1
|
Sadique Hussain M, Gupta G, Ghaboura N, Moglad E, Hassan Almalki W, Alzarea SI, Kazmi I, Ali H, MacLoughlin R, Loebenberg R, Davies N, Kumar Singh S, Dua K. Exosomal ncRNAs in liquid biopsies for lung cancer. Clin Chim Acta 2024; 565:119983. [PMID: 39368685 DOI: 10.1016/j.cca.2024.119983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 09/30/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]
Abstract
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) 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.
Collapse
Affiliation(s)
- Md Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Nehmat Ghaboura
- Department of Pharmacy Practice, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Alkharj 11942, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haider Ali
- Division of Translational Health Research, Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Ronan MacLoughlin
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Leinster D02 YN77, Ireland; School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, Leinster D02 PN40, Ireland
| | - Raimar Loebenberg
- University of Alberta, Faculty of Pharmacy and Pharmaceutical Sciences, Edmonton, AB, T6G2N8, Canada
| | - Neal Davies
- University of Alberta, Faculty of Pharmacy and Pharmaceutical Sciences, Edmonton, AB, T6G2N8, Canada
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, P.O. Box: 123, Broadway, Ultimo, NSW, 2007, Australia
| |
Collapse
|
2
|
Rahimi S, Balusamy SR, Perumalsamy H, Ståhlberg A, Mijakovic I. CRISPR-Cas target recognition for sensing viral and cancer biomarkers. Nucleic Acids Res 2024; 52:10040-10067. [PMID: 39189452 PMCID: PMC11417378 DOI: 10.1093/nar/gkae736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024] Open
Abstract
Nucleic acid-based diagnostics is a promising venue for detection of pathogens causing infectious diseases and mutations related to cancer. However, this type of diagnostics still faces certain challenges, and there is a need for more robust, simple and cost-effective methods. Clustered regularly interspaced short palindromic repeats (CRISPRs), the adaptive immune systems present in the prokaryotes, has recently been developed for specific detection of nucleic acids. In this review, structural and functional differences of CRISPR-Cas proteins Cas9, Cas12 and Cas13 are outlined. Thereafter, recent reports about applications of these Cas proteins for detection of viral genomes and cancer biomarkers are discussed. Further, we highlight the challenges associated with using these technologies to replace the current diagnostic approaches and outline the points that need to be considered for designing an ideal Cas-based detection system for nucleic acids.
Collapse
Affiliation(s)
- Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Sri Renukadevi Balusamy
- Department of Food Science and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Republic of Korea
| | - Haribalan Perumalsamy
- Center for Creative Convergence Education, Hanyang University, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, South Korea
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
3
|
Kfoury M, Bonnet C, Delanoy N, Howarth K, Marzac C, Rouleau E, Micol JB, Leary A. Dynamic changes in TP53 mutated circulating tumor DNA predicts outcome of patients with high-grade ovarian carcinomas. Int J Gynecol Cancer 2024:ijgc-2024-005581. [PMID: 39313297 DOI: 10.1136/ijgc-2024-005581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024] Open
Abstract
There is a lack of biomarkers to predict outcome following initial treatment in patients with high-grade ovarian cancer. We hypothesized that monitoring TP53 mutation (TP53m) in circulating tumor DNA (ctDNA) could be a tumor-specific biomarker. Patients enrolled in a prospective study (NCT03010124) consented to analysis of biological samples through the disease course. ctDNA was extracted and analyzed to detect the presence of TP53m Next-generation sequencing was performed on tumor tissue to detect TP53m and on whole blood to detect clonal hematopoiesis of indeterminate potential (CHIP).A total of 102 samples were sequentially collected from 26 patients. ctDNA was detected in all patients at diagnosis. The same TP53m was found in ctDNA and tumor tissue in 77% of patients. TP53m in ctDNA was not CHIP related. During neoadjuvant chemotherapy, increasing ctDNA was associated with failure to achieve complete interval cytoreductive surgery in 60% of patients. Rising ctDNA or de novo TP53m seemed to be associated with a trend for worst survival compared with decrease or complete clearance: progression-free survival 10 versus 26.5 months, HR 3.2. Despite macroscopically complete surgery, 30% of patients had detectable ctDNA post-operatively and had worse survival than those with undetectable ctDNA. Monitoring TP53m in ctDNA during chemotherapy or after surgery could help guide the best adjuvant therapy.
Collapse
Affiliation(s)
- Maria Kfoury
- Medical Oncology Department, Institut Gustave-Roussy, Villejuif, Île-de-France, France
- Medical Oncology Department, Institut Paoli-Calmettes, Marseille, France
| | - Clément Bonnet
- Medical Oncology Department, Institut Curie, Paris, France
| | - Nicolas Delanoy
- Medical Oncology Department, Université de Paris, Paris, France
| | | | | | - Etienne Rouleau
- Medical Biology and Pathology Department, Institut Gustave-Roussy, Villejuif, Île-de-France, France
| | - Jean-Baptiste Micol
- Université Paris-Saclay, Gif-sur-Yvette, France
- Hematology Department, Institut Gustave-Roussy, Villejuif, Île-de-France, France
| | - Alexandra Leary
- Medical Oncology Department, Institut Gustave-Roussy, Villejuif, Île-de-France, France
| |
Collapse
|
4
|
Müller J, Hartwig C, Sonntag M, Bitzer L, Adelmann C, Vainshtein Y, Glanz K, Decker SO, Brenner T, Weber GF, von Haeseler A, Sohn K. A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma. Genome Res 2024; 34:gr.279326.124. [PMID: 39271293 PMCID: PMC11444180 DOI: 10.1101/gr.279326.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/12/2024] [Indexed: 09/15/2024]
Abstract
Here, we present a method for enrichment of double-stranded cfDNA with an average length of ∼40 bp from cfDNA for high-throughput DNA sequencing. This class of cfDNA is enriched at gene promoters and binding sites of transcription factors or structural DNA-binding proteins, so that a genome-wide DNA footprint is directly captured from liquid biopsies. In short double-stranded cfDNA from healthy individuals, we find significant enrichment of 203 transcription factor motifs. Additionally, short double-stranded cfDNA signals at specific genomic regions correlate negatively with DNA methylation, positively with H3K4me3 histone modifications and gene transcription. The diagnostic potential of short double-stranded cell-free DNA (cfDNA) in blood plasma has not yet been recognized. When comparing short double-stranded cfDNA from patient samples of pancreatic ductal adenocarcinoma with colorectal carcinoma or septic with postoperative controls, we identify 136 and 241 differentially enriched loci, respectively. Using these differentially enriched loci, the disease types can be clearly distinguished by principal component analysis, demonstrating the diagnostic potential of short double-stranded cfDNA signals as a new class of biomarkers for liquid biopsies.
Collapse
Affiliation(s)
- Jan Müller
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
- Max Perutz Labs, Vienna Biocenter Campus, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Structural and Computational Biology, Center of Integrative Bioinformatics Vienna, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Christina Hartwig
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
- Institute for Interfacial Engineering and Plasma Technology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Mirko Sonntag
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
- Interfaculty Graduate School of Infection Biology and Microbiology, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Lisa Bitzer
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Christopher Adelmann
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Yevhen Vainshtein
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Karolina Glanz
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Sebastian O Decker
- Heidelberg University, Medical Faculty Heidelberg, Department of Anesthesiology, 69120 Heidelberg, Germany
| | - Thorsten Brenner
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Georg F Weber
- Department of Surgery, Friedrich-Alexander University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Arndt von Haeseler
- Center of Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
- University of Vienna, Faculty of Computer Science Bioinformatics and Computational Biology, 1090 Vienna, Austria
| | - Kai Sohn
- Innovation Field In-vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany;
| |
Collapse
|
5
|
Abramovic I, Pezelj I, Dumbovic L, Skara Abramovic L, Vodopic T, Bulimbasic S, Stimac G, Bulic-Jakus F, Kulis T, Katusic Bojanac A, Tomas D, Ulamec M, Sincic N. LGALS3 cfDNA methylation in seminal fluid as a novel prostate cancer biomarker outperforming PSA. Prostate 2024; 84:1128-1137. [PMID: 38824441 DOI: 10.1002/pros.24749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND The unmet challenge in prostate cancer (PCa) management is to discriminate it from benign prostate hyperplasia (BPH) due to the lack of specific diagnostic biomarkers. Contemporary research on potential PCa biomarkers is directed toward methylated cell-free DNA (cfDNA) from liquid biopsies since epigenetic mechanisms are strongly involved in PCa development. METHODS In the present research, cfDNA methylation of the LGALS3 gene in blood and seminal plasma of PCa and BPH patients was assessed using pyrosequencing, as well as LGALS3 DNA methylation in tissue biopsies. Liquid biopsy samples were taken from patients with clinical suspicion of PCa, who were subsequently divided into two groups, that is, 42 with PCa and 55 with BPH, according to the histopathological analysis. RESULTS Statistically significant higher cfDNA methylation of LGALS3 in seminal plasma of BPH than in PCa patients was detected by pyrosequencing. ROC curve analysis showed that it could distinguish PCa and BPH patients with 56.4% sensitivity and 70.4% specificity, while PSA did not differ between the two patient groups. In contrast, there was no statistically significant difference in LGALS3 cfDNA methylation in blood plasma between the two patient groups. In prostate tumor tissue, there was a statistically significant DNA hypermethylation of LGALS3 compared to surrounding nontumor tissue and BPH tissue. CONCLUSIONS The DNA hypermethylation of the LGALS3 gene represents an event specific to PCa development. In conclusion, LGALS3 cfDNA methylation in seminal fluid discriminates early PCa and BPH presenting itself as a powerful novel PCa biomarker highly outperforming PSA.
Collapse
Affiliation(s)
- Irena Abramovic
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive & Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ivan Pezelj
- Department of Urology, University Clinical Hospital Center Sestre Milosrdnice, Zagreb, Croatia
| | - Leo Dumbovic
- Department of Urology, University Clinical Hospital Center Sestre Milosrdnice, Zagreb, Croatia
| | - Lucija Skara Abramovic
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive & Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tonci Vodopic
- Department of Pathology, Cytology and Forensic Medicine, Varazdin General Hospital, Varazdin, Croatia
| | - Stela Bulimbasic
- Department of Pathology and Cytology, University Hospital Centre Zagreb, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Goran Stimac
- Department of Urology, University Clinical Hospital Center Sestre Milosrdnice, Zagreb, Croatia
| | - Floriana Bulic-Jakus
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive & Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tomislav Kulis
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
- Department of Urology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive & Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Davor Tomas
- Ljudevit Jurak Clinical Department of Pathology & Cytology, Sestre Milosrdnice University Clinical Hospital Center, Zagreb, Croatia
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive & Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
- Ljudevit Jurak Clinical Department of Pathology & Cytology, Sestre Milosrdnice University Clinical Hospital Center, Zagreb, Croatia
- Department of Pathology, University of Zagreb School of Dental Medicine, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
- Scientific Centre of Excellence for Reproductive & Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
- BIMIS-Biomedical Research Center Salata, University of Zagreb School of Medicine, Zagreb, Croatia
| |
Collapse
|
6
|
Alexander EM, Miller HA, Egger ME, Smith ML, Yaddanapudi K, Linder MW. The Correlation between Plasma Circulating Tumor DNA and Radiographic Tumor Burden. J Mol Diagn 2024:S1525-1578(24)00179-X. [PMID: 39181324 DOI: 10.1016/j.jmoldx.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/05/2024] [Accepted: 07/15/2024] [Indexed: 08/27/2024] Open
Abstract
Conventional blood-based biomarkers and radiographic imaging are excellent for use in monitoring different aspects of malignant disease, but given their specific shortcomings, their integration with other, complementary markers such as plasma circulating tumor DNA (ctDNA) will be beneficial toward a precision medicine-driven future. Plasma ctDNA analysis utilizes the measurement of cancer-specific molecular alterations in a variety of bodily fluids released by dying tumor cells to monitor and profile response to therapy, and is being employed in several clinical scenarios. Plasma concentrations of ctDNA have been reported to correlate with tumor burden. However, the strength of this association is generally poor and highly variable, confounding the interpretation of longitudinal plasma ctDNA measurements in conjunction with routine radiographic assessments. Herein is discussed what is currently understood with respect to the fundamental characteristics of tumor growth that dictate plasma ctDNA concentrations, with a perspective on its interpretation in conjunction with radiographically determined tumor burden assessments.
