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Grewal US, Gaddam SJ, Beg MS, Brown TJ. Targeted therapies in advanced biliary malignancies: a clinical review. Expert Rev Anticancer Ther 2024; 24:869-880. [PMID: 39083012 DOI: 10.1080/14737140.2024.2387612] [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: 03/27/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
INTRODUCTION Despite several therapeutic advancements, the proportion of patients with advanced biliary tract cancers (BTC) surviving 5 years from diagnosis remains dismal. The increasing recognition of targetable genetic alterations in BTCs has ushered in a new era in the treatment of these patients. Newer therapeutic agents targeting mutations such as isocitrate dehydrogenase (IDH), fibroblastic growth factor receptor (FGFR), human epidermal growth factor receptor (HER), and so on have established a new standard of care for treatment upon progression on frontline therapy in patients with disease harboring these mutations. AREAS COVERED The current review aims to concisely summarize progress with various targeted therapy options for BTC. We also briefly discuss future directions in clinical and translational research for the adoption of a personalized approach for the treatment of unresectable or advanced BTC. EXPERT OPINION Several new agents continue to emerge as feasible treatment options for patients with advanced BTC harboring targetable mutations. There is a growing need to identify mechanisms to conquer primary and acquired resistance to these agents. The identification of potential biomarkers that predict response to targeted therapy may be helpful in adopting a more tailored approach. All patients receiving treatment for advanced BTC should undergo tissue genomic profiling at diagnosis.
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Affiliation(s)
- Udhayvir S Grewal
- Division of Hematology and Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Shiva J Gaddam
- Division of Hematology and Oncology, Department of Medicine, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | | | - Timothy J Brown
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Batool SM, Escobedo AK, Hsia T, Ekanayake E, Khanna SK, Gamblin AS, Zheng H, Skog J, Miller JJ, Stemmer-Rachamimov AO, Cahill DP, Balaj L, Carter BS. Clinical utility of a blood based assay for the detection of IDH1.R132H-mutant gliomas. Nat Commun 2024; 15:7074. [PMID: 39152110 PMCID: PMC11329733 DOI: 10.1038/s41467-024-51332-7] [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: 02/09/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
Glioma represents the most common central nervous system neoplasm in adults. Current classification scheme utilizes molecular alterations, particularly IDH1.R132H, to stratify lesions into distinct prognostic groups. Identification of the single nucleotide variant through traditional tissue biopsy assessment poses procedural risks and does not fully reflect the heterogeneous and evolving tumor landscape. Here, we introduce a liquid biopsy assay, mt-IDH1dx. The blood-based test allows minimally invasive detection of tumor-derived extracellular vesicle RNA using only 2 ml plasma volume. We perform rigorous, blinded validation testing across the study population (n = 133), comprising of IDH1.R132H patients (n = 80), IDH1 wild-type gliomas (n = 44), and age matched healthy controls (n = 9). Results from our plasma testing demonstrate an overall sensitivity of 75.0% (95% CI: 64.1%-84.0%), specificity 88.7% (95% CI: 77.0%-95.7%), positive predictive value 90.9%, and negative predictive value 70.1% compared to the tissue gold standard. In addition to fundamental diagnostic applications, the study also highlights the utility of mt-IDH1dx platform for blood-based monitoring and surveillance, offering valuable prognostic information. Finally, the optimized workflow enables rapid and efficient completion of both tumor tissue and plasma testing in under 4 hours from the time of sampling.
