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liquid biopsies and exosomal ncRNA: Transforming pancreatic cancer diagnostics and therapeutics

CLINICA CHIMICA ACTA 2025年 567卷 120105页

作者： Balaraman, Ashok Kumar Moglad, Ehssan Afzal, Muhammad Babu, M. Arockia Goyal, Kavita Roopashree, R. Kaur, Irwanjot Kumar, Sachin Kumar, M. Ravi Chauhan, Ashish Singh Hemalatha, S. Gupta, Gaurav Ali, Haider Univ Cyberjaya Persiaran Bestari Cyber 11 Cyberjaya 63000 Selangor Malaysia Prince Sattam Bin Abdulaziz Univ Coll Pharm Dept Pharmacol Al Kharj 11942 Saudi Arabia Dept Pharmaceut Sci Batterjee Med Coll Pharm Program POB 6231 Jeddah 21442 Saudi Arabia GLA Univ Inst Pharmaceut Res Mathura Uttar Pradesh India Graph Era Deemed Univ Dept Biotechnol Bell Rd clement town Dehra Dun Uttarakhand India JAIN Deemed Univ Sch Sci Dept Chem & Biochem Bangalore Karnataka India Vivekananda Global Univ Dept Allied Healthcare & Sci Jaipur 303012 Rajasthan India NIMS Univ Rajasthan NIMS Inst Pharm Jaipur India Raghu Engn Coll Dept Chem Visakhapatnam 531162 Andhra Prades India Uttaranchal Univ Div Res & Innovat Dehra Dun 248007 Uttarakhand India Deemed Univ Sri Ramachandra Inst Higher Educ & Res Sri Ramachandra Fac Pharm Chennai Tamil Nadu India Chitkara Univ Chitkara Coll Pharm Ctr Res Impact & Outcome Rajpura 140401 Punjab India Ajman Univ Ctr Med & Bioallied Hlth Sci Res Ajman U Arab Emirates Saveetha Univ Saveetha Med Coll & Hosp Saveetha Inst Med & Tech Sci Ctr Global Hlth Res Chennai India

Pancreatic cancer is a highly fatal malignancy due to poor early detection rate and resistance to conventional therapies. This review examines the potential for liquid biopsy as a transformative technology to identify diagnostic and therapeutic targets in pancreatic cancer. Specifically, we explore emerging biomarkers such as exosomal non-coding RNAs (ncRNAs), circulating tumor DNA (ctDNA), and circulating tumor cells (CTCs). Tumor-derived exosomes contain nucleic acid and protein that reflect the unique molecular landscape of the malignancy and can serve as an alternative diagnostic approach vs traditional biomarkers like CA19-9. Herein we highlight exosomal miRNAs, lncRNAs, and other ncRNAs alongside ctDNA and CTC-based strategies, evaluating their combined ability to improve early detection, disease monitoring and treatment response. Furthermore, the therapeutic implications of ncRNAs such as lncRNA UCA1 and miR-3960 in chemoresistance and progression are also discussed via suppression of EZH2 and PTEN/AKT pathways. Emerging therapeutic strategies that target the immune response, epithelial-mesenchymal transition (EMT) and drug resistance are explored. This review demonstrates a paradigm shift in pancreatic cancer management toward personalized, less invasive and more effective approaches.

关键词： Pancreatic cancer liquid biopsies Biomarkers ncRNAs miRNAs lncRNAs

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Rapid and Sensitive Digital Droplet PCR Assays for Detecting HPV16 DNA in liquid biopsies

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JOURNAL OF MEDICAL VIROLOGY 2025年第1期97卷 e70146页

作者： Loo, Suet Kee Feng, Jian Reeder, Carly Elias, Danny Azmi Xu, Zhongping Huang, Yufei Contrera, Kevin J. Zevallos, Jose P. Ferris, Robert Gao, Shou-Jiang Univ Pittsburgh UPMC Hillman Canc Ctr Canc Virol ProgramSch Med Pittsburgh PA 15260 USA Univ Pittsburgh Sch Med Dept Microbiol & Mol Genet Pittsburgh PA 15260 USA Univ Pittsburgh UPMC Hillman Canc Ctr Pittsburgh PA 15260 USA Univ Pittsburgh Dept Otolaryngol Pittsburgh PA 15260 USA Univ Pittsburgh Sch Med Dept Med Pittsburgh PA USA

