messenger RNA enables non‐invasive pan‐tumour monitoring of melanoma therapy independent of the mutational genotype

Albrecht¹,

Höwner²,

Griewank³

et al. 2022

Clinical & Translational Med

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Background Plasma‐derived tumour‐specific cell‐free nucleic acids are increasingly utilized as a minimally invasive, real‐time biomarker approach in many solid tumours. Circulating tumour DNA of melanoma‐specific mutations is currently the best studied liquid biopsy biomarker for melanoma. However, the combination of hotspot genetic alterations covers only around 80% of all melanoma patients. Therefore, alternative approaches are needed to enable the follow‐up of all genotypes, including wild‐type. Methods We identified KPNA2 , DTL , BACE2 and DTYMK messenger RNA (mRNA) upregulated in melanoma versus nevi tissues by unsupervised data mining ( N = 175 melanoma, N = 20 normal skin, N = 6 benign nevi) and experimentally confirmed differential mRNA expression in vitro ( N = 18 melanoma, N = 8 benign nevi). Circulating cell‐free RNA (cfRNA) was analysed in 361 plasma samples (collected before and during therapy) from 100 melanoma patients and 18 healthy donors. Absolute cfRNA copies were quantified on droplet digital PCR. Results KPNA2 , DTL , BACE2 and DTYMK cfRNA demonstrated high diagnostic accuracy between melanoma patients’ and healthy donors’ plasma (AUC > 86%, p < .0001). cfRNA copies increased proportionally with increasing tumour burden independently of demographic variables and even remained elevated in individuals with radiological absence of disease. Re‐analysis of single‐cell transcriptomes revealed a pan‐tumour origin of cfRNA, including endothelial, cancer‐associated fibroblasts, macrophages and B cells beyond melanoma cells as cellular sources. Low baseline cfRNA levels were associated with significantly longer progression‐free survival (PFS) ( KPNA2 HR = .54, p = .0362; DTL HR = .60, p = .0349) and overall survival ( KPNA2 HR = .52, p = .0237; BACE2 HR = .55, p = .0419; DTYMK HR = .43, p = .0393). Lastly, we found that cfRNA copies significantly increased during therapy in non‐responders compared to responders regardless of therapy and mutational subtypes and that the increase of KPNA2 (HR = 1.73, p = .0441) and DTYMK (HR = 1.82, p = .018) cfRNA during therapy was predictive of shorter PFS. Conclusions In sum, we identified a new panel of cfRNAs for...

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Plasma RNA Integrity Analysis

Cited by 11 publications

References 13 publications

Presence and Characterization of Cell-Free Seminal RNA in Healthy Individuals: Implications for Noninvasive Disease Diagnosis and Gene Expression Studies of the Male Reproductive System

Presence and Characterization of Cell-Free Seminal RNA in Healthy Individuals: Implications for Noninvasive Disease Diagnosis and Gene Expression Studies of the Male Reproductive System

The Circulating Transcriptome as a Source of Biomarkers for Melanoma

Circulating cell‐free messenger RNA enables non‐invasive pan‐tumour monitoring of melanoma therapy independent of the mutational genotype

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