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Affiliation(s)
- Syeda Maheen Batool
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sirena K Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hui Zheng
- Center for Biostatistics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Johan Skog
- Exosome Diagnostics, a Bio-Techne Brand, Waltham, MA, USA
| | - Julie J Miller
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Liu X, Wang Q, Li J, Diao Z, Hou J, Huo D, Hou C. Simultaneous Detection of Micro-RNAs by a Disposable Biosensor via the Click Chemistry Connection Strategy. Anal Chem 2024; 96:10577-10585. [PMID: 38887964 DOI: 10.1021/acs.analchem.4c01120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Simultaneous detection of multiple breast cancer-associated miRNAs significantly raises the accuracy and reliability of early diagnosis. In this work, disposable carbon fiber paper serves as the biosensing interface, linking DNA probes via click chemistry to efficiently capture targets and signals efficiently. DNA probes have multiple recognition domains that trigger a cascade reaction through the helper probes and targets, resulting in two signals output. The signals are centrally encapsulated in the pore of the MIL-88(Fe)-NH2. The signal carriers are directed by signal probes to the recognition domains that correspond to the DNA probes. The biosensor is selective and stable, and it can quantify miRNA-21 and miRNA-155 simultaneously with detection limits of 0.64 and 0.54 fmol/L, respectively. Furthermore, it demonstrates satisfactory performance in tests conducted with normal human serum and cell lysate. Overall, this method makes a satisfactory exploration to realize an inexpensive and sensitive biosensor for multiple biomarkers.
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Affiliation(s)
- Xiaofang Liu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Qun Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Jiawei Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Zhan Diao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Jingzhou Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing 401331, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
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Wang H, Zhang Y, Zhang H, Cao H, Mao J, Chen X, Wang L, Zhang N, Luo P, Xue J, Qi X, Dong X, Liu G, Cheng Q. Liquid biopsy for human cancer: cancer screening, monitoring, and treatment. MedComm (Beijing) 2024; 5:e564. [PMID: 38807975 PMCID: PMC11130638 DOI: 10.1002/mco2.564] [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: 04/23/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
Currently, tumor treatment modalities such as immunotherapy and targeted therapy have more stringent requirements for obtaining tumor growth information and require more accurate and easy-to-operate tumor information detection methods. Compared with traditional tissue biopsy, liquid biopsy is a novel, minimally invasive, real-time detection tool for detecting information directly or indirectly released by tumors in human body fluids, which is more suitable for the requirements of new tumor treatment modalities. Liquid biopsy has not been widely used in clinical practice, and there are fewer reviews of related clinical applications. This review summarizes the clinical applications of liquid biopsy components (e.g., circulating tumor cells, circulating tumor DNA, extracellular vesicles, etc.) in tumorigenesis and progression. This includes the development process and detection techniques of liquid biopsies, early screening of tumors, tumor growth detection, and guiding therapeutic strategies (liquid biopsy-based personalized medicine and prediction of treatment response). Finally, the current challenges and future directions for clinical applications of liquid biopsy are proposed. In sum, this review will inspire more researchers to use liquid biopsy technology to promote the realization of individualized therapy, improve the efficacy of tumor therapy, and provide better therapeutic options for tumor patients.
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Affiliation(s)
- Hao Wang
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Yi Zhang
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Hao Zhang
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Hui Cao
- Department of PsychiatryThe School of Clinical Medicine, Hunan University of Chinese MedicineChangshaChina
- Department of PsychiatryBrain Hospital of Hunan Province (The Second People’s Hospital of Hunan Province)ChangshaChina
| | - Jinning Mao
- Health Management CenterThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xinxin Chen
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Liangchi Wang
- Department of NeurosurgeryFengdu People's Hospital, ChongqingChongqingChina
| | - Nan Zhang
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Peng Luo
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Ji Xue
- Department of NeurosurgeryTraditional Chinese Medicine Hospital Dianjiang ChongqingChongqingChina
| | - Xiaoya Qi
- Health Management CenterThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Xiancheng Dong
- Department of Cerebrovascular DiseasesDazhou Central HospitalSichuanChina
| | - Guodong Liu
- Department of NeurosurgeryThe Second Affiliated Hospital, Chongqing Medical UniversityChongqingChina
| | - Quan Cheng
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaChina
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Filatova AA, Alekseeva LA, Sen’kova AV, Savin IA, Sounbuli K, Zenkova MA, Mironova NL. Tumor- and Fibroblast-Derived Cell-Free DNAs Differently Affect the Progression of B16 Melanoma In Vitro and In Vivo. Int J Mol Sci 2024; 25:5304. [PMID: 38791341 PMCID: PMC11120878 DOI: 10.3390/ijms25105304] [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: 03/28/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
It is widely postulated that the majority of pathologically elevated extracellular or cell-free DNA (cfDNA) in cancer originates from tumor cells; however, evidence has emerged regarding the significant contributions of other cells from the tumor microenvironment. Here, the effect of cfDNA originating from murine B16 melanoma cells and L929 fibroblasts on B16 cells was investigated. It was found that cfDNAL929 increased the viability and migration properties of B16 cells in vitro and their invasiveness in vivo. In contrast, cfDNAB16 exhibited a negative effect on B16 cells, reducing their viability and migration in vitro, which in vivo led to decreased tumor size and metastasis number. It was shown that cell treatment with both cfDNAs resulted in an increase in the expression of genes encoding DNases and the oncogenes Braf, Kras, and Myc. cfDNAL929-treated cells were shown to experience oxidative stress. Gene expression changes in the case of cfDNAB16 treatment are well correlated with the observed decrease in proliferation and migration of B16 cells. The obtained data may indicate the possible involvement of fibroblast DNA in the tumor microenvironment in tumor progression and, potentially, in the formation of new tumor foci due to the transformation of normal cells.