The combination of cell-free DNA (cfDNA) and digital droplet PCR (ddPCR) has significantly advanced the noninvasive screening, diagnosis, and monitoring of diseases, enabling highly sensitive and absolute quantification of target nucleic acids even in the presence of high background DNA. However, widespread adoption of ddPCR is hindered by higher costs, extended processing times, and the requirement for cfDNA purification, which adds expense and variability. To address these limitations, we developed two optimized ddPCR-based assays tailored for enhanced sensitivity, cost-efficiency, and ease of use. Our highly sensitive ddPCR assay for human papilloma virus (HPV)16 DNA detection in purified cfDNA from liquid biopsies from head and neck cancer patients significantly improved sensitivity by increasing cfDNA concentration by 8.5-fold, sample volume loading by 22-fold, and total cfDNA amount tested by 1200-fold without the need for restriction enzyme digestion. In parallel, we established a rapid ddPCR assay using unpurified cfDNA processed by heat treatment and centrifugation, achieving detection concordance rates of 55.6%, 66.7%, and 95.8% for plasma, serum, and surgical drain fluid (SDF), respectively, compared to purified cfDNA. Together, these complementary workflows, one optimized for unpurified cfDNA and the other for purified cfDNA, make ddPCR detection of specific targets in cfDNA more cost-effective, time-efficient, and standardizable across laboratories, paving the way for broader adoption in clinical diagnostics.

关键词： ddPCR digital PCR assay direct detection HPV16 detection liquid biopsies rapid and sensitive assay

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Exosomal ncRNAs in liquid biopsies for lung cancer

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CLINICA CHIMICA ACTA 2025年 565卷 119983页

作者： Hussain, Md Sadique Gupta, Gaurav Ghaboura, Nehmat Moglad, Ehssan Almalki, Waleed Hassan Alzarea, Sami I. Kazmi, Imran Ali, Haider MacLoughlin, Ronan Loebenberg, Raimar Davies, Neal M. Singh, Sachin Kumar Dua, Kamal Uttaranchal Univ Uttaranchal Inst Pharmaceut Sci Dehra Dun India Chitkara Univ Chitkara Coll Pharm Ctr Res Impact & Outcome Rajpura 140401 Punjab India Ajman Univ Ctr Med & Bioallied Hlth Sci Res Ajman U Arab Emirates Batterjee Med Coll Dept Pharm Practice Pharm Program POB 6231 Jeddah 21442 Saudi Arabia Prince Sattam Bin Abdulaziz Univ Coll Pharm Dept Pharmaceut POB 173 Alkharj 11942 Saudi Arabia Umm Al Qura Univ Coll Pharm Dept Pharmacol Mecca Saudi Arabia Jouf Univ Coll Pharm Dept Pharmacol Sakaka 72341 Al Jouf Saudi Arabia King Abdulaziz Univ Fac Sci Dept Biochem Jeddah 21589 Saudi Arabia Saveetha Inst Med & Tech Sci Saveetha Med Coll Ctr Global Hlth Res Div Translat Hlth Res Chennai India Kyrgyz State Med Coll Dept Pharmacol Bishkek Kyrgyzstan Royal Coll Surgeons Ireland Sch Pharm & Biomol Sci Dublin D02 YN77 Leinster Ireland Trinity Coll Dublin Sch Pharm & Pharmaceut Sci Dublin D02 PN40 Leinster Ireland Univ Alberta Fac Pharm & Pharmaceut Sci Edmonton AB T6G 2N8 Canada Lovely Profess Univ Sch Pharmaceut Sci Phagwara 144411 Punjab India Univ Technol Sydney Fac Hlth Australian Res Ctr Complementary & Integrat Med Ultimo NSW 2007 Australia Univ Technol Sydney Grad Sch Hlth Discipline Pharm POB 123 Broadway NSW 2007 Australia Aerogen Ltd Res & Dev Sci & Emerging Technol Galway H91 HE94 Ireland