Collapse
Affiliation(s)
- Evan M Alexander
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky
| | - Hunter A Miller
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky
| | - Michael E Egger
- Hiram C. Polk, Jr, MD, Department of Surgery, University of Louisville, Louisville, Kentucky; UofL Health-Brown Cancer Center, University of Louisville, Louisville, Kentucky
| | - Melissa L Smith
- UofL Health-Brown Cancer Center, University of Louisville, Louisville, Kentucky; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky; Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky
| | - Kavitha Yaddanapudi
- UofL Health-Brown Cancer Center, University of Louisville, Louisville, Kentucky; Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky; Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky; UofL Health-Brown Cancer Center, University of Louisville, Louisville, Kentucky.
| |
Collapse
|
7
|
Long Z, Gao Y, Han Z, Yuan H, Yu Y, Pei B, Jia Y, Ye J, Shi Y, Zhang M, Zhao Y, Wu D, Wang F. Discovery and Validation of Methylation Signatures in Circulating Cell-Free DNA for the Detection of Colorectal Cancer. Biomolecules 2024; 14:996. [PMID: 39199384 PMCID: PMC11353097 DOI: 10.3390/biom14080996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/25/2024] [Accepted: 08/09/2024] [Indexed: 09/01/2024] Open
Abstract
This study was conducted with the primary objective of assessing the performance of cfDNA methylation in the detection of colorectal cancer (CRC). Five tumor tissue, 20 peripheral blood leucocyte, and 169 cfDNA samples were collected for whole-genome bisulfite sequencing (WGBS) analysis. Bioinformatic analysis was conducted to identify differentially methylated regions (DMRs) and their functional characteristics. Quantitative methylation-specific PCR (qMSP) was used to validate the methylation levels of DMRs in the tissues and leucocytes. cfDNA samples from CRC patients and healthy controls were used to evaluate the performance of the DMR analysis. WGBS analysis revealed a decrease in DNA methylation levels in the CpG context in CRC tumor tissues compared with adjacent normal tissues. A total of 132 DMRs in cfDNA were identified as potential markers for diagnosing CRC. In a cohort of 95 CRC patients and 74 healthy controls, a combination of the three DMRs (DAB1, PPP2R5C, and FAM19A5) yielded an AUC of 0.763, achieving 64.21% sensitivity and 78.38% specificity in discriminating CRC patients from healthy controls. This study provides insights into DNA methylation patterns in CRC and identifies a set of DMRs in cfDNA with potential diagnostic value for CRC. These DMRs hold promise as biomarkers for CRC detection, offering promise for non-invasive CRC diagnosis. Further research is warranted to validate these findings in larger cohorts.
Collapse
Affiliation(s)
- Zhiping Long
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yu Gao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Zhen Han
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Heli Yuan
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yue Yu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Bing Pei
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yanjie Jia
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Jingyu Ye
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Ying Shi
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Min Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| | - Di Wu
- Department of Colorectal Surgery, Tumor Hospital of Harbin Medical University, Harbin Medical University, Harbin 150081, China
| | - Fan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin 150028, China; (Z.L.); (Y.G.); (Z.H.); (H.Y.); (Y.Y.); (B.P.); (Y.J.); (J.Y.); (Y.S.); (M.Z.)
| |
Collapse
|
8
|
Tung KTS, Tsang HW, Ngo U, Wong RS, Chow CHY, Tso WHY, Yam JCS, Chan GCF, Ip P. A systematic review on the applicability of cell-free DNA level as an obesity biomarker. Obes Rev 2024; 25:e13765. [PMID: 38770721 DOI: 10.1111/obr.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/19/2024] [Accepted: 04/06/2024] [Indexed: 05/22/2024]
Abstract
Obesity has become a global health concern in recent decades. Utilizing biomarkers presents a promising approach to comprehensively monitor the progress of obesity and its associated health conditions. This review aims to synthesize the available evidence on the correlation between cfDNA level and obesity and to provide insights into the applicability of using cfDNA level as a tool for monitoring progression of obesity. Searches were performed in PubMed and Embase on April 1, 2022. Data and other relevant information were extracted and compiled into a structured table for further analysis. Among 1170 articles screened, 11 articles were included in this review and assessed qualitatively. The results demonstrated that existing evidence mainly focused on three populations, including healthy individuals, cancer patients and pregnant women. Majority of the studies on healthy individuals identified a significant association between cfDNA level and body weight status but not among cancer patients. Varying results were observed among pregnant women at different gestational trimesters. Our review summarized some preliminary evidence on the association between cfDNA level and obesity. More cohort studies in larger scale with comprehensive assessment have to be conducted to examine the applicability of cfDNA as a biomarker for severity and disease progression of obesity.
Collapse
Affiliation(s)
- Keith T S Tung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hing Wai Tsang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ulrike Ngo
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rosa S Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Special Education and Counselling (SEC), The Education University of Hong Kong, Hong Kong SAR, China
| | - Clare H Y Chow
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Winnie H Y Tso
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Jason C S Yam
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Godfrey C F Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
| |
Collapse
|
9
|
Tanaka A, Wakayama K, Fukuda Y, Ohta S, Homma T, Ando K, Nishihara Y, Nakano R, Zhao J, Suzuki Y, Kyotani Y, Yano H, Kasahara K, Chung KP, Sagara H, Yoshizumi M, Nakahira K. Increased levels of circulating cell-free DNA in COVID-19 patients with respiratory failure. Sci Rep 2024; 14:17399. [PMID: 39075117 PMCID: PMC11286760 DOI: 10.1038/s41598-024-68433-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 07/23/2024] [Indexed: 07/31/2024] Open
Abstract
Cell-free DNA (cfDNA) is released from injured cells and aggravates inflammation. Patients with coronavirus disease (COVID-19) often develop pneumonia and respiratory failure, and require oxygen therapy (OT), including mechanical ventilation (MV). It remains unclear whether cfDNA predicts the risk of receiving OT or MV in COVID-19 patients. Therefore, we hypothesized that circulating cfDNA levels could reflect the severity of respiratory failure and determine a therapeutic approach for oxygenation in patients with COVID-19. We analyzed cfDNA levels in serum samples from 95 hospitalized patients with COVID-19 at Showa University Hospital (Tokyo, Japan). cfDNA levels were assessed by measuring the copy numbers of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) using quantitative real-time PCR (qPCR). Both cf-nDNA and cf-mtDNA levels were negatively correlated with adjusted SpO2 for FiO2 (SpO2/FiO2 ratio). Elevated cf-nDNA and cf-mtDNA levels were associated with the requirement for OT or MV during patient admission. Multivariate logistic regression analysis revealed that cf-nDNA and cf-mtDNA levels were independent risk factors for OT and MV. These results suggest that both serum cf-nDNA and cf-mtDNA could serve as useful early biomarkers to indicate the necessity of OT or MV in patients with COVID-19.
Collapse
Affiliation(s)
- Akihiko Tanaka
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Katsuki Wakayama
- Department of Pharmacology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Yosuke Fukuda
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Shin Ohta
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Tetsuya Homma
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Koichi Ando
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
- Division of Internal Medicine, Showa University Dental Hospital Medical Clinic, Tokyo, Japan
| | - Yuji Nishihara
- Department of Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Jing Zhao
- Department of Pharmacology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Yoji Kyotani
- Department of Pharmacology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Kei Kasahara
- Department of Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Kuei-Pin Chung
- Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, 100225, Taiwan
| | - Hironori Sagara
- Division of Respiratory Medicine and Allergology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Masanori Yoshizumi
- Department of Pharmacology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Kiichi Nakahira
- Department of Pharmacology, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
10
|
Markandran K, Clemente KNM, Tan E, Attal K, Chee QZ, Cheung C, Chen CK. The Future of Kawasaki Disease Diagnosis: Liquid Biopsy May Hold the Key. Int J Mol Sci 2024; 25:8062. [PMID: 39125631 PMCID: PMC11311979 DOI: 10.3390/ijms25158062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/13/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
Kawasaki disease (KD) is a febrile illness characterised by systemic inflammation of small- and medium-sized blood vessels, which commonly occurs in young children. Although self-limiting, there is a risk of developing coronary artery lesions as the disease progresses, with delay in diagnosis and treatment. Unfortunately, the diagnosis of KD continues to remain a clinical dilemma. Thus, this article not only summarises the key research gaps associated with KD, but also evaluates the possibility of using circulating endothelial injury biomarkers, such as circulating endothelial cells, endothelial microparticles and vascular endothelial cell-free DNA, as diagnostic and prognostic tools for KD: a "liquid biopsy" approach. The challenges of translating liquid biopsies to use in KD and the opportunities for improvement in its diagnosis and management that such translation may provide are discussed. The use of endothelial damage markers, which are easily obtained via blood collection, as diagnostic tools is promising, and we hope this will be translated to clinical applications in the near future.
Collapse
Affiliation(s)
- Kasturi Markandran
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (K.M.)
| | - Kristine Nicole Mendoza Clemente
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (K.M.)
| | - Elena Tan
- School of Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Karan Attal
- School of Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Qiao Zhi Chee
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive, Nanyang Technological University, Singapore 636921, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; (K.M.)
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
| |
Collapse
|
11
|
Rodríguez-Ces AM, Rapado-González Ó, Salgado-Barreira Á, Santos MA, Aroso C, Vinhas AS, López-López R, Suárez-Cunqueiro MM. Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis. Diagnostics (Basel) 2024; 14:1465. [PMID: 39061602 PMCID: PMC11276058 DOI: 10.3390/diagnostics14141465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to June 2024. Seventy-two study units from forty-six studies, comprising 4286 cancer patients, were identified and evaluated. The Quality Assessment for Studies of Diagnostic Accuracy-2 (QUADAS-2) was used to assess study quality. Meta-regression analysis was employed to investigate the underlying factors contributing to heterogeneity, alongside an evaluation of publication bias. The bivariate random-effect model was utilized to compute the primary diagnostic outcomes and their corresponding 95% confidence intervals (CIs). The pooled sensitivity, specificity, and positive and negative likelihood ratios of cfDI in cancer diagnosis were 0.70 and 0.77, 3.26 and 0.34, respectively. The overall area under the curve was 0.84, with a diagnostic odds ratio of 10.63. This meta-analysis suggested that the cfDI index has a promising potential as a non-invasive and accurate diagnostic tool for cancer. Study registration: The study was registered at PROSPERO (reference No. CRD42021276290).
Collapse
Affiliation(s)
- Ana María Rodríguez-Ces
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP@RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ángel Salgado-Barreira
- Department of Public Health, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiology and Public Health—CIBERESP), 28029 Madrid, Spain
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
| | - María Arminda Santos
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Carlos Aroso
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Ana Sofia Vinhas
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
| |
Collapse
|
12
|
Falahat P, Scheidt U, Pörner D, Schwab S. Recent Insights in Noninvasive Diagnostic for the Assessment of Kidney and Cardiovascular Outcome in Kidney Transplant Recipients. J Clin Med 2024; 13:3778. [PMID: 38999343 PMCID: PMC11242869 DOI: 10.3390/jcm13133778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Kidney transplantation improves quality of life and prolongs survival of patients with end-stage kidney disease. However, kidney transplant recipients present a higher risk for cardiovascular events compared to the general population. Risk assessment for graft failure as well as cardiovascular events is still based on invasive procedures. Biomarkers in blood and urine, but also new diagnostic approaches like genetic or molecular testing, can be useful tools to monitor graft function and to identify patients of high cardiovascular risk. Many biomarkers have been introduced, whereas most of these biomarkers have not been implemented in clinical routine. Here, we discuss recent developments in biomarkers and diagnostic models in kidney transplant recipients. Because many factors impact graft function and cardiovascular risk, it is most likely that no biomarker will meet the highest demands and standards. We advocate to shift focus to the identification of patients benefitting from molecular and genetic testing as well as from analysis of more specific biomarkers instead of finding one biomarker fitting to all patients.
