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Heydari Z, Moeinvaziri F, Mirazimi SMA, Dashti F, Smirnova O, Shpichka A, Mirzaei H, Timashev P, Vosough M. Alteration in DNA methylation patterns: Epigenetic signatures in gastrointestinal cancers. Eur J Pharmacol 2024; 973:176563. [PMID: 38593929 DOI: 10.1016/j.ejphar.2024.176563] [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: 01/22/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Abnormalities in epigenetic modifications can cause malignant transformations in cells, leading to cancers of the gastrointestinal (GI) tract, which accounts for 20% of all cancers worldwide. Among the epigenetic alterations, DNA hypomethylation is associated with genomic instability. In addition, CpG methylation and promoter hypermethylation have been recognized as biomarkers for different malignancies. In GI cancers, epigenetic alterations affect genes responsible for cell cycle control, DNA repair, apoptosis, and tumorigenic-specific signaling pathways. Understanding the pattern of alterations in DNA methylation in GI cancers could help scientists discover new molecular-based pharmaceutical treatments. This study highlights alterations in DNA methylation in GI cancers. Understanding epigenetic differences among GI cancers may improve targeted therapies and lead to the discovery of new diagnostic biomarkers.
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Affiliation(s)
- Zahra Heydari
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Farideh Moeinvaziri
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyed Mohammad Ali Mirazimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Dashti
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Kashan University of Medical Sciences, Kashan, Iran
| | - Olga Smirnova
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Anastasia Shpichka
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Peter Timashev
- Institute for Regenerative Medicine, Sechenov University, Moscow, Russia; World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia; Chemistry Department, Lomonosov Moscow State University, Moscow, Russia.
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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2
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Mahmood U, Carrier E, Khan K. Neoadjuvant management of locally advanced pancreatic ductal adenocarcinoma - Heading towards a promising change in treatment paradigm. Cancer Treat Rev 2024; 127:102750. [PMID: 38703592 DOI: 10.1016/j.ctrv.2024.102750] [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: 04/01/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Traditional chemotherapy-based adjuvant therapies for locally advanced pancreatic ductal adenocarcinoma (PDAC) have been associated with poor clinical outcomes driven partly by its complex anatomy and molecular heterogeneity. Treatment for PDAC is challenged by presence of a dense tumour microenvironment involving an interplay of multiple tumoural and stromal components which promote metastatic oncogenic behaviour. PDAC also involves aberrations in multiple signalling pathways with paucity of treatment options against the most common mutations including KRAS, TP53, CDKN2A andSMAD4. However, recent discovery of new mechanisms implicated in pancreatic carcinogenesis have led to identification of promising mechanistic therapeutic targets such as NET1 and ULK1. Early evidence also suggests the utility of targeting multiple DNA repair processes, modulators of DNA replication and major DNA damage response regulators. We explore the clinical rationale behind a neoadjuvant therapeutic strategy and emerging predictors of survival benefit associated with this approach. We also discuss challenges and opportunities originating from recent clinical trials evaluating neoadjuvant treatments composed of various combinations of radiotherapy, chemotherapy and immunotherapeutic regimens that have aimed to address some of these biological challenges. Selective treatment of patients harbouring specific genomic aberrations with targeted agents and immunotherapy can translate into optimum survival outcomes in PDAC. We also share perspectives on emerging prospective clinical evidence regarding stromal modifying agents, such as Tumour Growth Factor-Beta and Connective Tissue Growth Factor inhibitors along with novel vaccination-based approaches in improving PDAC outcomes.
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Affiliation(s)
- Umair Mahmood
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK
| | - Ewa Carrier
- Department of Clinical Development, FibroGen, Inc., San Francisco, CA, USA
| | - Khurum Khan
- Department of Gastrointestinal Oncology, University College Hospital NHS Foundation Trust (UCLH), London NW1 2BU, UK; University College London Cancer Institute, London WC1E 6DD, UK.
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3
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Huang C, Hecht EM, Soloff EV, Tiwari HA, Bhosale PR, Dasayam A, Galgano SJ, Kambadakone A, Kulkarni NM, Le O, Liau J, Luk L, Rosenthal MH, Sangster GP, Goenka AH. Imaging for Early Detection of Pancreatic Ductal Adenocarcinoma: Updates and Challenges in the Implementation of Screening and Surveillance Programs. AJR Am J Roentgenol 2024. [PMID: 38809122 DOI: 10.2214/ajr.24.31151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is one of the most aggressive cancers. It has a poor 5-year survival rate of 12%, partly because most cases are diagnosed at advanced stages, precluding curative surgical resection. Early-stage PDA has significantly better prognoses due to increased potential for curative interventions, making early detection of PDA critically important to improved patient outcomes. We examine current and evolving early detection concepts, screening strategies, diagnostic yields among high-risk individuals, controversies, and limitations of standard-of-care imaging.