Exosomal non-coding RNAs (ncRNAs) have become essential contributors to advancing and treating lung cancers (LCs). The development of liquid biopsies that utilize exosomal ncRNAs (exo-ncRNAs) exo-ncRNAs) offers an encouraging method for diagnosing, predicting, and treating LC. This thorough overview examines the dual function of exo-- ncRNAs as both indicators for early diagnosis and avenues for LC treatment. Exosomes are tiny vesicles secreted by various cells, including cancerous cells, enabling connection between cells by delivering ncRNAs. These ncRNAs, which encompass circular RNAs, long ncRNAs, and microRNAs, participate in the modulation of gene expression and cellular functions. In LC, certain exo-ncRNAs are linked to tumour advancement, spread, and treatment resistance, positioning them as promising non-invasive indicators in liquid biopsies. Additionally, targeting these ncRNAs offers potential for innovative treatment approaches, whether by suppressing harmful ncRNAs or reinstating the activity of tumour-suppressing ones. This review emphasizes recent developments in the extraction and analysis of exo-ncRNAs, their practical applications in LC treatment, and the challenges and prospects for translating these discoveries into clinical usage. Through this detailed examination of the current state of the art, we aim to highlight the significant potential of exo-ncRNAs for LC diagnostics and treatments.

关键词： Diagnosis Cancer indicators liquid biopsies Lung cancer Prognosis Therapeutic targets

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liquid biopsies in psychiatric disorders: identifying peripheral biomarkers of brain health

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Neural regeneration research 2025年第2期21卷 2025 Jan 13页

作者： Jennifer L Payne Sarven Sabunciyan Department of Psychiatry and Neurobehavioral Sciences University of Virginia Charlottesville VA USA (Payne JL). Department of Pediatrics Johns Hopkins School of Medicine Baltimore MD USA (Sabunciyan S).

The inability to access brain tissue has greatly hindered our ability to study and care for individuals suffering from psychiatric and neurological *** have questioned efforts to develop peripheral blood biomarkers in neurological and psychiatric disorders based on the assertion that disease pathology is limited to the *** discovery that all tissues,including the brain,release extracellular vesicles(Raposo and Stoorvogel,2013)and cell free DNAs(Chan et al.,2013)into various body fluids has provided a potential way to measure activity from inaccessible tissues like the central nervous system(CNS)and has given rise to the term“liquid biopsy.”The development of liquid biopsies that can diagnose and predict the course of psychiatric and neurological disorders would be *** ability to predict episodic events such as mania,depression,and risk for suicide would be particularly useful for psychiatric care as it would enable the development of interventions that prevent mortality and improve ***,biomarkers that are informative about drug response and aid in treatment decisions would be a significant advance in psychiatric care as it would prevent patients from having to endure multiple courses of ineffective treatments and side effects.

关键词： develop peripheral blood biomarkers liquid biopsies study care individuals cell free dnas chan extracellular vesicles raposo body fluids neurological psychiatric disorders peripheral biomarkers

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liquid biopsies to Select Patients for Perioperative Chemotherapy in Muscle-invasive Bladder Cancer: A Systematic Review

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EUROPEAN UROLOGY ONCOLOGY 2021年第2期4卷 204-214页

作者： de Kruijff, Ingeborg E. Beije, Nick Martens, John W. M. de Wit, Ronald Boormans, Joost L. Sleijfer, Stefan Erasmus MC Erasmus MC Canc Inst Dept Med Oncol & Canc Genom Netherlands Rotterdam Netherlands Erasmus MC Erasmus MC Canc Inst Dept Urol Rotterdam Netherlands

Context: Neoadjuvant chemotherapy (NAC) is considered the standard treatment for muscle-invasive bladder cancer (MIBC). However, its overall survival benefit is limited and toxicity is significant;hence, NAC has not been adopted universally. Objective: To systematically evaluate whether biomarkers can guide the administration of perioperative chemotherapy in MIBC patients. Evidence acquisition: A systematic search of the PubMed database was performed according to the Preferred Reporting Items for Systematic Reviews and Meta analyses (PRISMA). In total, 215 papers were screened and 22 were selected to assess the potential clinical value of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) in selecting MIBC patients for perioperative chemotherapy. Evidence synthesis: We found that the presence of one or more CTCs before radical cystectomy, as determined by the CellSearch technique, is a robust marker for poor recurrence-free and overall survival. Consequently, whether NAC can be withheld in patients without the presence of CTCs is a subject of ongoing investigation. Studies investigating various approaches to detect cfDNA showed that cfDNA is present in the blood of MIBC patients, but varying results on its prognostic value have been reported. Successful cfDNA-based approaches are likely to encompass at least a multitude of genes using next-generation sequencing, as there are generally few hotspot somatic mutations in MIBC. Conclusions: liquid biopsies hold promise in selecting MIBC patients for perioperative chemotherapy, but instead of more proof-of-principle studies, prospective studies investigating true clinical applicability for treatment decision making are urgently needed. Patient summary: liquid biopsies appear to be a promising tool to guide the administration of chemotherapy in patients with muscle-invasive bladder cancer;however, the optimal way to implement these remains to be determined. (c) 2020 European Association of Urology. Published by Elsev