Collapse
Affiliation(s)
- Peyman Falahat
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| | - Uta Scheidt
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| | - Daniel Pörner
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| | - Sebastian Schwab
- Department of Internal Medicine I, Nephrology Section, University of Bonn, 53121 Bonn, Germany
| |
Collapse
|
13
|
Gromek P, Senkowska Z, Płuciennik E, Pasieka Z, Zhao LY, Gielecińska A, Kciuk M, Kłosiński K, Kałuzińska-Kołat Ż, Kołat D. Revisiting the standards of cancer detection and therapy alongside their comparison to modern methods. World J Methodol 2024; 14:92982. [PMID: 38983668 PMCID: PMC11229876 DOI: 10.5662/wjm.v14.i2.92982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/15/2024] [Accepted: 04/28/2024] [Indexed: 06/13/2024] Open
Abstract
In accordance with the World Health Organization data, cancer remains at the forefront of fatal diseases. An upward trend in cancer incidence and mortality has been observed globally, emphasizing that efforts in developing detection and treatment methods should continue. The diagnostic path typically begins with learning the medical history of a patient; this is followed by basic blood tests and imaging tests to indicate where cancer may be located to schedule a needle biopsy. Prompt initiation of diagnosis is crucial since delayed cancer detection entails higher costs of treatment and hospitalization. Thus, there is a need for novel cancer detection methods such as liquid biopsy, elastography, synthetic biosensors, fluorescence imaging, and reflectance confocal microscopy. Conventional therapeutic methods, although still common in clinical practice, pose many limitations and are unsatisfactory. Nowadays, there is a dynamic advancement of clinical research and the development of more precise and effective methods such as oncolytic virotherapy, exosome-based therapy, nanotechnology, dendritic cells, chimeric antigen receptors, immune checkpoint inhibitors, natural product-based therapy, tumor-treating fields, and photodynamic therapy. The present paper compares available data on conventional and modern methods of cancer detection and therapy to facilitate an understanding of this rapidly advancing field and its future directions. As evidenced, modern methods are not without drawbacks; there is still a need to develop new detection strategies and therapeutic approaches to improve sensitivity, specificity, safety, and efficacy. Nevertheless, an appropriate route has been taken, as confirmed by the approval of some modern methods by the Food and Drug Administration.
Collapse
Affiliation(s)
- Piotr Gromek
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Zuzanna Senkowska
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Zbigniew Pasieka
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Lin-Yong Zhao
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz 90-237, Lodzkie, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, Lodz 90-237, Lodzkie, Poland
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz 90-237, Lodzkie, Poland
| | - Karol Kłosiński
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Żaneta Kałuzińska-Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
| |
Collapse
|
14
|
Hu X, Zhang H, Wang Y, Lin Y, Li Q, Li L, Zeng G, Ou R, Cheng X, Zhang Y, Jin X. Effects of blood-processing protocols on cell-free DNA fragmentomics in plasma: Comparisons of one- and two-step centrifugations. Clin Chim Acta 2024; 560:119729. [PMID: 38754575 DOI: 10.1016/j.cca.2024.119729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Cell-free DNA (cfDNA) fragmentomic characteristics are promising analytes with abundant physiological signals for non-invasive disease diagnosis and monitoring. Previous studies on plasma cfDNA fragmentomics commonly employed a two-step centrifugation process for removing cell debris, involving a low-speed centrifugation followed by a high-speed centrifugation. However, the effects of centrifugation conditions on the analysis of cfDNA fragmentome remain uncertain. METHODS We collected blood samples from 10 healthy individuals and divided each sample into two aliquots for plasma preparation with one- and two-step centrifugation processes. We performed whole genome sequencing (WGS) of the plasma cfDNA in the two groups and comprehensively compared the cfDNA fragmentomic features. Additionally, we reanalyzed the fragmentomic features of cfDNA from 16 healthy individuals and 16 COVID-19 patients, processed through one- and two-step centrifugation in our previous study, to investigate the impact of centrifugation on disease signals. RESULTS Our results showed that there were no significant differences observed in the characteristics of nuclear cfDNA, including size, motif diversity score (MDS) of end motifs, and genome distribution, between plasma samples treated with one- and two-step centrifugation. The cfDNA size shortening in COVID-19 patients was observed in plasma samples with one- and two-step centrifugation methods. However, we observed a significantly higher relative abundance and longer size of cell-free mitochondrial DNA (mtDNA) in the one-step samples compared to the two-step samples. This difference in mtDNA caused by the one- and two-step centrifugation methods surpasses the pathological difference between COVID-19 patients and healthy individuals. CONCLUSIONS Our findings indicate that one-step low-speed centrifugation is a simple and potentially suitable method for analyzing nuclear cfDNA fragmentation characteristics. These results offer valuable guidance for cfDNA research in various clinical scenarios.
Collapse
Affiliation(s)
- Xintao Hu
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China; BGI Research, Shenzhen 518083, China
| | | | | | - Yu Lin
- BGI Research, Shenzhen 518083, China
| | - Qiuyan Li
- BGI Research, Shenzhen 518083, China
| | | | | | - Rijing Ou
- BGI Research, Shenzhen 518083, China
| | - Xinyu Cheng
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yan Zhang
- BGI Research, Shenzhen 518083, China.
| | - Xin Jin
- BGI Research, Shenzhen 518083, China; School of Medicine, South China University of Technology, Guangzhou 510006, China.
| |
Collapse
|
15
|
Gerdes C, Basmanav FB. Intercellular transfer of plasmid DNA between in vitro cultured HEK293 cells following transient transfection. Plasmid 2024; 131-132:102729. [PMID: 38876373 DOI: 10.1016/j.plasmid.2024.102729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
Gene overexpression by transient transfection of in vitro cultured model cell lines with plasmid DNA is a commonly used method for studying molecular aspects of human biology and pathobiology. However, there is accumulating evidence suggesting that human cells may actively secrete fragments of DNA and the implications of this phenomenon for in vitro cultured cells transiently transfected with foreign nucleic acids has been overlooked. Therefore, in the current study we investigated whether a cell-to-cell transmission of acquired plasmid DNA takes place in a commonly used human cell line model. We transiently transfected HEK293 cells with EGFP encoding plasmids to serve as donor cells and either co-cultured these with stably mCherry expressing recipient cells in different set-ups or transferred their culture medium to the recipient cells. We found that recipient cells produced EGFP after being co-cultured with donor cells but not when they were exposed to their culture medium. The employment of different co-culture set-ups excluded that the observed effect stemmed from technical artefacts and provided evidence that an intercellular plasmid transfer takes place requiring physical proximity between living cells. This phenomenon could represent a significant biological artefact for certain studies such as those addressing protein transmissions in prion diseases.
Collapse
Affiliation(s)
- Christoph Gerdes
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, D-37073 Göttingen, Germany; Hannover Medical School, Department of Gastroenterology, Hepatology, Infectiology and Endocrinology, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - F Buket Basmanav
- University Medical Center Göttingen, Institute for Neuro- and Sensory Physiology, D-37073 Göttingen, Germany; Campus Laboratory for Advanced Imaging, Microscopy and Spectroscopy, University of Göttingen, D-37073 Göttingen, Germany; Institute of X-ray Physics, University of Göttingen, 37073 Göttingen, Germany; Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany.
| |
Collapse
|
16
|
Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
Collapse
Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
17
|
Wu X, Chen Y, Kreutz A, Silver B, Tokar EJ. Pluripotent stem cells for target organ developmental toxicity testing. Toxicol Sci 2024; 199:163-171. [PMID: 38547390 PMCID: PMC11131012 DOI: 10.1093/toxsci/kfae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
Prenatal developmental toxicity research focuses on understanding the potential adverse effects of environmental agents, drugs, and chemicals on the development of embryos and fetuses. Traditional methods involve animal testing, but ethical concerns and the need for human-relevant models have prompted the exploration of alternatives. Pluripotent stem cells (PSCs) are versatile cells with the unique ability to differentiate into any cell type, serving as a foundational tool for studying human development. Two-dimensional (2D) PSC models are often chosen for their ease of use and reproducibility for high-throughput screening. However, they lack the complexity of an in vivo environment. Alternatively, three-dimensional (3D) PSC models, such as organoids, offer tissue architecture and intercellular communication more reminiscent of in vivo conditions. However, they are complicated to produce and analyze, usually requiring advanced and expensive techniques. This review discusses recent advances in the use of human PSCs differentiated into brain and heart lineages and emerging tools and methods that can be combined with PSCs to help address important scientific questions in the area of developmental toxicology. These advancements and new approach methods align with the push for more relevant and predictive developmental toxicity assessment, combining innovative techniques with organoid models to advance regulatory decision-making.
Collapse
Affiliation(s)
- Xian Wu
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, North Carolina 27709, USA
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834, USA
| | - Yichang Chen
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Anna Kreutz
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, North Carolina 27709, USA
- Inotiv, Research Triangle Park, North Carolina 27560, USA
| | - Brian Silver
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Erik J Tokar
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, North Carolina 27709, USA
| |
Collapse
|
18
|
Bleckman RF, Haag CMSC, Rifaela N, Beukema G, Mathijssen RHJ, Steeghs N, Gelderblom H, Desar IME, Cleven A, Ter Elst A, Schuuring E, Reyners AKL. Levels of circulating tumor DNA correlate with tumor volume in gastro-intestinal stromal tumors: an exploratory long-term follow-up study. Mol Oncol 2024. [PMID: 38790141 DOI: 10.1002/1878-0261.13644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 05/26/2024] Open
Abstract
Patients with gastro-intestinal stromal tumors (GISTs) undergoing tyrosine kinase inhibitor therapy are monitored with regular computed tomography (CT) scans, exposing patients to cumulative radiation. This exploratory study aimed to evaluate circulating tumor DNA (ctDNA) testing to monitor treatment response and compare changes in ctDNA levels with RECIST 1.1 and total tumor volume measurements. Between 2014 and 2021, six patients with KIT proto-oncogene, receptor tyrosine kinase (KIT) exon-11-mutated GIST from whom long-term plasma samples were collected prospectively were included in the study. ctDNA levels of relevant plasma samples were determined using the KIT exon 11 digital droplet PCR drop-off assay. Tumor volume measurements were performed using a semi-automated approach. In total, 94 of 130 clinically relevant ctDNA samples were analyzed. Upon successful treatment response, ctDNA became undetectable in all patients. At progressive disease, ctDNA was detectable in five out of six patients. Higher levels of ctDNA correlated with larger tumor volumes. Undetectable ctDNA at the time of progressive disease on imaging was consistent with lower tumor volumes compared to those with detectable ctDNA. In summary, ctDNA levels seem to correlate with total tumor volume at the time of progressive disease. Our exploratory study shows promise for including ctDNA testing in treatment follow-up.
Collapse
Affiliation(s)
- Roos F Bleckman
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Charlotte M S C Haag
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Naomi Rifaela
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Gerrieke Beukema
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Ingrid M E Desar
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen Cleven
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Arja Ter Elst
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ed Schuuring
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Anna K L Reyners
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| |
Collapse
|
19
|
Ara H, Tarek SA, Biswas MK, Al-Din SMS, Hoque E, Hasan KME, Hossain AKMM, Faruque SB, Haque Y, Sharafuddin SM. Investigating the Z-scan technique for quantifying circulating cell-free DNA (ccfDNA) extracted from blood plasma as a potential biomarker for various cancers. Biomed Phys Eng Express 2024; 10:045029. [PMID: 38718773 DOI: 10.1088/2057-1976/ad4890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The Z-scan technique is a nonlinear optical method that has found applications in characterizing various materials, particularly those exhibiting nonlinear optical response (NLOR). This study applies the continuous wave (CW) Z-scan technique to examine the NLOR in terms of the nonlinear optical phase shifts(ΔΦ0) exhibited by the ccfDNA extracted from blood plasma samples collected from a group constituting 30 cancer-diagnosed patients and another group constituting 30 non-diagnosed individuals. The cancer group exhibited significantly higherΔΦ0versus incident power slopes compared to the non-cancer group (0.34 versus 0.12) providing a clear distinction between the two groups. The receiver operating characteristic (ROC) curve analysis of the results indicates a clear separation between cancer and non-cancer groups, along with a 94% accuracy rate of the data. The Z-scan results are corroborated by spectrophotometric analysis, revealing a consistent trend in the concentration values of ccfDNA samples extracted from both cancerous and non-cancerous samples, measuring 3.24 and 1.41 respectively. Additionally, more sensitive fluorometric analyses of the respective samples demonstrate significantly higher concentrations of ccfDNA in the cancer group, further affirming the correlation with the Z-scan results. The study suggests that the Z-scan technique holds promise as an effective method for cancer detection, potentially contributing to improved oncology diagnosis and prognosis in the future.