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Affiliation(s)
- Alina A. Filatova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila A. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Innokenty A. Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Khetam Sounbuli
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Nadezhda L. Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
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6
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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.
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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
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Libert DM, Zhu Y, Wang A, Allard GM, Cheng-Yi Lowe A. Detection of effusion tumor cells under different storage and processing conditions. Cancer Cytopathol 2024; 132:297-308. [PMID: 38373107 DOI: 10.1002/cncy.22803] [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: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Circulating tumor cells (CTCs) shed into blood provide prognostic and/or predictive information. Previously, the authors established an assay to detect carcinoma cells from pleural fluid, termed effusion tumor cells (ETCs), by employing an immunofluorescence-based CTC-identification platform (RareCyte) on air-dried unstained ThinPrep (TP) slides. To facilitate clinical integration, they evaluated different slide processing and storage conditions, hypothesizing that alternative comparable conditions for ETC detection exist. METHODS The authors enumerated ETCs on RareCyte, using morphology and mean fluorescence intensity (MFI) cutoffs of >100 arbitrary units (a.u.) for epithelial cellular adhesion molecule (EpCAM) and <100 a.u. for CD45. They analyzed malignant pleural fluid from three patients under seven processing and/or staining conditions, three patients after short-term storage under three conditions, and seven samples following long-term storage at -80°C. MFI values of 4',6-diamidino-2-phenylindol, cytokeratin, CD45, and EpCAM were compared. RESULTS ETCs were detected in all conditions. Among the different processing conditions tested, the ethanol-fixed, unstained TP was most similar to the previously established air-dried, unstained TP protocol. All smears and Pap-stained TPs had significantly different marker MFIs from the established condition. After short-term storage, the established condition showed comparable results, but ethanol-fixed and Pap-stained slides showed significant differences. ETCs were detectable after long-term storage at -80°C in comparable numbers to freshly prepared slides, but most marker MFIs were significantly different. CONCLUSIONS It is possible to detect ETCs under different processing and storage conditions, lending promise to the application of this method in broader settings. Because of decreased immunofluorescence-signature distinctions between cells, morphology may need to play a larger role.
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Affiliation(s)
- Diane M Libert
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Yili Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Aihui Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Grace M Allard
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Alarice Cheng-Yi Lowe
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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Allen TA. The Role of Circulating Tumor Cells as a Liquid Biopsy for Cancer: Advances, Biology, Technical Challenges, and Clinical Relevance. Cancers (Basel) 2024; 16:1377. [PMID: 38611055 PMCID: PMC11010957 DOI: 10.3390/cancers16071377] [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: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer remains a leading cause of mortality worldwide, with metastasis significantly contributing to its lethality. The metastatic spread of tumor cells, primarily through the bloodstream, underscores the importance of circulating tumor cells (CTCs) in oncological research. As a critical component of liquid biopsies, CTCs offer a non-invasive and dynamic window into tumor biology, providing invaluable insights into cancer dissemination, disease progression, and response to treatment. This review article delves into the recent advancements in CTC research, highlighting their emerging role as a biomarker in various cancer types. We explore the latest technologies and methods for CTC isolation and detection, alongside novel approaches to characterizing their biology through genomics, transcriptomics, proteomics, and epigenetic profiling. Additionally, we examine the clinical implementation of these findings, assessing how CTCs are transforming the landscape of cancer diagnosis, prognosis, and management. By offering a comprehensive overview of current developments and potential future directions, this review underscores the significance of CTCs in enhancing our understanding of cancer and in shaping personalized therapeutic strategies, particularly for patients with metastatic disease.