关键词： Cell-free DNA Circulating tumor cells Muscle-invasive bladder cancer liquid biopsies Perioperative therapy

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liquid biopsies in pancreatic cancer

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EXPERT REVIEW OF ANTICANCER THERAPY 2019年第10期19卷 869-878页

作者： Kamyabi, Nabiollah Bernard, Vincent Maitra, Anirban UT MD Anderson Canc Ctr Dept Translat Mol Pathol Houston TX 77030 USA UT MD Anderson Canc Ctr Sheikh Ahmed Ctr Pancreat Canc Res Houston TX 77030 USA

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a disease of high lethality. Invasive tissue biopsies of primary or metastatic lesions remain the gold standard for diagnosis, but repeated sampling is infeasible. Noninvasive liquid biopsies offer new opportunities for early diagnosis for high-risk cohorts, and for the longitudinal analysis of tumor evolution and progression in patients on therapy. liquid biopsies can capture tumor-associated components, such as circulating tumor DNA (ctDNA), extracellular vesicles (EVs), and circulating tumor cells (CTCs), each of which provides genomic and molecular information about the underlying PDAC that can potentially inform clinical decisions. Areas covered: Here, we reviewed current knowledge and recent technological advances regarding liquid biopsy in PDAC and mention the pitfalls and benefits in each methodology. We also discuss clinical correlative studies for diagnosis and prognosis in PDAC. Expert opinion:In pancreatic cancer where tissue samples are limited and repeated tissue biopsies are mostly invasive and infeasible, liquid biopsies opened a new window for tumor diagnosis, molecular stratification, and treatment monitoring. While none of the isolation and analysis methods have gained widespread clinical acceptance, it is imperative that the advantages and limitations of each platform for isolation and analysis of tumor associated components are taken into consideration.

关键词： Cell-free DNA circulating tumor cells extracellular vesicles liquid biopsies pancreatic cancer

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liquid biopsies in patients with diffuse glioma

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ACTA NEUROPATHOLOGICA 2015年第6期129卷 849-865页

作者： Best, Myron G. Sol, Nik Zijl, Sebastiaan Reijneveld, Jaap C. Wesseling, Pieter Wurdinger, Thomas Vrije Univ Amsterdam Med Ctr Canc Ctr Amsterdam Neurooncol Res Grp NL-1081 HV Amsterdam Netherlands Vrije Univ Amsterdam Med Ctr Canc Ctr Amsterdam Dept Neurosurg NL-1081 HV Amsterdam Netherlands Vrije Univ Amsterdam Med Ctr Canc Ctr Amsterdam Dept Pathol NL-1081 HV Amsterdam Netherlands Vrije Univ Amsterdam Med Ctr Canc Ctr Amsterdam Dept Neurol NL-1081 HV Amsterdam Netherlands Radboud Univ Nijmegen Med Ctr Dept Pathol NL-6525 ED Nijmegen Netherlands Harvard Univ Massachusetts Gen Hosp Sch Med Dept Neurol Boston MA USA ThromboDx BV Amsterdam Netherlands

Diffuse gliomas are the most common malignant primary tumors of the central nervous system. Like other neoplasms, these gliomas release molecular information into the circulation. Tumor-derived biomarkers include proteins, nucleic acids, and tumor-derived extracellular vesicles that accumulate in plasma, serum, blood platelets, urine and/or cerebrospinal fluid. Recently, also circulating tumor cells have been identified in the blood of glioma patients. Circulating molecules, vesicles, platelets, and cells may be useful as easily accessible diagnostic, prognostic and/or predictive biomarkers to guide patient management. Thereby, this approach may help to circumvent problems related to tumor heterogeneity and sampling error at the time of diagnosis. Also, liquid biopsies may allow for serial monitoring of treatment responses and of changes in the molecular characteristics of gliomas over time. In this review, we summarize the literature on blood-based biomarkers and their potential value for improving the management of patients with a diffuse glioma. Incorporation of the study of circulating molecular biomarkers in clinical trials is essential for further assessment of the potential of liquid biopsies in this context.