Collapse
Affiliation(s)
- H Ara
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - S A Tarek
- American International University-Bangladesh, Dhaka, Bangladesh
| | - M K Biswas
- Sunamgonj Govt. College, Sunamgonj, Bangladesh
| | - S M S Al-Din
- Invent Technologies Ltd, Banani, Dhaka, Bangladesh
| | - E Hoque
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - K M E Hasan
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - A K M M Hossain
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - S B Faruque
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Y Haque
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - S M Sharafuddin
- Department of Physics, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| |
Collapse
|
20
|
Silver BB, Brooks A, Gerrish K, Tokar EJ. Isolation and Characterization of Cell-Free DNA from Cerebral Organoids. Int J Mol Sci 2024; 25:5522. [PMID: 38791569 PMCID: PMC11121789 DOI: 10.3390/ijms25105522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Early detection of neurological conditions is critical for timely diagnosis and treatment. Identifying cellular-level changes is essential for implementing therapeutic interventions prior to symptomatic disease onset. However, monitoring brain tissue directly through biopsies is invasive and poses a high risk. Bodily fluids such as blood or cerebrospinal fluid contain information in many forms, including proteins and nucleic acids. In particular, cell-free DNA (cfDNA) has potential as a versatile neurological biomarker. Yet, our knowledge of cfDNA released by brain tissue and how cfDNA changes in response to deleterious events within the brain is incomplete. Mapping changes in cfDNA to specific cellular events is difficult in vivo, wherein many tissues contribute to circulating cfDNA. Organoids are tractable systems for examining specific changes consistently in a human background. However, few studies have investigated cfDNA released from organoids. Here, we examined cfDNA isolated from cerebral organoids. We found that cerebral organoids release quantities of cfDNA sufficient for downstream analysis with droplet-digital PCR and whole-genome sequencing. Further, gene ontology analysis of genes aligning with sequenced cfDNA fragments revealed associations with terms related to neurodevelopment and autism spectrum disorder. We conclude that cerebral organoids hold promise as tools for the discovery of cfDNA biomarkers related to neurodevelopmental and neurological disorders.
Collapse
Affiliation(s)
- Brian B. Silver
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
- Molecular Genomics Core, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
| | - Ashley Brooks
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
| | - Kevin Gerrish
- Molecular Genomics Core, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA;
| | - Erik J. Tokar
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| |
Collapse
|
21
|
Mondal D, Shinde S, Sinha V, Dixit V, Paul S, Gupta RK, Thakur S, Vishvakarma NK, Shukla D. Prospects of liquid biopsy in the prognosis and clinical management of gastrointestinal cancers. Front Mol Biosci 2024; 11:1385238. [PMID: 38770216 PMCID: PMC11103528 DOI: 10.3389/fmolb.2024.1385238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
Gastrointestinal (GI) cancers account for one-fourth of the global cancer incidence and are incriminated to cause one-third of cancer-related deaths. GI cancer includes esophageal, gastric, liver, pancreatic, and colorectal cancers, mostly diagnosed at advanced stages due to a lack of accurate markers for early stages. The invasiveness of diagnostic methods like colonoscopy for solid biopsy reduces patient compliance as it cannot be frequently used to screen patients. Therefore, minimally invasive approaches like liquid biopsy may be explored for screening and early identification of gastrointestinal cancers. Liquid biopsy involves the qualitative and quantitative determination of certain cancer-specific biomarkers in body fluids such as blood, serum, saliva, and urine to predict disease progression, therapeutic tolerance, toxicities, and recurrence by evaluating minimal residual disease and its correlation with other clinical features. In this review, we deliberate upon various tumor-specific cellular and molecular entities such as circulating tumor cells (CTCs), tumor-educated platelets (TEPs), circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), exosomes, and exosome-derived biomolecules and cite recent advances pertaining to their use in predicting disease progression, therapy response, or risk of relapse. We also discuss the technical challenges associated with translating liquid biopsy into clinical settings for various clinical applications in gastrointestinal cancers.
Collapse
Affiliation(s)
- Deepankar Mondal
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| | - Sapnita Shinde
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| | - Vibha Sinha
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| | - Vineeta Dixit
- Department of Botany, Sri Sadguru Jagjit Singh Namdhari College, Garhwa, Jharkhand, India
| | - Souvik Paul
- Department of Surgical Gastroenterology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Rakesh Kumar Gupta
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | | | | | - Dhananjay Shukla
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh, India
| |
Collapse
|
22
|
Bønløkke S, Steiniche T, Sorensen BS, Nyvang G, Lindegaard JC, Blaakær J, Bertelsen J, Fuglsang K, Strube ML, Lenz S, Stougaard M. Circulating cell-free HPV DNA is a strong marker for disease severity in cervical cancer. Mol Oncol 2024; 18:1231-1244. [PMID: 37853962 PMCID: PMC11076984 DOI: 10.1002/1878-0261.13538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023] Open
Abstract
For cervical cancer (CC), circulating cell-free HPV DNA (ccfHPV) may establish disease severity. Furthermore, HPV integration has been correlated to viral load and survival. In this study, pre-treatment plasma from 139 CC cases (50 primary surgery patients, 22 primary surgery + adjuvant oncological therapy patients, and 67 primary oncological therapy patients) was collected (2018-2020). Furthermore, plasma from 25 cervical intraepithelial neoplasia grade 3 patients and 15 healthy women (negative controls) were collected. Two next-generation sequencing (NGS) panels were used to establish ccfHPV presence and human papillomavirus type 16 (HPV16) integration status. ccfHPV was detected in four primary surgery (8.0%), eight primary surgery + adjuvant oncology (36.4%), and 54 primary oncology (80.6%) patients. For primary oncology patients with HPV16-related cancer (n = 37), more ccfHPVneg than ccfHPVpos patients had HPV16 integration (P = 0.04), and in patients with HPV16 integration (n = 13), ccfHPVpos patients had higher disease stages than ccfHPVneg patients (P = 0.05). In summary, ccfHPV presence is related to disease severity and may add to the debated Sedlis criteria used for identifying patients for adjuvant oncological therapy. However, ccfHPV detection is influenced by HPV integration status and disease stage, and these factors need to be considered in ccfHPVneg patients.
Collapse
Affiliation(s)
- Sara Bønløkke
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of PathologyAarhus University HospitalDenmark
| | - Torben Steiniche
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of PathologyAarhus University HospitalDenmark
| | - Boe Sandahl Sorensen
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of Clinical BiochemistryAarhus University HospitalDenmark
| | | | | | - Jan Blaakær
- Department of Obstetrics and GynecologyOdense University HospitalDenmark
- Department of Clinical ResearchUniversity of Southern DenmarkOdense MDenmark
| | | | - Katrine Fuglsang
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of Obstetrics and GynecologyAarhus University HospitalDenmark
| | | | - Suzan Lenz
- Private Gynecological Clinic “Suzan Lenz Gynækolog”CopenhagenDenmark
| | - Magnus Stougaard
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of PathologyAarhus University HospitalDenmark
| |
Collapse
|
23
|
Oehr P. Novel Tools for Single Comparative and Unified Evaluation of Qualitative and Quantitative Bioassays: SS/PV-ROC and SS-J/PV-PSI Index-ROC Curves with Integrated Concentration Distributions, and SS-J/PV-PSI Index Cut-Off Diagrams. Diagnostics (Basel) 2024; 14:951. [PMID: 38732365 PMCID: PMC11082985 DOI: 10.3390/diagnostics14090951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/10/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Background: This investigation is both a study of potential non-invasive diagnostic approaches for the bladder cancer biomarker UBC® Rapid test and a study including novel comparative methods for bioassay evaluation and comparison that uses bladder cancer as a useful example. The objective of the paper is not to investigate specific data. It is used only for demonstration, partially to compare ROC methodologies and also to show how both sensitivity/specificity and predictive values can be used in clinical diagnostics and decision making. This study includes ROC curves with integrated cut-off distribution curves for a comparison of sensitivity/specificity (SS) and positive/negative predictive values (PPV/NPV or PV), as well as SS-J index/PV-PSI index-ROC curves and SS-J/PV-PSI index cut-off diagrams (J = Youden, PSI = Predictive Summary Index) for the unified direct comparison of SS-J/PV results achieved via quantitative and/or qualitative bioassays and an identification of optimal separate or unified index cut-off points. Patients and Methods: According to the routine diagnostics, there were 91 patients with confirmed bladder cancer and 1152 patients with no evidence of bladder cancer, leading to a prevalence value of 0.073. This study performed a quantitative investigation of used-up test cassettes from the visual UBC® Rapid qualitative point-of-care assay, which had already been applied in routine diagnostics. Using a photometric reader, quantitative data could also be obtained from the test line of the used cassettes. Interrelations between SS and PV values were evaluated using cumulative distribution analysis (CAD), SS/PV-ROC curves, SS-J/PV-PSI index-ROC curves, and the SS-J/PV-PSI index cut-off diagram. The maximum unified SS-J/PV-PSI index value and its corresponding cut-off value were determined and calculated with the SS-J/PV-PSI index cut-off diagram. Results: The use of SS/PV-ROC curves with integrated cut-off concentration distribution curves provides improved diagnostic information compared to "traditional" ROC curves. The threshold distributions integrated as curves into SS/PV-ROC curves and SS-J/PV-PSI index-ROC curves run in opposite directions. In contrast to the SS-ROC curves, the PV-ROC and the novel PV-PSI index-ROC curves had neither an area under the curve (AUC) nor a range from 0% to 100%. The cut-off level of the qualitative assay was 7.5 µg/L, with a sensitivity of 65.9% and a specificity of 63.3%, and the PPV was 12.4% and the NPV was 95.9%, at a threshold value of 12.5 µg/L. Based on these set concentrations, the reader-based evaluation revealed a graphically estimated 5% increase in sensitivity and a 13% increase in specificity, as compared to the visual qualitative POC test. In the case of predictive values, there was a gain of 8% for PPV and 10% for NPV. The index values and cut-offs were as follows: visual SS-J index, 0.328 and 35 µg/L; visual PV-PSI index, 0.083 and 5.4 µg/L; maximal reader Youden index, 0.0558 and 250 µg/L; and maximal PV-PSI index, 0.459 and 250 µg/L, respectively. The maximum unified SS-J/PV-PSI index value was 0.32, and the cut-off was 43 µg/L. The reciprocal SS-J index correctly detected one out of three patients, while the reciprocal PV-PSI index gave one out of twelve patients a correct diagnosis. Conclusions: ROC curves including cut-off distribution curves supplement the information lost in "traditionally plotted" ROC curves. The novel sets of ROC and index-ROC curves and the new SS/PV index cut-off diagrams enable the simultaneous comparison of sensitivity/specificity and predictive value profiles of diagnostic tools and the identification of optimal cut-off values at maximal index values, even in a unifying SS/PV approach. Because the curves within an SS-J/PV-PSI index cut-off diagram are distributed over the complete cut-off range of a quantitative assay, this field is open for special clinical considerations, with the need to vary the mentioned clinical diagnostic parameters. Complete or partial areas over the x-axis (AOX) can be calculated for summarized quantitative or qualitative effectivity evaluations with respect to single and/or unified SS-J and PV-PSI indices and with respect to single, several, or several unified assays. The SS-J/PV-PSI index-AOX approach is a new tool providing additional joint clinical information, and the reciprocal SS-J indices can predict the number of patients with a correct diagnosis and the number of persons who need to be examined in order to correctly predict a diagnosis of the disease. These methods could be used in applications like medical or plant epidemiology, machine learning algorithms, and neural networks.
Collapse
Affiliation(s)
- Peter Oehr
- Faculty of Medicine, University of Bonn, 53113 Bonn, Germany
| |
Collapse
|
24
|
Davidson BA, Miranda AX, Reed SC, Bergman RE, Kemp JDJ, Reddy AP, Pantone MV, Fox EK, Dorand RD, Hurley PJ, Croessmann S, Park BH. An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release. Commun Biol 2024; 7:441. [PMID: 38600351 PMCID: PMC11006667 DOI: 10.1038/s42003-024-06129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABTRACT Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.