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Affiliation(s)
- Chenchan Huang
- Department of Radiology, NYU Langone Health, 660 First Avenue, 3rd floor, New York, NY 10016
| | - Elizabeth M Hecht
- Department of Radiology, Weill Cornell Medicine, New York, NY, 520 East 70th Street, Starr 8a-29, New York, NY 10021
| | - Erik V Soloff
- Department of Radiology, University of Washington, 1959 NE Pacific St., Box 357233, Seattle WA 98195-7115
| | - Hina Arif Tiwari
- Department of Radiology, University of Arizona College of Medicine, Banner University Medicine, 1501 N. Campbell Avenue, PO Box 245067, Tucson, AZ 85724-5067
| | - Priya R Bhosale
- Department of Radiology, The University of Texas MD Anderson Cancer Center, 1515 Holcomb Street Bellaire Texas 77401
| | - Anil Dasayam
- Department of Radiology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, PA 15213
| | - Samuel J Galgano
- Department of Radiology, University of Alabama at Birmingham, 619 19th St S, JT N454, Birmingham, AL 35249
| | - Avinash Kambadakone
- Department of Radiology, Massachusetts General Hospital, 55 Fruit Street, White 270, Boston, MA-02114
| | - Naveen M Kulkarni
- Department of Radiology, Medical College of Wisconsin, 8752 William Coffey Dr., Milwaukee, WI 53226
| | - Ott Le
- Department of Radiology, The University of Texas MD Anderson Cancer Center, 1515 Holcomb Street Bellaire Texas 77401
| | - Joy Liau
- Department of Radiology, University of California at San Diego, 200 W. Arbor Drive #8756; San Diego, CA 92103-8756
| | - Lyndon Luk
- Department of Radiology, Columbia University Medical Center, 622 West 168th Street, New York, NY 10032
| | - Michael H Rosenthal
- Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline AvenueBoston, MA 02215
| | - Guillermo P Sangster
- Department of Radiology, OLSU Health Shreveport, 1501 Kings Hwy, Shreveport, LA 71103
| | - Ajit H Goenka
- Department of Radiology, Mayo Clinic, 200 First Street SW, Charlton 1, Rochester, MN 55905
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4
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Ahmed TM, Kawamoto S, Lopez-Ramirez F, Yasrab M, Hruban RH, Fishman EK, Chu LC. Early detection of pancreatic cancer in the era of precision medicine. Abdom Radiol (NY) 2024:10.1007/s00261-024-04358-w. [PMID: 38761272 DOI: 10.1007/s00261-024-04358-w] [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: 03/31/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/20/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related mortality and it is often diagnosed at advanced stages due to non-specific clinical presentation. Disease detection at localized disease stage followed by surgical resection remains the only potentially curative treatment. In this era of precision medicine, a multifaceted approach to early detection of PDAC includes targeted screening in high-risk populations, serum biomarkers and "liquid biopsies", and artificial intelligence augmented tumor detection from radiologic examinations. In this review, we will review these emerging techniques in the early detection of PDAC.
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Affiliation(s)
- Taha M Ahmed
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Satomi Kawamoto
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Felipe Lopez-Ramirez
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Mohammad Yasrab
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elliot K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Linda C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, MD, USA.
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5
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He M, Pan Y, You C, Gao H. CircRNAs in cancer therapy tolerance. Clin Chim Acta 2024; 558:119684. [PMID: 38649011 DOI: 10.1016/j.cca.2024.119684] [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: 03/20/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
The rapidly expanding field of circular RNA (circ-RNA) research has opened new avenues in cancer diagnostics and treatment, highlighting the role of serum circRNAs as potential biomarkers for assessing tumor therapy resistance. This review comprehensively compiles existing knowledge regarding the biogenesis, function, and clinical relevance of circRNAs, emphasizing their stability, abundance, and cell type-specific expression profiles, which make them ideal candidates for noninvasive early biomarkers in cancer treatment. We explored the roles of circRNAs in oncogenesis and tumor progression and their complex interactions with patient responses to various cancer treatments, such as chemotherapy, radiotherapy, targeted therapy, and immunotherapy. Through the analysis of data from recent studies and clinical trials, we underscore the prognostic significance of serum circRNAs in predicting therapeutic outcomes, their involvement in resistance mechanisms, and their capacity to inform personalized treatment approaches. Additionally, this review addresses the obstacles inherent in circRNA research, including the need for standardized protocols for circRNA extraction and quantification and the elucidation of the clinical significance of circRNAs. Furthermore, our investigation extends to future prospects, including embedding circRNA profiling into regular clinical workflows and pioneering circRNA-based therapeutic approaches. We underscore the transformative potential of serum circRNAs in enhancing cancer diagnosis, improving the accuracy of therapy tolerance predictions, and ultimately fostering the advent of precision oncology.