关键词： Malignant glioma Minimally invasive biomarkers liquid biopsies Molecular diagnostics

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Clinical applications of (epi)genetics in gastroenteropancreatic neuroendocrine neoplasms: Moving towards liquid biopsies

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REVIEWS IN ENDOCRINE & METABOLIC DISORDERS 2019年第3期20卷 333-351页

作者： Boons, Gitta Vandamme, Timon Peeters, Marc Van Camp, Guy Op de Beeck, Ken Univ Antwerp Ctr Oncol Res CORE Univ Pl 1 B-2610 Antwerp Belgium Antwerp Univ Hosp Univ Pl 1 B-2610 Antwerp Belgium Univ Antwerp Ctr Med Genet Prins Boudewijnlaan 43 B-2650 Edegem Belgium Antwerp Univ Hosp Prins Boudewijnlaan 43 B-2650 Edegem Belgium Erasmus MC Div Endocrinol Dept Internal Med Dr Molewaterpl 50 NL-3015 GE Rotterdam Netherlands

High-throughput analysis, including next-generation sequencing and microarrays, have strongly improved our understanding of cancer biology. However, genomic data on rare cancer types, such as neuroendocrine neoplasms, has been lagging behind. Neuroendocrine neoplasms (NENs) develop from endocrine cells spread throughout the body and are highly heterogeneous in biological behavior. In this challenging disease, there is an urgent need for new therapies and new diagnostic, prognostic, follow-up and predictive biomarkers to aid patient management. The last decade, molecular data on neuroendocrine neoplasms of the gastrointestinal tract and pancreas, termed gastroenteropancreatic NENs (GEP-NENs), has strongly expanded. The aim of this review is to give an overview of the recent advances on (epi)genetic level and highlight their clinical applications to address the current needs in GEP-NENs. We illustrate how molecular alterations can be and are being used as therapeutic targets, how mutations in DAXX/ATRX and copy number variations could be used as prognostic biomarkers, how far we are in identifying predictive biomarkers and how genetics can contribute to GEP-NEN classification. Finally, we discuss recent studies on liquid biopsies in the field of GEP-NENs and illustrate how liquid biopsies can play a role in patient management. In conclusion, molecular studies have suggested multiple potential biomarkers, but further validation is ongoing.

关键词： Gastroenteropancreatic Neuroendocrine Neoplasms Genetics Epigenetics Biomarkers liquid biopsies

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Exploring the tumor genomic landscape of aggressive prostate cancer by whole-genome sequencing of tissue or liquid biopsies

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INTERNATIONAL JOURNAL OF CANCER 2024年第2期155卷 298-313页

作者： Weiss, Simone Lamy, Philippe Rusan, Maria Norgaard, Maibritt Ulhoi, Benedicte Parm Knudsen, Michael Kassentoft, Christine Gaasdal Farajzadeh, Leila Jensen, Jorgen Bjerggaard Pedersen, Jakob Skou Borre, Michael Sorensen, Karina Dalsgaard Aarhus Univ Hosp Dept Mol Med Aarhus Denmark Aarhus Univ Dept Clin Med Aarhus Denmark Aarhus Univ Hosp Dept Clin Immunol Aarhus Denmark Aarhus Univ Hosp Dept Pathol Aarhus Denmark Aarhus Univ Dept Biomed Aarhus Denmark Godstrup Hosp Dept Urol Godstrup Denmark Aarhus Univ Bioinformat Res Ctr Aarhus Denmark Aarhus Univ Hosp Dept Urol Aarhus Denmark Aarhus Univ Dept Clin Med Palle Juul Jensens Blvd 82 DK-8200 Aarhus N Denmark