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Zhao Y, Ma C, Cai R, Xin L, Li Y, Ke L, Ye W, Ouyang T, Liang J, Wu R, Lin Y. NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection. Nat Commun 2024; 15:2463. [PMID: 38504100 PMCID: PMC10951220 DOI: 10.1038/s41467-024-46837-0] [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: 08/29/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, consistently identified by NMR and MS, and reflected in 16 serum and 10 urine metabolic signatures in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperform clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and are effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613).
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Affiliation(s)
- Yan Zhao
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Central Laboratory, Clinical Research Center, Shantou Central Hospital, Shantou, Guangdong, China
| | - Changchun Ma
- Radiation Oncology Department, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Rongzhi Cai
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Lijing Xin
- Animal Imaging and Technology Core, Center for Biomedical Imaging, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Lixin Ke
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Wei Ye
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ting Ouyang
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jiahao Liang
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Renhua Wu
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Yan Lin
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
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10
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Pru JK. Defining liquid biopsy parameters in postmenopausal women for disease diagnosis. Menopause 2024; 31:169-170. [PMID: 38385728 DOI: 10.1097/gme.0000000000002330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Affiliation(s)
- James K Pru
- From the Program in Reproductive Biology, University of Wyoming, Laramie, WY
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11
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Min Y, Deng W, Yuan H, Zhu D, Zhao R, Zhang P, Xue J, Yuan Z, Zhang T, Jiang Y, Xu K, Wu D, Cai Y, Suo C, Chen X. Single extracellular vesicle surface protein-based blood assay identifies potential biomarkers for detection and screening of five cancers. Mol Oncol 2024; 18:743-761. [PMID: 38194998 PMCID: PMC10920081 DOI: 10.1002/1878-0261.13586] [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: 05/15/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Extracellular vesicles (EVs) and EV proteins are promising biomarkers for cancer liquid biopsy. Herein, we designed a case-control study involving 100 controls and 100 patients with esophageal, stomach, colorectal, liver, or lung cancer to identify common and type-specific biomarkers of plasma-derived EV surface proteins for the five cancers. EV surface proteins were profiled using a sequencing-based proximity barcoding assay. In this study, five differentially expressed proteins (DEPs) and eight differentially expressed protein combinations (DEPCs) showed promising performance (area under curve, AUC > 0.900) in pan-cancer identification [e.g., TENM2 (AUC = 0.982), CD36 (AUC = 0.974), and CD36-ITGA1 (AUC = 0.971)]. Our classification model could properly discriminate between cancer patients and controls using DEPs (AUC = 0.981) or DEPCs (AUC = 0.965). When distinguishing one cancer from the other four, the accuracy of the classification model using DEPCs (85-92%) was higher than that using DEPs (78-84%). We validated the performance in an additional 14 cancer patients and 14 controls, and achieved an AUC value of 0.786 for DEPs and 0.622 for DEPCs, highlighting the necessity to recruit a larger cohort for further validation. When clustering EVs into subpopulations, we detected cluster-specific proteins highly expressed in immune-related tissues. In the context of colorectal cancer, we identified heterogeneous EV clusters enriched in cancer patients, correlating with tumor initiation and progression. These findings provide epidemiological and molecular evidence for the clinical application of EV proteins in cancer prediction, while also illuminating their functional roles in cancer physiopathology.
