Patient-specific alterations in blood plasma cfRNA profiles enable accurate classification of cancer patients and controls DOI Creative Commons
Annelien Morlion, Philippe Decruyenaere, Kathleen Schoofs

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 28, 2023

Abstract Circulating nucleic acids in blood plasma form an attractive resource to study human health and disease. Here, we applied mRNA capture sequencing of cell-free RNA from 266 cancer patients cancer-free controls (discovery n = 208, 25 types; replication 58, 3 types). We observed type-specific as well pan-cancer alterations transcriptomes compared controls. Differentially abundant RNAs were heterogenous among cohorts, hampering identification robust biomarkers. Therefore, developed a novel method that compares each individual patient reference control population identify so-called biomarker tail genes. The number genes sample enables distinguishing potential this approach was confirmed additional cohorts 65 donors (2 lymphoma types) 24 urine (bladder cancer). Together, our findings demonstrate heterogeneity propose case-specific can be exploited for classification purposes.

Language: Английский

The systematic role of pancreatic cancer exosomes: distant communication, liquid biopsy and future therapy DOI Creative Commons
Cheng‐Feng Qin, Tianyu Li, Lin Chen

et al.

Cancer Cell International, Journal Year: 2024, Volume and Issue: 24(1)

Published: July 25, 2024

Abstract Pancreatic cancer remains one of the most lethal diseases worldwide. Cancer-derived exosomes, benefiting from protective role lipid membrane, exhibit remarkable stability in circulatory system. These released by tumor microenvironment, contain various biomolecules such as proteins, RNAs, and lipids that plays a pivotal mediating distant communication between local pancreatic other organs or tissues. They facilitate transfer oncogenic factors to sites, contributing compromised body immune system, metastasis, diabetes, cachexia, promoting microenvironment conducive growth metastasis patients. Beyond their intrinsic roles, circulating exosomes peripheral blood can be detected accurate liquid biopsy. This approach offers novel promising method for diagnosis management cancer. Consequently, are not only crucial mediators systemic cell-cell during progression but also hold great potential precise tools treatment. Exosome-based biopsy therapy represent advancements treatment Exosomes serve drug delivery vehicles, enhancing targeting efficacy anticancer treatments, modulating facilitating gene editing suppress growth. Ongoing research focuses on biomarker identification, systems, clinical trials validate safety exosome-based therapies, offering new possibilities early precision Leveraging therapeutic including ability deliver targeted drugs modulate responses, opens avenues innovative strategies.

Language: Английский

Citations

6
Utilizing nullomers in cell-free RNA for early cancer detection DOI Creative Commons
Austin Montgomery,

Georgios Christos Tsiatsianis,

Ioannis Mouratidis

et al.

Cancer Gene Therapy, Journal Year: 2024, Volume and Issue: 31(6), P. 861 - 870

Published: Feb. 14, 2024

Abstract Early detection of cancer can significantly improve patient outcomes; however, sensitive and highly specific biomarkers for are currently missing. Nullomers the shortest sequences that absent from human genome but emerge due to somatic mutations in cancer. We examine over 10,000 whole exome sequencing matched tumor-normal samples characterize nullomer emergence across exonic regions genome. also identify emerging mutational hotspots within tumor genes. Finally, we provide evidence identification nullomers cell-free RNA peripheral blood samples, enabling multiple types. show classification models with an AUC greater than 0.9, including a hepatocellular carcinoma classifier 0.99.

Language: Английский

Citations

5
A Comprehensive Review on Circulating cfRNA in Plasma: Implications for Disease Diagnosis and Beyond DOI Creative Commons

Pengqiang Zhong,

Lu Bai,

Mengzhi Hong

et al.

Diagnostics, Journal Year: 2024, Volume and Issue: 14(10), P. 1045 - 1045

Published: May 17, 2024

Circulating cfRNA in plasma has emerged as a fascinating area of research with potential applications disease diagnosis, monitoring, and personalized medicine. RNA sequencing technology allows for the non-invasive collection important information about expression target genes, eliminating need biopsies. This comprehensive review aims to provide detailed overview current knowledge advancements study cfRNA, focusing on its diverse landscape biological functions, detection methods, diagnostic prognostic various diseases, challenges, future perspectives.

Language: Английский

Citations

5
Depletion‐assisted multiplexed cell‐free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles DOI Creative Commons
Hongke Wang,

Qing Zhan,

Menɡ Ninɡ

et al.

Clinical and Translational Medicine, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

Abstract Background Cell‐free long RNAs in human plasma and extracellular vesicles (EVs) have shown promise as biomarkers liquid biopsy, despite their fragmented nature. Methods To investigate these cell‐free (cfRNAs), we developed a cost‐effective cfRNA sequencing method called DETECTOR‐seq (depletion‐assisted multiplexed total RNA sequencing). utilised meticulously tailored set of customised guide to remove large amounts unwanted (i.e., ribosomal mitochondrial RNAs) plasma. Early barcoding strategy was implemented reduce costs minimise requirements. Results Using DETECTOR‐seq, conducted comprehensive analysis transcriptomes both whole EVs. Our revealed discernible distributions types Plasma exhibited pronounced enrichment structured circular RNAs, tRNAs, Y viral while EVs showed messenger (mRNAs) signal recognition particle (srpRNAs). Functional pathway highlighted splicing‐related ribonucleoproteins (RNPs) antimicrobial humoral response genes plasma, demonstrated transcriptional activity, cell migration antigen receptor‐mediated immune signals. study indicates the comparable potential cfRNAs from distinguishing cancer patients colorectal lung cancer) healthy donors. And microbial classifying specific types. Conclusions EV paired samples provides valuable insights for determining need purification cfRNA‐based studies. We envision cost effectiveness efficiency will empower transcriptome‐wide investigations fields biopsy. Keypoints sequencing) enabled efficient depletion sequences derived Distinct (cfRNA) signatures versus were revealed. Both capable normal individuals, better classification than cfRNAs.