Treatment resistance remains a major issue in aggressive prostate cancer (PC), and novel genomic biomarkers may guide better treatment selection. Circulating tumor DNA (ctDNA) can provide minimally invasive information about tumor genomes, but the genomic landscape of aggressive PC based on whole-genome sequencing (WGS) of ctDNA remains incompletely characterized. Thus, we here performed WGS of tumor tissue (n = 31) or plasma ctDNA (n = 10) from a total of 41 aggressive PC patients, including 11 hormone-naive, 15 hormone-sensitive, and 15 castration-resistant patients. Across all variant types, we found progressively more altered tumor genomic profiles in later stages of aggressive PC. The potential driver genes most frequently affected by single-nucleotide variants or insertions/deletions included the known PC-related genes TP53, CDK12, and PTEN and the novel genes COL13A1, KCNH3, and SENP3. Etiologically, aggressive PC was associated with age-related and DNA repair-related mutational signatures. Copy number variants most frequently affected 14q11.2 and 8p21.2, where no well-recognized PC-related genes are located, and also frequently affected regions near the known PC-related genes MYC, AR, TP53, PTEN, and BRCA1. Structural variants most frequently involved not only the known PC-related genes TMPRSS2 and ERG but also the less extensively studied gene in this context, PTPRD. Finally, clinically actionable variants were detected throughout all stages of aggressive PC and in both plasma and tissue samples, emphasizing the potential clinical applicability of WGS of minimally invasive plasma samples. Overall, our study highlights the feasibility of using liquid biopsies for comprehensive genomic characterization as an alternative to tissue biopsies in advanced/aggressive PC. Circulating tumor DNA can provide valuable information about tumor genomes in a minimally invasive manner. This study using whole-genome sequencing of tumor tissue and plasma circulating tumor DNA

关键词： ctDNA genomics liquid biopsies prostate cancer whole-genome sequencing

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The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review

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EUROPEAN JOURNAL OF PEDIATRICS 2020年第2期179卷 191-202页

作者： Van Paemel, Ruben Vlug, Roos De Preter, Katleen Van Roy, Nadine Speleman, Frank Willems, Leen Lammens, Tim Laureys, Genevieve Schleiermacher, Gudrun Tytgat, Godelieve A. M. Astrahantseff, Kathy Deubzer, Hedwig De Wilde, Bram Ghent Univ Hosp Ctr Med Genet Ghent Belgium CRIG Ghent Belgium Ghent Univ Hosp Dept Pediat Hematol Oncol & Stem Cell Transplanta C Heymanslaan 10 B-9000 Ghent Belgium PSL Res Univ Inst Curie INSERM Res CtrLab Genet & Biol CancU830 Paris France PSL Res Univ Inst Curie SiRIC RTOP Rech Translationelle Oncol Pediat Translat Res DeptRes Ctr Paris France Inst Curie Hosp Grp Dept Pediat Oncol Paris France Princess Maxima Ctr Pediat Oncol Utrecht Netherlands Charite Univ Med Berlin Dept Pediat Hematol & Oncol Berlin Germany BIH Berlin Germany ECRC Neuroblastoma Res Grp Berlin Germany

Cell-free DNA profiling using patient blood is emerging as a non-invasive complementary technique for cancer genomic characterization. Since these liquid biopsies will soon be integrated into clinical trial protocols for pediatric cancer treatment, clinicians should be informed about potential applications and advantages but also weaknesses and potential pitfalls. Small retrospective studies comparing genetic alterations detected in liquid biopsies with tumor biopsies for pediatric solid tumor types are encouraging. Molecular detection of tumor markers in cell-free DNA could be used for earlier therapy response monitoring and residual disease detection as well as enabling detection of pathognomonic and therapeutically relevant genomic alterations. Conclusion: Existing analyses of liquid biopsies from children with solid tumors increasingly suggest a potential relevance for molecular diagnostics, prognostic assessment, and therapeutic decision-making. Gaps remain in the types of tumors studied and value of detection methods applied. Here we review the current stand of liquid biopsy studies for pediatric solid tumors with a dedicated focus on cell-free DNA analysis. There is legitimate hope that integrating fully validated liquid biopsy-based innovations into the standard of care will advance patient monitoring and personalized treatment of children battling solid cancers.

关键词： liquid biopsies Pediatric solid tumors Cell-free DNA profiling

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