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Affiliation(s)
- Yuxin Min
- Department of Epidemiology, School of Public HealthFudan UniversityShanghaiChina
| | - Wenjiang Deng
- Department of Medical Epidemiology and BiostatisticsKarolinska InstituteStockholmSweden
| | - Huangbo Yuan
- State Key Laboratory of Genetic Engineering, School of Life ScienceHuman Phenome Institute, Fudan UniversityShanghaiChina
| | - Dongliang Zhu
- Department of Epidemiology, School of Public HealthFudan UniversityShanghaiChina
| | - Renjia Zhao
- State Key Laboratory of Genetic Engineering, School of Life ScienceHuman Phenome Institute, Fudan UniversityShanghaiChina
| | - Pengyan Zhang
- Department of Epidemiology, School of Public HealthFudan UniversityShanghaiChina
| | - Jiangli Xue
- Fudan University Taizhou Institute of Health SciencesTaizhouChina
| | - Ziyu Yuan
- Fudan University Taizhou Institute of Health SciencesTaizhouChina
| | - Tiejun Zhang
- Department of Epidemiology, School of Public HealthFudan UniversityShanghaiChina
- Fudan University Taizhou Institute of Health SciencesTaizhouChina
- Yiwu Research Institute of Fudan UniversityChina
| | - Yanfeng Jiang
- State Key Laboratory of Genetic Engineering, School of Life ScienceHuman Phenome Institute, Fudan UniversityShanghaiChina
- Fudan University Taizhou Institute of Health SciencesTaizhouChina
| | - Kelin Xu
- Department of Biostatistics, School of Public HealthFudan UniversityShanghaiChina
| | - Di Wu
- Vesicode ABStockholmSweden
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Key Laboratory of Genitourinary Tumor, Department of UrologyThe First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen Institute of Translational MedicineShenzhenChina
| | - Chen Suo
- Department of Epidemiology, School of Public HealthFudan UniversityShanghaiChina
- Fudan University Taizhou Institute of Health SciencesTaizhouChina
- Shanghai Institute of Infectious Disease and BiosecurityShanghaiChina
| | - Xingdong Chen
- Fudan University Taizhou Institute of Health SciencesTaizhouChina
- Yiwu Research Institute of Fudan UniversityChina
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and National Clinical Research Center for Aging and Medicine, Huashan HospitalFudan UniversityShanghaiChina
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Sandau US, Wiedrick JT, McFarland TJ, Galasko DR, Fanning Z, Quinn JF, Saugstad JA. Analysis of the longitudinal stability of human plasma miRNAs and implications for disease biomarkers. Sci Rep 2024; 14:2148. [PMID: 38272952 PMCID: PMC10810819 DOI: 10.1038/s41598-024-52681-5] [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: 08/17/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
There is great interest in developing clinical biomarker assays that can aid in non-invasive diagnosis and/or monitoring of human diseases, such as cancer, cardiovascular disease, and neurological diseases. Yet little is known about the longitudinal stability of miRNAs in human plasma. Here we assessed the intraindividual longitudinal stability of miRNAs in plasma from healthy human adults, and the impact of common factors (e.g., hemolysis, age) that may confound miRNA data. We collected blood by venipuncture biweekly over a 3-month period from 22 research participants who had fasted overnight, isolated total RNA, then performed miRNA qPCR. Filtering and normalization of the qPCR data revealed amplification of 134 miRNAs, 74 of which had high test-retest reliability and low percentage level drift, meaning they were stable in an individual over the 3-month time period. We also determined that, of nuisance factors, hemolysis and tobacco use have the greatest impact on miRNA levels and variance. These findings support that many miRNAs show intraindividual longitudinal stability in plasma from healthy human adults, including some reported as candidate biomarkers for Alzheimer's disease.
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Affiliation(s)
- Ursula S Sandau
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Jack T Wiedrick
- Biostatistics and Design Program, Oregon Health and Science University, Portland, OR, USA
| | - Trevor J McFarland
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Douglas R Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Zoe Fanning
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Joseph F Quinn
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Julie A Saugstad
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, USA.
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