Collapse
Affiliation(s)
- Brad A Davidson
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Adam X Miranda
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah C Reed
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Riley E Bergman
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Justin D J Kemp
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Anvith P Reddy
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Morgan V Pantone
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ethan K Fox
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - R Dixon Dorand
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Paula J Hurley
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah Croessmann
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ben Ho Park
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
| |
Collapse
|
25
|
Giudice V, Ianniello M, De Novellis D, Pezzullo L, Petrillo N, Serio B, D'Addona M, Della Corte AM, Rizzo M, Cuffa B, Castaldi MA, Savarese P, Mori A, Castiello R, Fico A, Savarese G, Selleri C. Non-invasive prenatal test identifies circulating cell-free DNA chromosomal abnormalities derived from clonal hematopoiesis in aggressive hematological malignancies. Clin Exp Med 2024; 24:69. [PMID: 38578383 PMCID: PMC10997720 DOI: 10.1007/s10238-024-01313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
Liquid biopsy is a minimally invasive diagnostic tool for identification of tumor-related mutations in circulating cell-free DNA (cfDNA). The aim of this study was to investigate feasibility, sensitivity, and specificity of non-invasive prenatal test (NIPT) for identification of chromosomal abnormalities in cfDNA from a total of 77 consecutive patients with non-Hodgkin B-cell lymphomas, Hodgkin lymphoma (HL), or plasma cell dyscrasia. In this case series, half of patients had at least one alteration, more frequently in chromosome 6 (23.1%), chromosome 9 (20.5%), and chromosomes 3 and 18 (16.7%), with losses of chromosome 6 and gains of chromosome 7 negatively impacting on overall survival (OS), with a 5-year OS of 26.9% and a median OS of 14.6 months, respectively (P = 0.0009 and P = 0.0004). Moreover, B-cell lymphomas had the highest NIPT positivity, especially those with aggressive lymphomas, while patients with plasma cell dyscrasia with extramedullary disease had a higher NIPT positivity compared to conventional cytogenetics analysis and a worse outcome. Therefore, we proposed a NIPT-based liquid biopsy a complementary minimally invasive tool for chromosomal abnormality detection in hematological malignancies. However, prospective studies on larger cohorts are needed to validate clinical utility of NIPT-based liquid biopsy in routinely clinical practice.
Collapse
Affiliation(s)
- Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy
| | | | - Danilo De Novellis
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy
| | - Luca Pezzullo
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | | | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Matteo D'Addona
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy
| | - Anna Maria Della Corte
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Michela Rizzo
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Bianca Cuffa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Maria Antonietta Castaldi
- Gynecology and Obstetrics Unit, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | | | - Alessio Mori
- Ames Center s.r.l, Casalnuovo di Naples, Naples, Italy
| | | | - Antonio Fico
- Ames Center s.r.l, Casalnuovo di Naples, Naples, Italy
| | | | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy.
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy.
| |
Collapse
|
26
|
Zhong Y, Tan GW, Bult J, Veltmaat N, Plattel W, Kluiver J, Enting R, Diepstra A, van den Berg A, Nijland M. Detection of circulating tumor DNA in plasma of patients with primary CNS lymphoma by digital droplet PCR. BMC Cancer 2024; 24:407. [PMID: 38566053 PMCID: PMC10985975 DOI: 10.1186/s12885-024-12191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) are rare mature B-cell lymphoproliferative diseases characterized by a high incidence of MYD88 L265P and CD79B Y196 hotspot mutations. Diagnosis of PCNSL can be challenging. The aim of the study was to analyze the detection rate of the MYD88 L265P and CD79B Y196 mutation in cell free DNA (cfDNA) in plasma of patients with PCNSL. METHODS We analyzed by digital droplet PCR (ddPCR) to determine presence of the MYD88 L265P and CD79B Y196 hotspot mutations in cfDNA isolated from plasma of 24 PCNSL patients with active disease. Corresponding tumor samples were available for 14 cases. Based on the false positive rate observed in 8 healthy control samples, a stringent cut-off for the MYD88 L265P and CD79B Y196 mutation were set at 0.3% and 0.5%, respectively. RESULTS MYD88 L265P and CD79B Y196 mutations were detected in 9/14 (64%) and 2/13 (15%) tumor biopsies, respectively. In cfDNA samples, the MYD88 L265P mutation was detected in 3/24 (12.5%), while the CD79B Y196 mutation was not detected in any of the 23 tested cfDNA samples. Overall, MYD88 L265P and/or CD79B Y196 were detected in cfDNA in 3/24 cases (12.5%). The detection rate of the combined analysis did not improve the single detection rate for either MYD88 L265P or CD79B Y196. CONCLUSION The low detection rate of MYD88 L265P and CD79B Y196 mutations in cfDNA in the plasma of PCNSL patients argues against its use in routine diagnostics. However, detection of MYD88 L265P by ddPCR in cfDNA in the plasma could be considered in challenging cases.
Collapse
Affiliation(s)
- Yujie Zhong
- Department of Hematology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Geok Wee Tan
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Johanna Bult
- Department of Hematology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nick Veltmaat
- Department of Hematology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wouter Plattel
- Department of Hematology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Roelien Enting
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel Nijland
- Department of Hematology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| |
Collapse
|
27
|
Lin S, Wang S, Xu B. Fragmentation patterns of cell-free DNA and somatic mutations in the urine of metastatic breast cancer patients. J Cancer Res Ther 2024; 20:563-569. [PMID: 38454812 DOI: 10.4103/jcrt.jcrt_1359_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/08/2023] [Indexed: 03/09/2024]
Abstract
BACKGROUND Urinary cell-free deoxyribonucleic acid (DNA) (ucfDNA) holds promise as a biomarker; however, its potential remains largely unexplored. We examined the fragmentation pattern of ucfDNA and identified somatic mutations within urine samples from metastatic breast cancer (MBC) patients. METHODS Urine and blood specimens were collected before treatment from 45 MBC patients and posttreatment urine samples from 16 of the 45 patients at the China National Cancer Center. Somatic mutations and tumor mutational burden (TMB) in the urine and plasma of 10 patients were analyzed by next-generation sequencing (NGS). Fragmentation patterns of cfDNA were displayed using electropherograms. Differences in the extracted amount of cfDNA, length of cfDNA fragments, and TMB between urine and plasma were compared using a Wilcoxon test. RESULTS The fragmentation patterns of ucfDNA were categorized as follows: (1) profile A (n = 26) containing a short peak (100-200 bp) and a long peak (>1500 bp); (2) profile B (n = 8) containing only a long peak; and (3) profile C (n = 11) containing flat pattern. For profile A patients, the short-peaked ucfDNA circulating in the bloodstream was much shorter compared with plasma cfDNA (149 vs. 171 bp, Wilcoxon test, P = 0.023). The fragmentation patterns in lung metastasis patients exhibited a higher propensity toward profile C ( P = 0.002). After treatment, 87.5% of the patients exhibited consistent fragmentation patterns. The concordance rate for somatic mutations in the plasma and urine was 30%, and the median TMB of urine and plasma was not significantly different. CONCLUSIONS This study established a fragmentation pattern for ucfDNA and detected somatic mutations in the urine of MBC patients. These results suggest the potential application of ucfDNA as a biomarker for MBC.
Collapse
Affiliation(s)
- Shaoyan Lin
- Department of Clinical Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Shusen Wang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| |
Collapse
|
28
|
Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024; 96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital sequencing has made previously challenging applications possible by significantly improving sensitivity and specificity to now allow detection of rare sequence variants, even at single molecule level. Digital sequencing utilizes unique molecular identifiers (UMIs) to minimize sequencing-induced errors and quantification biases. Here, we discuss the principles of UMIs and how they are used in digital sequencing. We outline the properties of different UMI types and the consequences of various UMI approaches in relation to experimental protocols and bioinformatics. Finally, we describe how digital sequencing can be applied in specific research fields, focusing on cancer management where it can be used in screening of asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring treatment efficacy and early detection of treatment resistance as well as relapse.
Collapse
Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Firaol Tamiru Kebede
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
| |
Collapse
|
29
|
Lee JY, Jeon S, Jun HR, Sung CO, Jang SJ, Choi CM, Chun SM. Revolutionizing Non-Small Cell Lung Cancer Diagnosis: Ultra-High-Sensitive ctDNA Analysis for Detecting Hotspot Mutations with Long-term Stored Plasma. Cancer Res Treat 2024; 56:484-501. [PMID: 37871897 PMCID: PMC11016651 DOI: 10.4143/crt.2023.712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/22/2023] [Indexed: 10/25/2023] Open
Abstract
PURPOSE Circulating cell-free DNA (cfDNA) has great potential in clinical oncology. The prognostic and predictive values of cfDNA in non-small cell lung cancer (NSCLC) have been reported, with epidermal growth factor receptor (EGFR), KRAS, and BRAF mutations in tumor-derived cfDNAs acting as biomarkers during the early stages of tumor progression and recurrence. However, extremely low tumor-derived DNA rates hinder cfDNA application. We developed an ultra-high-sensitivity lung version 1 (ULV1) panel targeting BRAF, KRAS, and EGFR hotspot mutations using small amounts of cfDNA, allowing for semi-quantitative analysis with excellent limit-of-detection (0.05%). MATERIALS AND METHODS Mutation analysis was performed on cfDNAs extracted from the plasma of 104 patients with NSCLC by using the ULV1 panel and targeted next-generation sequencing (CT-ULTRA), followed by comparison analysis of mutation patterns previously screened using matched tumor tissue DNA. RESULTS The ULV1 panel demonstrated robust selective amplification of mutant alleles, enabling the detection of mutations with a high degree of analytical sensitivity (limit-of-detection, 0.025%-0.1%) and specificity (87.9%-100%). Applying ULV1 to NSCLC cfDNA revealed 51.1% (23/45) samples with EGFR mutations, increasing with tumor stage: 8.33% (stage I) to 78.26% (stage IV). Semi-quantitative analysis proved effective for low-mutation-fraction clinical samples. Comparative analysis with PANAMutyper EGFR exhibited substantial concordance (κ=0.84). CONCLUSION Good detection sensitivity (~80%) was observed despite the limited volume (1 mL) and long-term storage (12-50 months) of plasma used and is expected to increase with high cfDNA inputs. Thus, the ULV1 panel is a fast and cost-effective method for early diagnosis, treatment selection, and clinical follow-up of patients with NSCLC.
Collapse
Affiliation(s)
- Ji-Young Lee
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Seoul, Korea
| | - Seyeon Jeon
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Seoul, Korea
| | - Ha Ra Jun
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Seoul, Korea
| | - Chang Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang-Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| |
Collapse
|
30
|
Das D, Avssn R, Chittela RK. A phenol-chloroform free method for cfDNA isolation from cell conditioned media: development, optimization and comparative analysis. Anal Biochem 2024; 687:115454. [PMID: 38158107 DOI: 10.1016/j.ab.2023.115454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The non-invasive invasive nature of cell-free DNA (cfDNA) as diagnostic, prognostic, and theragnostic biomarkers has gained immense popularity in recent years. The clinical utility of cfDNA biomarkers may depend on understanding their origin and biological significance. Apoptosis, necrosis, and/or active release are possible mechanisms of cellular DNA release into the cell-free milieu. In-vitro cell culture models can provide useful insights into cfDNA biology. The yields and quality of cfDNA in the cell conditioned media (CCM) are largely dependent on the extraction method used. Here, we developed a phenol-chloroform-free cfDNA extraction method from CCM and compared it with three others published cfDNA extraction methods and four commercially available kits. Real-Time PCR (qPCR) targeting two different loci and a fluorescence-based Qubit assay were performed to quantify the extracted cfDNA. The absolute concentration of the extracted cfDNA varies with the target used for the qPCR assay; however, the relative trend remains similar for both qPCR assays. The cfDNA yield from CCM provided by the developed method was found to be either higher or comparable to the other methods used. In conclusion, we developed a safe, rapid and cost-effective cfDNA extraction protocol with minimal hands-on time; with no compromise in cfDNA yields.
Collapse
Affiliation(s)
- Dhruv Das
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India
| | - Rao Avssn
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Rajani Kant Chittela
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India.
| |
Collapse
|
31
|
Egger ME, Alexander E, Van Meter T, Kong M, Maung AA, Valdes R, Hall MB, Linder MW. Corresponding ctDNA and tumor burden dynamics in metastatic melanoma patients on systemic treatment. Transl Oncol 2024; 42:101883. [PMID: 38306914 PMCID: PMC10850110 DOI: 10.1016/j.tranon.2024.101883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Radiographic imaging is the current standard for monitoring progression of tumor-burden and therapeutic resistance in patients with metastatic melanoma. Plasma circulating tumor DNA (ctDNA) has shown promise as a survelience tool, but longitudinal data on the dynamics between plasma ctDNA concentrations and radiographic imaging is lacking. We evaluated the relationship between longitudinal radiographic measures of tumor burden and ctDNA concentrations in plasma on 30 patients with metastatic melanoma on systemic treatment. In 9 patients with no radiographic evidence of disease over a total of 15 time points, ctDNA concentrations were undetectable. In 21 patients with radiographic tumor burden, ctDNA was detected in 81 % of 58 time points. Plasma ctDNA concentrations demonstrated a modest positive correlation with total tumor burden (TTB) measurements (R2= 0.49, p < 0.001), with the greatest degree of correlation observed under conditions of progressive disease (PD) (R2 = 0.91, p = 0.032). Plasma ctDNA concentrations were significantly greater at times of RECIST v1.1 progression (PD; 22.1 % ± 5.7 %) when compared to samples collected during stable disease (SD; 4.99 % ± 3.0 %) (p = 0.012); this difference was independent of total tumor burden (p = 0.997). Changes in plasma ctDNA showed a strong correlation with changes in TTB (R2= 0.88, p<0.001). These data suggest that measurements of plasma ctDNA during therapy are a better surrogate for responding versus non-responding disease compared to absolute tumor burden.