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Affiliation(s)
- Miao He
- The Second Hospital of Lanzhou University, Laboratory Medicine Center, Lanzhou 730030, PR China; The Second Clinical Medical School, Lanzhou University, Lanzhou 730030, PR China
| | - Yunyan Pan
- The Second Hospital of Lanzhou University, Laboratory Medicine Center, Lanzhou 730030, PR China
| | - Chongge You
- The Second Hospital of Lanzhou University, Laboratory Medicine Center, Lanzhou 730030, PR China.
| | - Hongwei Gao
- The Second Hospital of Lanzhou University, Laboratory Medicine Center, Lanzhou 730030, PR China.
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6
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Kinane DF, Gabert J, Xynopoulos G, Guzeldemir-Akcakanat E. Strategic approaches in oral squamous cell carcinoma diagnostics using liquid biopsy. Periodontol 2000 2024. [PMID: 38676371 DOI: 10.1111/prd.12567] [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: 11/01/2023] [Revised: 02/06/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024]
Abstract
Liquid biopsy is a noninvasive diagnostic technique used for monitoring cancer utilizing specific genetic biomarkers present in bodily fluids, such as blood, saliva, or urine. These analyses employ multiple biomolecular sources including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and exosomes (that contain DNA fragments) to detect genetic biomarkers that can predict, disclose, and/or monitor cancers. Levels of these biomarkers can inform on the presence of cancer, its genetic characteristics, and its potential treatment response and also provide predictive genetic predisposition information for specific cancers including oral squamous cell carcinomas (OSCC). Liquid biopsies can aid cancer management as they offer real-time dynamic information on the response to say chemotherapy or radiotherapy and recurrence following surgical excision. Unlike traditional tissue biopsies, which are invasive with a degree of morbidity and require specific tumor location sampling, liquid biopsies are noninvasive and can be repeated frequently. For oral squamous cell carcinoma, on which this review focuses, liquid biopsy of blood or saliva can be valuable in predicting susceptibility, providing early detection, and monitoring the disease's progression and response to therapy. This review gives a general narrative overview of the technology, its current medical usage, and advantages and disadvantages compared with current techniques and discusses a range of current potential biomarkers for disclosing OSCC and predicting its risk. Oral squamous cell carcinoma is all too often detected in the late stages. In future, liquid biopsy may provide an effective screening process such that cancers including OSCC will be detected in the early stages rather than later when prognosis is poor and morbidity and debilitation are greater. In this screening process, periodontists and hygienists have a critical role in that they are adept in examining mucosa, they see patients with shared risk factors for periodontitis and OSCC, namely smoking and poor oral hygiene, and they see patients frequently such that OSCC examinations should be a routine part of the recall visit. With this additional screening manpower, oral medicine and oral surgery colleagues will detect OSCC earlier and this coupled with new techniques such as liquid biopsy may greatly decrease global morbidity in OSCC.