Language: Английский

Citations

5
Circulating small extracellular vesicle-based miRNA classifier for follicular thyroid carcinoma: a diagnostic study DOI
Genpeng Li, Hongke Wang,

Jinjing Zhong

et al.

British Journal of Cancer, Journal Year: 2024, Volume and Issue: 130(6), P. 925 - 933

Published: Jan. 18, 2024

Language: Английский

Citations

4
Introduction: navigating the landscape of cancer biomarkers DOI

J. N. Baruah,

Sthiti Porna Dutta, Partha Pratim Das

et al.

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 41

Published: Jan. 1, 2025

Language: Английский

Citations

0
Detection of reproducible liver cancer specific ligand-receptor signaling in blood DOI Creative Commons
Aram Safrastyan, Damian Wollny

Frontiers in Bioinformatics, Journal Year: 2025, Volume and Issue: 4

Published: Jan. 9, 2025

Cell-cell communication mediated by ligand-receptor interactions (LRI) is critical to coordinating diverse biological processes in homeostasis and disease. Lately, our understanding of these has greatly expanded through the inference cellular communication, utilizing RNA extracted from bulk tissue or individual cells. Considering challenge obtaining biopsies for approaches, we considered potential studying cell-free obtained blood. To test feasibility this approach, used BulkSignalR algorithm across 295 samples compared LRI profiles multiple cancer types healthy donors. Interestingly, detected specific reproducible LRIs particularly blood liver patients We found an increase magnitude hepatocyte interactions, notably autocrine patients. Additionally, a robust panel 30 cancer-specific presents bridge linking pathogenesis discernible markers. In summary, approach shows plausibility detecting builds upon transcriptomes.

Language: Английский

Citations

0
Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring DOI Creative Commons

Xinxin Wang,

Shaogang Li,

Rijing Ou

et al.

RNA Biology, Journal Year: 2025, Volume and Issue: unknown

Published: March 20, 2025

Circulating cell-free RNA (cfRNA) has emerged as a promising analyte for disease detection. However, the comprehensive profiling of diverse cfRNA types remains under-characterized. Here, we applied new wide-spectrum sequencing method and simultaneously captured rRNA, tRNA, mRNA, miRNA, lncRNA, all mitochondrial RNA. The compositions, size distributions, highly abundant genes were analyzed each type cfRNA. We depicted cell origin profiles 66 generally healthy individuals found that BMI showed significant impact on kidney-derived proportion. Three with some liver problems identified because relatively high levels hepatocyte-specific abundance different types, including miRNA significantly correlated function test results. individual variances enriched in pathways associated common diseases such diseases, virus infections, cancers, metabolic diseases. This study provided displayed potential biomarker health monitoring.

Language: Английский

Citations

0
Comprehensive evaluation of methods for identifying tissues or cell types of origin of the plasma cell-free transcriptome DOI Creative Commons
Tingyu Yang,

Yulong Qin,

Shuo Yan

et al.

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19241 - e19241

Published: April 17, 2025

Plasma cell-free RNA (cfRNA) is derived from cells in various tissues and organs throughout the body reflects physiological pathological conditions. Identifying origins of cfRNA essential for comprehending its variations. Only a few tools are designed deconvolution, most studies have relied on traditional bulk methods. In this study, we employed human tissue cell transcriptomic data as reference sets evaluated performance seven deconvolution methods cfRNA. We compared analysis results types origin plasma chose to use single-cell sequencing (scRNA-seq) conduct further evaluation Subsequently, assessed accuracy robustness by utilizing simulated generated scRNA-seq. also methods’ real analyzing correlation between predicted proportions corresponding clinical indicators. Moreover, effectiveness revealing impacts diseases cancer classification models based they provided. summary, our study provides valuable insights into analysis, enhancing potential biomedical research.

Language: Английский

Citations

0
Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study DOI Creative Commons

Zhongkun Zhou,

Yunhao Ma, Dekui Zhang

et al.

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

ABSTRACT Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of human microbiome plays important roles in occurrence development CRC. Recently, blood has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 feces 120 samples are collected, including healthy individuals, adenoma patients, patients. The cfDNA fecal genome subjected to shotgun metagenome sequencing. After removing sequences, microbial sequences analyzed. Based differential microbes functions, random forest (RF) models constructed diagnosis. results show that alterations signatures captured under low coverage (even at 3×). RF based markers achieve high area curve (AUC) values patients (0.8849) (0.9824). When fragmentation pattern combined with KEGG markers, higher AUC obtained. Furthermore, compared microbiome, shows different community composition, whereas their changes pathways similar. Pathogenic bacteria Fusobacterium nucleatum ( F. ) increased gradually from group groups. Additionally, positive correlation Cumulatively, integration promising IMPORTANCE cell-free DNA enter used diagnosis, potential colorectal association gut not explored. account less than 1% total sequences. among Machine learning these characteristics accuracy, especially when they integrated patterns. great difference between microbiomes indicates may originate organs. Therefore, study provides new insights into composition functions proposes non-invasive tool.

Language: Английский

Citations

0