Collapse
Affiliation(s)
- Michael E Egger
- Department of Surgery, Division of Surgical Oncology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Evan Alexander
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Tracy Van Meter
- Department of Radiology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Maiying Kong
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, Louisville, KY, USA; Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA
| | - Aye Aye Maung
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, Louisville, KY, USA; Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA
| | - Roland Valdes
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA; Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa Barousse Hall
- UofL Health Brown Cancer Center, Louisville, KY, USA; Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA; UofL Health Brown Cancer Center, Louisville, KY, USA.
| |
Collapse
|
32
|
Lai HF, Wang SE, Chen SC, Shyr BS, Shyr YM, Shyr BU. The emerging role of cell-free DNA as a molecular marker for duodenal adenocarcinoma. J Chin Med Assoc 2024; 87:422-427. [PMID: 38391235 DOI: 10.1097/jcma.0000000000001079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Duodenal adenocarcinoma is rare and its prognostic factors remain controversial. In our study, the role of cell-free deoxyribonucleic acid (cfDNA) as prognostic factor in duodenal adenocarcinoma was evaluated. METHODS From June 2003 to July 2021, plasma samples were collected from 41 patients with duodenal adenocarcinoma. Plasma cfDNA was assessed in combination with clinicopathological and biochemical characteristics. Univariate and multivariate analyses were conducted to identify independent prognostic factors for overall survival with a Cox proportional hazards regression model. RESULTS The 1- and 5-year survival rates of the patients with high plasma cfDNA level (>9288 copies/mL) group were 58.7% and 17.6%, respectively, which were much lower than patients with low cfDNA level (≤9288 copies/mL), with 95.2% and 64.6%. In univariate analysis, high cfDNA level, lymph node involvement, lymphovascular invasion, and tumor stage were associated with decreased survival. When subjected to multivariate analysis, only high cfDNA level showed significance in influencing the overall survival of duodenal cancer. CONCLUSION cfDNA analysis is simple and noninvasive. High cfDNA level is a strong independent prognostic factor for decreased overall survival and it should be integrated into clinical care.
Collapse
Affiliation(s)
- Hon-Fan Lai
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital and National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | | | | | | | | | | |
Collapse
|
33
|
Çelik B, Peker Eyüboğlu İ, Koca S, Uğurlu MÜ, Alan Ö, Güllü Amuran G, Akin Telli T, Yumuk F, Akkiprik M. Correlation between plasma ccfDNA, mtDNA changes, CTCs, and epithelial-mesenchymal transition in breast cancer patients undergoing NACT. Turk J Med Sci 2024; 54:652-665. [PMID: 39295614 PMCID: PMC11407343 DOI: 10.55730/1300-0144.5834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 08/23/2024] [Accepted: 03/11/2024] [Indexed: 09/21/2024] Open
Abstract
Background/aim Breast cancer is the most prevalent cancer in women, emphasizing need for noninvasive blood biomarkers to aid in treatment selection. Previous studies have demonstrated elevated levels of plasma circulating cell-free DNA (ccfDNA) in breast cancer patients. Both ccfDNA and mitochondrial DNA (mtDNA) are fragments released into the bloodstream. In this study, we investigated effectiveness of ccfDNA and mtDNA as indicators of treatment response and explored their potential as monitoring biomarkers. Additionally, we compared these markers with circulating tumor cell (CTC) data and assessed their relationship with epithelial-mesenchymal transition (EMT). Materials and methods Thirty-six female breast cancer patients and 21 healthy females were included in the study. Quantitative polymerase chain reaction (qPCR) was performed on plasma samples to measure levels of ND1, ND4, ALU115, ALU247, and GAPDH, and DNA integrity was determined by calculating ratios of ALU247/ALU115 and ND4/ND1. Results After treatment, patients had a significant decrease in ccfDNA levels and a significant increase in mtDNA copy number (mtDNAcn). However, there was no significant change in ccfDNA and mtDNA integrity. When comparing all groups, patients exhibited higher levels of ALU115 and ALU247 compared to controls. Moreover, patients demonstrated significantly lower ccfDNA integrity than controls. Conclusion This study represents the first comprehensive investigation of plasma ccfDNA levels, mtDNAcn, and integrities collectively. Furthermore, it is the first study to explore the relationship between these markers and CTCs, cancer stem cell markers, treatment response, and metastatic status. Our findings suggest that plasma ccfDNA and mtDNA may serve as potential biomarkers for assessing chemotherapy response and can be employed alone or in combination with other biomarkers to monitor treatment efficacy in breast cancer patients.
Collapse
Affiliation(s)
- Betül Çelik
- Department of Medical Biology and Genetics, Health Sciences Institute, Marmara University, İstanbul, Turkiye
| | - İrem Peker Eyüboğlu
- Department of Medical Biology, School of Medicine, Marmara University, İstanbul, Turkiye
| | - Sinan Koca
- Department of Medical Oncology, Ümraniye Education Research Hospital, İstanbul, Turkiye
| | - M Ümit Uğurlu
- Department of General Surgery, School of Medicine, Marmara University, İstanbul, Turkiye
| | - Özkan Alan
- Department of Medical Oncology, School of Medicine, Marmara University, İstanbul, Turkiye
| | - Gökçe Güllü Amuran
- Department of Medical Biology, School of Medicine, Marmara University, İstanbul, Turkiye
| | - Tuğba Akin Telli
- Department of Medical Oncology, School of Medicine, Marmara University, İstanbul, Turkiye
| | - Fulden Yumuk
- Department of Medical Oncology, School of Medicine, Marmara University, İstanbul, Turkiye
| | - Mustafa Akkiprik
- Department of Medical Biology, School of Medicine, Marmara University, İstanbul, Turkiye
| |
Collapse
|
34
|
Wever BMM, Steenbergen RDM. Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities. Mol Oncol 2024. [PMID: 38462745 DOI: 10.1002/1878-0261.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/27/2024] [Indexed: 03/12/2024] Open
Abstract
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor-derived cell-free DNA. We also provide future recommendations for technical advancements in urine-based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell-free DNA.
Collapse
Affiliation(s)
- Birgit M M Wever
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| |
Collapse
|
35
|
Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
Collapse
Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
36
|
Abdul Wahab MR, Palaniyandi T, Viswanathan S, Baskar G, Surendran H, Gangadharan SGD, Sugumaran A, Sivaji A, Kaliamoorthy S, Kumarasamy S. Biomarker-specific biosensors revolutionise breast cancer diagnosis. Clin Chim Acta 2024; 555:117792. [PMID: 38266968 DOI: 10.1016/j.cca.2024.117792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Breast cancer is the most common cancer among women across the globe. In order to treat breast cancer successfully, it is crucial to conduct a comprehensive assessment of the condition during its initial stages. Although mammogram screening has long been a common method of breast cancer screening, high rates of type I error and type II error results as well as radiation exposure have always been of concern. The outgrowth cancer mortality rate is primarily due to delayed diagnosis, which occurs most frequently in a metastatic III or IV stage, resulting in a poor prognosis after therapy. Traditional detection techniques require identifying carcinogenic properties of cells, such as DNA or RNA alterations, conformational changes and overexpression of certain proteins, and cell shape, which are referred to as biomarkers or analytes. These procedures are complex, long-drawn-out, and expensive. Biosensors have recently acquired appeal as low-cost, simple, and super sensitive detection methods for analysis. The biosensor approach requires the existence of biomarkers in the sample. Thus, the development of novel molecular markers for diverse forms of cancer is a rising complementary affair. These biosensor devices offer two major advantages: (1) a tiny amount of blood collected from the patient is sufficient for analysis, and (2) it could help clinicians swiftly select and decide on the best therapy routine for the individual. This review will include updates on prospective cancer markers and biosensors in cancer diagnosis, as well as the associated detection limitations, with a focus on biosensor development for marker detection.
Collapse
Affiliation(s)
| | - Thirunavukkarasu Palaniyandi
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India; Department of Anatomy, Biomedical Research Unit and Laboratory Animal Centre, Saveetha Dental College and Hospital, SIMATS, Saveetha University, Chennai, India.
| | - Sandhiya Viswanathan
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Gomathy Baskar
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Hemapreethi Surendran
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - S G D Gangadharan
- Department of Medical Oncology, Madras Medical College, R. G. G. G. H., Chennai, Tamil Nadu, India
| | - Abimanyu Sugumaran
- Department of Pharmaceutical Sciences, Assam University, (A Central University), Silchar, Assam, India
| | - Asha Sivaji
- Department of Biochemistry, DKM College for Women, Vellore, India
| | - Senthilkumar Kaliamoorthy
- Department of Electronics and Communication Engineering, Dr. M.G.R Educational and Research Institute, Chennai, Tamil Nadu, India
| | - Saravanan Kumarasamy
- Department of Electrical and Electronics Engineering, Dr. M.G.R Educational and Research Institute, Chennai, Tamil Nadu, India
| |
Collapse
|
37
|
Chantre-Justino M, Figueiredo MC, Alves G, Ornellas MHF. A pilot study on salivary HPV DNA detection to monitor active disease from patients with recurrent respiratory papillomatosis. Am J Otolaryngol 2024; 45:104157. [PMID: 38061173 DOI: 10.1016/j.amjoto.2023.104157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/04/2023] [Indexed: 03/16/2024]
Abstract
PURPOSE Recurrent respiratory papillomatosis (RRP) is a human papillomavirus (HPV)-related disease affecting the upper airway and saliva could be an important non-invasive sampling source for viral screening and clinical monitoring. We investigated whether HPV DNA could be detected in saliva (cellular pellets and supernatant) from RRP patients and influence on clinical manifestation of the disease. MATERIALS AND METHODS In this pilot study, saliva samples from 14 RRP patients were obtained in preoperative condition (n = 7) and in disease-free interval (DFI; n = 7). Healthy donors (n = 14) were also included. HPV DNA was investigated by polymerase chain reaction (PCR)-based assays. RESULTS From cellular pellets, HPV-positive saliva was only detected from preoperative collections (5/7; 71.4 %) and showed a mean cycle threshold (Ct) value of 24.33 (±1.25), whereas all patients in DFI were HPV-negative (Ct ≥ 32.16), revealing significant difference between these two clinical moments (p = 0.021). Patients in DFI and healthy donors showed similar Ct values. From saliva supernatant, detectable HPV cell-free DNA (cfDNA) occurred in 42.9 % (3/7) and 57.1 % (4/7) of preoperative collections using the commercial cfDNA kits from Norgen and Qiagen, respectively. Salivary cfDNA size distribution obtained by TapeStation analysis showed a predominant size range of 150 to 400 bp in both patients and healthy controls, corresponding to mononucleosomal and dinucleosomal fragments. CONCLUSIONS In conclusion, HPV DNA screening in saliva (both cellular pellets and cfDNA) may have clinical utility to monitor active disease of RRP patients.
