Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids

Liu, Zhongzhen; Wang, Taifu; Yang, Xi; Zhou, Qing; Zhu, Shuifang; Zeng, Juan; Chen, Haixiao; Sun, Jinghua; Li, Liqiang; Xu, Jinjin; Geng, Chunyu; Xu, Xun; Wang, Jian; Yang, Huanming; Zhu, Shida; Chen, Fang; Wang, Wen‐Jing

doi:10.1002/ctm2.987

Cited by 13 publications

(15 citation statements)

References 88 publications

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“…Protocols for handling RNA are improved constantly, in particular by the fields of single-cell transcriptomics and liquid biopsy. 21,32,33 Thus, diagnostic applications can also benefit from optimizations, particularly by the single-cell field. The implementation of these methods is cheap in regard to the low amounts of expensive reagents used (e.g.…”

Section: Discussionmentioning

confidence: 99%

RNA-based sensitive fungal pathogen detection

Micheel,

Aron,

Kelani

et al. 2023

Preprint

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Detecting fungal pathogens, a major cause of severe systemic infections, remains challenging due to the difficulty and time-consuming nature of diagnostic methods. This delay in identification hinders targeted treatment decisions and may lead to unnecessary use of broad-spectrum antibiotics. To expedite treatment initiation, one promising approach is to directly detect pathogen nucleic acids such as DNA, which is often preferred to RNA because of its inherent stability. However, a higher number of RNA molecules per cell makes RNA a more promising diagnostic target which is particularly prominent for highly expressed genes such as rRNA. Here, we investigated the utility of a minimal input-specialized reverse transcription protocol to increase diagnostic sensitivity. This proof-of-concept study demonstrates that fungal rRNA detection by the minimal input protocol is drastically more sensitive compared to detection of genomic DNA even with high levels of human RNA background. This approach can detect several of the most relevant human pathogenic fungal genera, such asAspergillus, Candida, andFusariumand thus represents a powerful, cheap, and easily adaptable addition to currently available diagnostic assays.

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Section: Discussionmentioning

confidence: 99%

RNA-based sensitive fungal pathogen detection

Micheel,

Aron,

Kelani

et al. 2023

Preprint

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“…Both ctDNA and ctRNA contain mutational information, but ctRNA can also provide information about the quantitative expression levels of genes of interest [ 47 ]. Similar to ctDNA, ctRNA is likely released from apoptotic or necrotic cells but may also be released in exosomes (discussed below), which protect them from degradation [ 46 , 48 ]. RNAs that are not encapsulated are also released into bodily fluids, but certain classes (e.g., mRNAs and lncRNAs) are more likely to be degraded by ribonucleases (RNases) [ 15 , 49 ].…”

Section: Sample Types and Materials For Biomarker Analysismentioning

confidence: 99%

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Brockley¹,

Souza

Forder³

et al. 2023

Cancers

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Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.

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“…cfRNAs are detected in the bloodstream and other body fluids. Similarly to ctDNAs, a subset of these may be released from tumor cells [115,116]. There are several classes of RNA that can be found in circulation, including messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs).…”

Section: Cell-free Rnas (Cfrnas)mentioning

confidence: 99%

“…Beyond the therapy response, measuring the levels of mRNAs from saliva in combination with the presence of CTCs has been shown to discern NSCLC patients from healthy controls [122]. However, due to the presence of ribonucleases in the blood, mRNAs are generally fragmented in circulation and thus give low-quality reads when analyzed by sequencing [116].…”

Section: Cell-free Rnas (Cfrnas)mentioning

confidence: 99%

Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis

Souza

Forder²,

Brockley³

et al. 2023

IJMS

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Liquid biopsies have emerged as a promising tool for the detection of metastases as well as local and regional recurrence in lung cancer. Liquid biopsy tests involve analyzing a patient’s blood, urine, or other body fluids for the detection of biomarkers, including circulating tumor cells or tumor-derived DNA/RNA that have been shed into the bloodstream. Studies have shown that liquid biopsies can detect lung cancer metastases with high accuracy and sensitivity, even before they are visible on imaging scans. Such tests are valuable for early intervention and personalized treatment, aiming to improve patient outcomes. Liquid biopsies are also minimally invasive compared to traditional tissue biopsies, which require the removal of a sample of the tumor for further analysis. This makes liquid biopsies a more convenient and less risky option for patients, particularly those who are not good candidates for invasive procedures due to other medical conditions. While liquid biopsies for lung cancer metastases and relapse are still being developed and validated, they hold great promise for improving the detection and treatment of this deadly disease. Herein, we summarize available and novel approaches to liquid biopsy tests for lung cancer metastases and recurrence detection and describe their applications in clinical practice.

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Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids

Cited by 13 publications

References 88 publications

RNA-based sensitive fungal pathogen detection

RNA-based sensitive fungal pathogen detection

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis

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