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Affiliation(s)
- Denis F Kinane
- Department of Periodontology, Dental School, University Bern, Bern, Switzerland
- ExpressTest, Cignpost Diagnostics Ltd., Farnborough, United Kingdom
| | | | | | - Esra Guzeldemir-Akcakanat
- Department of Periodontology, Faculty of Dentistry, Kocaeli University, İzmit, Turkey
- College of Dental Medicine, QU Health, Qatar University, Qatar, Qatar
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7
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Wang Z, Chen X, Qiu X, Chen Y, Wang T, Lv L, Guo X, Yang F, Tang M, Gu W, Luo Y. High-Fidelity Sensitive Tracing Circulating Tumor Cell Telomerase Activity. Anal Chem 2024; 96:5527-5536. [PMID: 38483815 DOI: 10.1021/acs.analchem.3c05749] [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: 04/10/2024]
Abstract
Dynamic tracing of intracellular telomerase activity plays a crucial role in cancer cell recognition and correspondingly in earlier cancer diagnosis and personalized precision therapy. However, due to the complexity of the required reaction system and insufficient loading of reaction components into cells, achieving a high-fidelity determination of telomerase activity is still a challenge. Herein, an Aptamer-Liposome mediated Telomerase activated poly-Molecular beacon Arborescent Nanoassembly(ALTMAN) approach was described for direct high-fidelity visualization of telomerase activity. Briefly, intracellular telomerase activates molecular beacons, causing their hairpin structures to unfold and produce fluorescent signals. Furthermore, multiple molecular beacons can self-assemble, forming arborescent nanostructures and leading to exponential amplification of fluorescent signals. Integrating the enzyme-free isothermal signal amplification successfully increased the sensitivity and reduced interference by leveraging the skillful design of the molecular beacon and the extension of the telomerase-activated TTAGGG repeat sequence. The proposed approach enabled ultrasensitive visualization of activated telomerase exclusively with a prominent detection limit of 2 cells·μL-1 and realized real-time imaging of telomerase activity in living cancer cells including blood samples from breast cancer patients and urine samples from bladder cancer patients. This approach opens an avenue for establishing a telomerase activity determination and in situ monitoring technique that can facilitate both telomerase fundamental biological studies and cancer diagnostics.
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Affiliation(s)
- Zining Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Xiaohui Chen
- Department of Clinical Laboratory, Fuling Hospital, Chongqing University, Chongqing 408099, P.R. China
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing 400044, P.R. China
| | - Xiaopei Qiu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Yi Chen
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Tian Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Linxi Lv
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Xinlin Guo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Fei Yang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Miao Tang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Wei Gu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, P.R. China
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing 400044, P.R. China
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8
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Zhao G, Jiang R, Shi Y, Gao S, Wang D, Li Z, Zhou Y, Sun J, Wu W, Peng J, Kuang T, Rong Y, Yuan J, Zhu S, Jin G, Wang Y, Lou W. Circulating cell-free DNA methylation-based multi-omics analysis allows early diagnosis of pancreatic ductal adenocarcinoma. Mol Oncol 2024. [PMID: 38561976 DOI: 10.1002/1878-0261.13643] [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: 08/05/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a 5-year survival rate of 7.2% in China. However, effective approaches for diagnosis of PDAC are limited. Tumor-originating genomic and epigenomic aberration in circulating free DNA (cfDNA) have potential as liquid biopsy biomarkers for cancer diagnosis. Our study aims to assess the feasibility of cfDNA-based liquid biopsy assay for PDAC diagnosis. In this study, we performed parallel genomic and epigenomic profiling of plasma cfDNA from Chinese PDAC patients and healthy individuals. Diagnostic models were built to distinguish PDAC patients from healthy individuals. Cancer-specific changes in cfDNA methylation landscape were identified, and a diagnostic model based on six methylation markers achieved high sensitivity (88.7% for overall cases and 78.0% for stage I patients) and specificity (96.8%), outperforming the mutation-based model significantly. Moreover, the combination of the methylation-based model with carbohydrate antigen 19-9 (CA19-9) levels further improved the performance (sensitivity: 95.7% for overall cases and 95.5% for stage I patients; specificity: 93.3%). In conclusion, our findings suggest that both methylation-based and integrated liquid biopsy assays hold promise as non-invasive tools for detection of PDAC.