Collapse
Affiliation(s)
- Mariana Chantre-Justino
- Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Research Division, National Institute of Traumatology and Orthopaedics (INTO), Rio de Janeiro 20940-070, Brazil.
| | - Marcelo Cardoso Figueiredo
- Respiratory Endoscopy and Head and Neck Surgery Service at Hospital Federal de Bonsucesso, Rio de Janeiro 21041-030, Brazil
| | - Gilda Alves
- Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Maria Helena Faria Ornellas
- Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| |
Collapse
|
38
|
Yang Q, Zhu X, Liu Y, He Z, Xu H, Zheng H, Huang Z, Wang D, Lin X, Guo P, Chen H. Reduced representative methylome profiling of cell-free DNA for breast cancer detection. Clin Epigenetics 2024; 16:33. [PMID: 38414041 PMCID: PMC10898043 DOI: 10.1186/s13148-024-01641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Whole-genome methylation sequencing of cfDNA is not cost-effective for tumor detection. Here, we introduce reduced representative methylome profiling (RRMP), which employs restriction enzyme for depletion of AT-rich sequence to achieve enrichment and deep sequencing of CG-rich sequences. METHODS We first verified the ability of RRMP to enrich CG-rich sequences using tumor cell genomic DNA and analyzed differential methylation regions between tumor cells and normal whole blood cells. We then analyzed cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals to detect breast cancer by building machine learning models. RESULTS RRMP captured 81.9% CpG islands and 75.2% gene promoters when sequenced to 10 billion base pairs, with an enrichment efficiency being comparable to RRBS. RRMP allowed us to assess DNA methylation changes between tumor cells and whole blood cells. Applying our approach to cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals, we developed machine learning models that could discriminate between breast cancer and non-breast cancer controls (AUC = 0.85), suggesting possibilities for truly non-invasive cancer detection. CONCLUSIONS We developed a new method to achieve reduced representative methylome profiling of cell-free DNA for tumor detection.
Collapse
Affiliation(s)
- Qingmo Yang
- The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xingqiang Zhu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Yulu Liu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhi He
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Huan Xu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Hailing Zheng
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhiming Huang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Dan Wang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Xiaofang Lin
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Ping Guo
- Xiamen Huazao Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
| | - Hongliang Chen
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| |
Collapse
|
39
|
Nguyen T, Jeong S, Kang SK, Han SW, Nguyen TMT, Lee S, Jung YJ, Kim YH, Park S, Bak GH, Ko YC, Choi EJ, Kim HY, Oh JW. 3D Superclusters with Hybrid Bioinks for Early Detection in Breast Cancer. ACS Sens 2024; 9:699-707. [PMID: 38294962 PMCID: PMC10897927 DOI: 10.1021/acssensors.3c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024]
Abstract
The surface-enhanced Raman scattering (SERS) technique has garnered significant interest due to its ultrahigh sensitivity, making it suitable for addressing the growing demand for disease diagnosis. In addition to its sensitivity and uniformity, an ideal SERS platform should possess characteristics such as simplicity in manufacturing and low analyte consumption, enabling practical applications in complex diagnoses including cancer. Furthermore, the integration of machine learning algorithms with SERS can enhance the practical usability of sensing devices by effectively classifying the subtle vibrational fingerprints produced by molecules such as those found in human blood. In this study, we demonstrate an approach for early detection of breast cancer using a bottom-up strategy to construct a flexible and simple three-dimensional (3D) plasmonic cluster SERS platform integrated with a deep learning algorithm. With these advantages of the 3D plasmonic cluster, we demonstrate that the 3D plasmonic cluster (3D-PC) exhibits a significantly enhanced Raman intensity through detection limit down to 10-6 M (femtomole-(10-17 mol)) for p-nitrophenol (PNP) molecules. Afterward, the plasma of cancer subjects and healthy subjects was used to fabricate the bioink to build 3D-PC structures. The collected SERS successfully classified into two clusters of cancer subjects and healthy subjects with high accuracy of up to 93%. These results highlight the potential of the 3D plasmonic cluster SERS platform for early breast cancer detection and open promising avenues for future research in this field.
Collapse
Affiliation(s)
- Thanh
Mien Nguyen
- Bio-IT
Fusion Technology Research Institute, Pusan
National University, Busan 46241, Republic
of Korea
| | - SinSung Jeong
- Telecommunication
System Technology, College of Engineering, Korea University, Seoul 02841, Republic
of Korea
| | - Seok Kyung Kang
- Department
of Surgery, Pusan National University Yangsan
Hospital, Pusan National University School of Medicine, Yangsan 49241, Republic of Korea
| | - Seung-Wook Han
- Department
of Nano Fusion Technology, Pusan National
University, Busan 46214, Republic of Korea
| | - Thu M. T. Nguyen
- Department
of Nano Fusion Technology, Pusan National
University, Busan 46214, Republic of Korea
| | - Seungju Lee
- Department
of Surgery, Pusan National University Yangsan
Hospital, Pusan National University School of Medicine, Yangsan 49241, Republic of Korea
| | - Youn Joo Jung
- Department
of Surgery, Pusan National University Yangsan
Hospital, Pusan National University School of Medicine, Yangsan 49241, Republic of Korea
| | - You Hwan Kim
- Department
of Nano Fusion Technology, Pusan National
University, Busan 46214, Republic of Korea
| | - Sunwoo Park
- Department
of Nano Fusion Technology, Pusan National
University, Busan 46214, Republic of Korea
| | - Gyeong-Ha Bak
- Department
of Nano Fusion Technology, Pusan National
University, Busan 46214, Republic of Korea
| | - Young-Chai Ko
- School
of Electrical and Computer Engineering, Korea University, Seoul 02841, Republic
of Korea
| | - Eun-Jung Choi
- Bio-IT
Fusion Technology Research Institute, Pusan
National University, Busan 46241, Republic
of Korea
| | - Hyun Yul Kim
- Department
of Surgery, Pusan National University Yangsan
Hospital, Pusan National University School of Medicine, Yangsan 49241, Republic of Korea
| | - Jin-Woo Oh
- Bio-IT
Fusion Technology Research Institute, Pusan
National University, Busan 46241, Republic
of Korea
- Department
of Nano Fusion Technology, Pusan National
University, Busan 46214, Republic of Korea
- Department
of Nanoenergy Engineering and Research Center for Energy Convergence
Technology, Pusan National University, Busan 46214, Republic of Korea
| |
Collapse
|
40
|
Wang HY, Lin WY, Zhou C, Yang ZA, Kalpana S, Lebowitz MS. Integrating Artificial Intelligence for Advancing Multiple-Cancer Early Detection via Serum Biomarkers: A Narrative Review. Cancers (Basel) 2024; 16:862. [PMID: 38473224 DOI: 10.3390/cancers16050862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The concept and policies of multicancer early detection (MCED) have gained significant attention from governments worldwide in recent years. In the era of burgeoning artificial intelligence (AI) technology, the integration of MCED with AI has become a prevailing trend, giving rise to a plethora of MCED AI products. However, due to the heterogeneity of both the detection targets and the AI technologies, the overall diversity of MCED AI products remains considerable. The types of detection targets encompass protein biomarkers, cell-free DNA, or combinations of these biomarkers. In the development of AI models, different model training approaches are employed, including datasets of case-control studies or real-world cancer screening datasets. Various validation techniques, such as cross-validation, location-wise validation, and time-wise validation, are used. All of the factors show significant impacts on the predictive efficacy of MCED AIs. After the completion of AI model development, deploying the MCED AIs in clinical practice presents numerous challenges, including presenting the predictive reports, identifying the potential locations and types of tumors, and addressing cancer-related information, such as clinical follow-up and treatment. This study reviews several mature MCED AI products currently available in the market, detecting their composing factors from serum biomarker detection, MCED AI training/validation, and the clinical application. This review illuminates the challenges encountered by existing MCED AI products across these stages, offering insights into the continued development and obstacles within the field of MCED AI.
Collapse
Affiliation(s)
- Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu 300044, Taiwan
- 20/20 GeneSystems, Gaithersburg, MD 20877, USA
| | - Wan-Ying Lin
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | | | - Zih-Ang Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | - Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | | |
Collapse
|
41
|
Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
Collapse
Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
42
|
Parida P, Baburaj G, Rao M, Lewis S, Damerla RR. Circulating cell-free DNA as a diagnostic and prognostic marker for cervical cancer. Int J Gynecol Cancer 2024; 34:307-316. [PMID: 37949487 DOI: 10.1136/ijgc-2023-004873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) is a promising tool for liquid biopsy-based tests. cfDNA has been reported to help in the diagnosis, quantification of minimal residual disease, prognosis, and identification of mutations conferring resistance in various types of cancers. Cervical cancer is the fourth most common cancer among women worldwide. High-risk human papillomavirus (hr-HPV) infections have been associated with almost all cervical cancers. Lack of HPV vaccines in national vaccination programs and irregular screening strategies in nations with low or moderate levels of human development index have led to cervical cancer becoming the second leading cause of cancer mortality in women. As HPV integration and overexpression of E6/E7 oncoprotein are crucial steps in the development of cancer, HPV cfDNA could potentially be used as a specific biomarker for the detection of cervical cancer. Many studies have used HPV cfDNA and other gene mutations or mRNA expression profiles for diagnosis and disease surveillance in patients with cervical cancer at various stages of disease progression. In this review we present an overview of different studies discussing the utility of cfDNA in cervical cancer and summarize the evidence supporting its potential use in diagnosis and treatment monitoring.
Collapse
Affiliation(s)
- Preetiparna Parida
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gayathri Baburaj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shirley Lewis
- Department of Radiotherapy and Oncology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Rama Rao Damerla
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
43
|
Ferdosnejad K, Zamani MS, Soroush E, Fateh A, Siadat SD, Tarashi S. Tuberculosis and lung cancer: metabolic pathways play a key role. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-20. [PMID: 38305273 DOI: 10.1080/15257770.2024.2308522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
Despite the fact that some cases of tuberculosis (TB) are undiagnosed and untreated, it remains a serious global public health issue. In the diagnosis, treatment, and control of latent and active TB, there may be a lack of effectiveness. An understanding of metabolic pathways can be fundamental to treat latent TB infection and active TB disease. Rather than targeting Mycobacterium tuberculosis, the control strategies aim to strengthen host responses to infection and reduce chronic inflammation by effectively enhancing host resistance to infection. The pathogenesis and progression of TB are linked to several metabolites and metabolic pathways, and they are potential targets for host-directed therapies. Additionally, metabolic pathways can contribute to the progression of lung cancer in patients with latent or active TB. A comprehensive metabolic pathway analysis is conducted to highlight lung cancer development in latent and active TB. The current study aimed to emphasize the association between metabolic pathways of tumor development in patients with latent and active TB. Health control programs around the world are compromised by TB and lung cancer due to their special epidemiological and clinical characteristics. Therefore, presenting the importance of lung cancer progression through metabolic pathways occurring upon TB infection can open new doors to improving control of TB infection and active TB disease while stressing that further evaluations are required to uncover this correlation.
Collapse
Affiliation(s)
| | | | - Erfan Soroush
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Tarashi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
44
|
Kim HH, Lee JC, Oh IJ, Kim EY, Yoon SH, Lee SY, Lee MK, Lee JE, Park CK, Lee KY, Lee SY, Kim SJ, Lim JH, Choi CM. Real-World Outcomes of Crizotinib in ROS1-Rearranged Advanced Non-Small-Cell Lung Cancer. Cancers (Basel) 2024; 16:528. [PMID: 38339278 PMCID: PMC10854608 DOI: 10.3390/cancers16030528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Real-world data on the use and outcomes of crizotinib in ROS1-rearranged non-small-cell lung cancer (NSCLC) are limited. This study aims to analyze the real-world efficacy of crizotinib in South Korea and explore the utilization of liquid biopsies that implement next-generation sequencing (NGS) using cell-free total nucleic acids. In this prospective multicenter cohort study, 40 patients with ROS1-rearranged NSCLC, either starting or already on crizotinib, were enrolled. Patients had a median age of 61 years, with 32.5% presenting brain/central nervous system (CNS) metastases at treatment initiation. At the data cutoff, 48.0% were still in treatment; four continued with it even after disease progression due to the clinical benefits. The objective response rate was 70.0%, with a median duration of response of 27.8 months. The median progression-free survival was 24.1 months, while the median overall survival was not reached. Adverse events occurred in 90.0% of patients, primarily with elevated transaminases, yet these were mostly manageable. The NGS assay detected a CD74-ROS1 fusion in 2 of the 14 patients at treatment initiation and identified emerging mutations, such as ROS1 G2032R, ROS1 D2033N, and KRAS G12D, during disease progression. These findings confirm crizotinib's sustained clinical efficacy and safety in a real-world context, which was characterized by a higher elderly population and higher rates of brain/CNS metastases. The study highlights the clinical relevance of liquid biopsy for detecting resistance mechanisms, suggesting its value in personalized treatment strategies.
Collapse
Affiliation(s)
- Hyeon Hwa Kim
- Division of Pulmonology and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea;
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical Centre, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea;
| | - In-Jae Oh
- Department of Internal Medicine, Chonnam National University Medical School and Hwasun Hospital, Gwangju 58128, Republic of Korea;
| | - Eun Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seong Hoon Yoon
- Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan 50612, Republic of Korea;
| | - Shin Yup Lee
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu 41404, Republic of Korea
| | - Min Ki Lee
- Division of Pulmonology, Allergy and Critical Care Medicine, Department of Internal Medicine, Pusan National University Hospital, Busan 49241, Republic of Korea;
| | - Jeong Eun Lee
- Division of Pulmonology, Department of Internal Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Chan Kwon Park
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 16247, Republic of Korea;
| | - Kye Young Lee
- Departments of Internal Medicine, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Republic of Korea;
| | - Sung Yong Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Seung Joon Kim
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 16247, Republic of Korea;
| | - Jun Hyeok Lim
- Department of Internal Medicine, Inha University Hospital, Incheon 22332, Republic of Korea
| | - Chang-min Choi
- Division of Pulmonology and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea;
- Department of Oncology, Asan Medical Centre, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea;
| |
Collapse
|
45
|
George NG, Rishi B, Singh A, Vishmaya S, Kumar R, Kushwaha N, Kaur M, Bhardwaj R, Jain A, Jain A, Chaudhry S, Misra A. Early prognosis prediction in acute myeloid and acute lymphoid leukemia patients using cell-free DNA concentration ratios. Front Mol Biosci 2024; 10:1333943. [PMID: 38317776 PMCID: PMC10840420 DOI: 10.3389/fmolb.2023.1333943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Background: Cell-free DNA (cfDNA) is a promising biomarker for disease prediction in many cancers, including acute leukemia (acute myeloid leukemia [AML] and acute lymphoblastic leukemia [ALL]). This study investigated the role of cfDNA in predicting relapse or unfavorable outcomes in acute leukemia patients upon initial diagnosis. Methods: Paired peripheral blood samples of 25 patients with ALL and AML were compared at baseline and induction/follow-up and clinically correlated with clinicopathological and outcome variables according to the risk category. cfDNA was isolated using commercial cfDNA extraction kits. The probability of poor outcomes in high-risk groups and a cut-off value for risk stratification minimal residual disease (MRD) positivity and outcome prediction were derived. Results: Twenty-five patients diagnosed with AML and ALL were risk-stratified based on NCI risk stratification, and of these 25 patients, 4 patients were of standard risk (SR) and 1 patient was of intermediate risk (IR), while a majority of patients (80%) were of high risk (HR). Of these, four HR patients passed away. The ratio of cfDNA reduction at baseline and the end of induction was a strong predictor of poor outcomes in high-risk patients, regardless of the MRD status. A cfDNA ratio score of 2.6 or higher at diagnosis/remission predicted poor outcomes, with higher accuracy than conventional MRD detection by flow cytometry. Conclusion: A higher cfDNA ratio at diagnosis/remission or at baseline predicts poor outcomes in acute leukemia patients. This pilot study suggests that cfDNA ratio scoring may be a useful tool for predicting prognosis in acute leukemia patients, regardless of the MRD status.
Collapse
Affiliation(s)
| | - Bhavika Rishi
- ICMR‐National Institute of Pathology, New Delhi, India
| | - Amitabh Singh
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sree Vishmaya
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Rakesh Kumar
- ICMR‐National Institute of Pathology, New Delhi, India
| | | | - Manpreet Kaur
- ICMR‐National Institute of Pathology, New Delhi, India
| | | | - Ankur Jain
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Aditi Jain
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sumita Chaudhry
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | | |
Collapse
|
46
|
Liu X, Mei F, Fang M, Jia Y, Zhou Y, Li C, Tian P, Lu C, Li G. Cerebrospinal fluid ctDNA testing shows an advantage over plasma ctDNA testing in advanced non-small cell lung cancer patients with brain metastases. Front Oncol 2024; 13:1322635. [PMID: 38269023 PMCID: PMC10806520 DOI: 10.3389/fonc.2023.1322635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
Background Brain metastases (BM), including brain parenchyma metastases (BPM) and leptomeningeal metastases (LM), are devastating metastatic complications in advanced cancer patients. Next-generation sequencing (NGS) is emerging as a new promising tool for profiling cancer mutation, which could facilitate the diagnosis of cancer. This retrospective study aimed to investigate the molecular genetic characteristics of non-small cell lung cancer (NSCLC) patients with BPM and LM using NGS. Methods Cerebrospinal fluid (CSF) samples and paired plasma samples were collected from 37 patients of NSCLC-BM. We profiled genetic mutation characteristics using NGS from NSCLC-BM by comparing CSF circulating tumour DNA (ctDNA) with plasma ctDNA and primary tumour tissues. Results Among the 37 patients with NSCLC-BM, 28 patients had LM with or without BPM, while 9 patients only had BPM. Driver and drug-resistant mutations in primary tumours with LM included: EGFR L858R (10, 35.7%), EGFR 19del (6, 21.4%), EGFR L858R+MET (1, 3.6%), EGFR L858R+S768I (1, 3.6%), ALK (2, 7.1%), ROS1 (1, 3.6%), negative (5, 17.9%), and unknown (2, 7.1%). In patients with NSCLC-LM, the detection rate and abundance of ctDNA in the CSF were significantly higher than those in paired plasma. The main driver mutations of NSCLC-LM remained highly consistent with those of the primary tumours, along with other unique mutations. Circulating tumour DNA was negative in the CSF samples of BPM patients. Patients with BMP had a higher ratio of EGFR 19del than L858R mutation (55.6% vs 11.1.%), whereas NSCLC patients with LM had a higher ratio of EGFR L858R than 19del mutation (50.0% vs 25.0%). Most patients with positive plasma ctDNA results were male (p = 0.058) and in an unstable state (p = 0.003). Conclusion Our study indicated that the CSF ctDNA detected by NGS may reflect the molecular characteristics and heterogeneity of NSCLC-LM. Timely screening of patients with NSCLC for CSF ctDNA, especially for patients with positive plasma ctDNA, may facilitate the early detection of LM. Furthermore, patients with the EGFR 19del may have a higher risk of developing BPM.
Collapse
Affiliation(s)
- Xiaocui Liu
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Neurology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei, China
| | - Fengjun Mei
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Mei Fang
- Department of Reproductive Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yaqiong Jia
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yazhu Zhou
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Chenxi Li
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Panpan Tian
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Chufan Lu
- Department of Neurology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guangrui Li
- Department of Neurology, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| |
Collapse
|
47
|
Bronkhorst AJ, Holdenrieder S. A pocket companion to cell-free DNA (cfDNA) preanalytics. Tumour Biol 2024; 46:S297-S308. [PMID: 37840517 DOI: 10.3233/tub-230011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The cumulative pool of cell-free DNA (cfDNA) molecules within bodily fluids represents a highly dense and multidimensional information repository. This "biological mirror" provides real-time insights into the composition, function, and dynamics of the diverse genomes within the body, enabling significant advancements in personalized molecular medicine. However, effective use of this information necessitates meticulous classification of distinct cfDNA subtypes with exceptional precision. While cfDNA molecules originating from different sources exhibit numerous genetic, epigenetic, and physico-chemical variations, they also share common features that complicate analyses. Considerable progress has been achieved in mapping the landscape of cfDNA features, their clinical correlations, and optimizing extraction procedures, analytical approaches, bioinformatics pipelines, and machine learning algorithms. Nevertheless, preanalytical workflows, despite their profound impact on cfDNA measurements, have not progressed at a corresponding pace. In this perspective article, we emphasize the pivotal role of robust preanalytical procedures in the development and clinical integration of cfDNA assays, highlighting persistent obstacles and emerging challenges.
Collapse
Affiliation(s)
- Abel J Bronkhorst
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, Munich, Germany
| |
Collapse
|
48
|
Yahya J, Baber M, Nabavizadeh N, Goodyear SM, Kardosh A. A Review of Circulating Tumor DNA as a Biomarker Guide for Total Neoadjuvant Therapy in Patients with Locally Advanced Rectal Cancer. J Gastrointest Cancer 2023; 54:1140-1150. [PMID: 36719559 PMCID: PMC10754735 DOI: 10.1007/s12029-022-00906-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2022] [Indexed: 02/01/2023]
Abstract
PURPOSE Non-operative management of patients with locally advanced rectal cancer (LARC) is emerging as a popular approach for patients that have no evidence of disease following neoadjuvant therapy. However, high rates of local recurrence or distant metastases have highlighted the urgent need for robust biomarker strategies to aid clinical management of these patients. METHODS This review summarizes recent advances in the utility of cell-free (cf) and circulating tumor (ct) DNA as potential biomarkers to help guide individualized non-operative management strategies for LARC patients receiving neoadjuvant therapy. RESULTS Liquid biopsies and the detection of cfDNA/ctDNA is an emerging technology with the potential to provide a non-invasive approach to monitor disease response and improve the identification of patients with LARC that would best benefit from non-operative management. CONCLUSIONS Substantial work is still needed before cfDNA/ctDNA monitoring can be widely adopted in the clinical setting. Studies reviewed herein highlight several areas of opportunity for improving the effectiveness and utility of cfDNA/ctDNA for managing patients with LARC.
Collapse
Affiliation(s)
- Jehan Yahya
- Department of Radiation Medicine, Oregon Health & Science University (OHSU), Portland, OR, USA
| | - Miriam Baber
- University of Kansas School of Medicine-Wichita, Wichita, KS, USA
| | - Nima Nabavizadeh
- Department of Radiation Medicine, Oregon Health & Science University (OHSU), Portland, OR, USA
- Knight Cancer Institute, OHSU, Portland, OR, USA
| | - Shaun M Goodyear
- Knight Cancer Institute, OHSU, Portland, OR, USA
- Division of Hematology and Oncology, School of Medicine, OHSU, Portland, OR, USA
| | - Adel Kardosh
- Knight Cancer Institute, OHSU, Portland, OR, USA.
- Division of Hematology and Oncology, School of Medicine, OHSU, Portland, OR, USA.
| |
Collapse
|
49
|
Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
Collapse
Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| |
Collapse
|
50
|
Miao Q, Zheng X, Li L, Zheng X, Zhang L, Jiang K, Wu S, Wang H, Wu B, Xu Y, Zhong Q, Zou Z, Zhang Q, Yang S, Li Y, Lin G. Cerebrospinal fluid circulating tumor DNA contributes to the detection and characterization of leptomeningeal metastasis in non-small cell lung cancer. J Neurooncol 2023; 165:517-525. [PMID: 38104049 DOI: 10.1007/s11060-023-04520-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
PURPOSE Cerebrospinal fluid (CSF) has revealed the unique genetic characteristics of leptomeningeal metastasis (LM) from non-small cell lung cancer (NSCLC). However, the research in this area is still very limited. METHODS Patients with LM from NSCLC (n = 80) were retrospectively analyzed. Circulating tumor DNA (ctDNA) in CSF was tested by next-generation sequencing (NGS), with paired extracranial tissue or plasma samples included for comparison. An independent non-LM cohort (n = 100) was also analyzed for comparative purposes. Clinical outcomes were compared with Kaplan-Meier log-rank test and Cox proportional hazards methodologies. RESULTS An overwhelming 93.8% of patients carried druggable mutations in NSCLC LM, with EGFR (78.8%) being the most prevalent. Notably, 4 patients who tested negative for driver genes in extracranial samples surprisingly showed EGFR mutations in their CSF and subsequently benefited from targeted therapy. There was a clear difference in genetic profiles between CSF and extracranial samples, with CSF showing more driver gene detections, increased Copy Number Variations (CNVs), and varied resistance mechanisms among individuals. Abnormalities in cell-cycle regulatory molecules were highly enriched in LM (50.9% vs 31.0%, p = 0.017), and CDKN2A/2B deletions were identified as an independent poor prognostic factor for LM patients, with a significant reduction in median OS (p = 0.013), supported by multivariate analysis (HR 2.63, 95% CI 1.32-5.26, p = 0.006). CONCLUSIONS CSF-based ctDNA analysis is crucial for detecting and characterizing genetic alterations in NSCLC LM. The distinct genetic profiles in CSF and extracranial tissues emphasize the need for personalized treatment approaches.
Collapse
Affiliation(s)
- Qian Miao
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Xinlong Zheng
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Lifeng Li
- Geneplus-Beijing Institute, Beijing, China
| | - Xiaobin Zheng
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Longfeng Zhang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Kan Jiang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Shiwen Wu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Haibo Wang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Biao Wu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yiquan Xu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Qiaofeng Zhong
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Zihua Zou
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Qiuyu Zhang
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
| | - Shanshan Yang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yujing Li
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Gen Lin
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China.
- Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China.
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou, China.
| |
Collapse
|