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Affiliation(s)
- Guochao Zhao
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Ying Shi
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Dansong Wang
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhilong Li
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Yuhong Zhou
- Department of Medical Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianlong Sun
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Wenchuan Wu
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaxi Peng
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Tiantao Kuang
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yefei Rong
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Yuan
- The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Shida Zhu
- BGI Genomics, BGI-Shenzhen, China
- Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, China
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital Affiliated to Navy Medical University, Shanghai, China
| | - Yuying Wang
- Envelope Health Biotechnology Co. Ltd., BGI-Shenzhen, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
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9
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Reshkin SJ, Cardone RA, Koltai T. Genetic Signature of Human Pancreatic Cancer and Personalized Targeting. Cells 2024; 13:602. [PMID: 38607041 PMCID: PMC11011857 DOI: 10.3390/cells13070602] [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: 02/12/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Pancreatic cancer is a highly lethal disease with a 5-year survival rate of around 11-12%. Surgery, being the treatment of choice, is only possible in 20% of symptomatic patients. The main reason is that when it becomes symptomatic, IT IS the tumor is usually locally advanced and/or has metastasized to distant organs; thus, early diagnosis is infrequent. The lack of specific early symptoms is an important cause of late diagnosis. Unfortunately, diagnostic tumor markers become positive at a late stage, and there is a lack of early-stage markers. Surgical and non-surgical cases are treated with neoadjuvant and/or adjuvant chemotherapy, and the results are usually poor. However, personalized targeted therapy directed against tumor drivers may improve this situation. Until recently, many pancreatic tumor driver genes/proteins were considered untargetable. Chemical and physical characteristics of mutated KRAS are a formidable challenge to overcome. This situation is slowly changing. For the first time, there are candidate drugs that can target the main driver gene of pancreatic cancer: KRAS. Indeed, KRAS inhibition has been clinically achieved in lung cancer and, at the pre-clinical level, in pancreatic cancer as well. This will probably change the very poor outlook for this disease. This paper reviews the genetic characteristics of sporadic and hereditary predisposition to pancreatic cancer and the possibilities of a personalized treatment according to the genetic signature.
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Affiliation(s)
- Stephan J. Reshkin
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy;
| | - Rosa Angela Cardone
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy;
| | - Tomas Koltai
- Oncomed, Via Pier Capponi 6, 50132 Florence, Italy
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10
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Kim YJ, Rho WY, Park SM, Jun BH. Optical nanomaterial-based detection of biomarkers in liquid biopsy. J Hematol Oncol 2024; 17:10. [PMID: 38486294 PMCID: PMC10938695 DOI: 10.1186/s13045-024-01531-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
Liquid biopsy, which is a minimally invasive procedure as an alternative to tissue biopsy, has been introduced as a new diagnostic/prognostic measure. By screening disease-related markers from the blood or other biofluids, it promises early diagnosis, timely prognostication, and effective treatment of the diseases. However, there will be a long way until its realization due to its conceptual and practical challenges. The biomarkers detected by liquid biopsy, such as circulating tumor cell (CTC) and circulating tumor DNA (ctDNA), are extraordinarily rare and often obscured by an abundance of normal cellular components, necessitating ultra-sensitive and accurate detection methods for the advancement of liquid biopsy techniques. Optical biosensors based on nanomaterials open an important opportunity in liquid biopsy because of their enhanced sensing performance with simple and practical properties. In this review article, we summarized recent innovations in optical nanomaterials to demonstrate the sensitive detection of protein, peptide, ctDNA, miRNA, exosome, and CTCs. Each study prepares the optical nanomaterials with a tailored design to enhance the sensing performance and to meet the requirements of each biomarker. The unique optical characteristics of metallic nanoparticles (NPs), quantum dots, upconversion NPs, silica NPs, polymeric NPs, and carbon nanomaterials are exploited for sensitive detection mechanisms. These recent advances in liquid biopsy using optical nanomaterials give us an opportunity to overcome challenging issues and provide a resource for understanding the unknown characteristics of the biomarkers as well as the mechanism of the disease.
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Affiliation(s)
- Young Jun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Won-Yeop Rho
- School of International Engineering and Science, Jeonbuk National University, Chonju, 54896, Republic of Korea
| | - Seung-Min Park
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, 637459, Singapore.
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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11
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Ben-Ami R, Wang QL, Zhang J, Supplee JG, Fahrmann JF, Lehmann-Werman R, Brais LK, Nowak J, Yuan C, Loftus M, Babic A, Irajizad E, Davidi T, Zick A, Hubert A, Neiman D, Piyanzin S, Gal-Rosenberg O, Horn A, Shemer R, Glaser B, Boos N, Jajoo K, Lee L, Clancy TE, Rubinson DA, Ng K, Chabot JA, Kastrinos F, Kluger M, Aguirre AJ, Jänne PA, Bardeesy N, Stanger B, O'Hara MH, Till J, Maitra A, Carpenter EL, Bullock AJ, Genkinger J, Hanash SM, Paweletz CP, Dor Y, Wolpin BM. Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer. Gut 2024; 73:639-648. [PMID: 38123998 PMCID: PMC10958271 DOI: 10.1136/gutjnl-2023-331074] [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: 09/05/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed. DESIGN To assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites. RESULTS Comparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92). CONCLUSION A combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.
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Affiliation(s)
- Roni Ben-Ami
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Qiao-Li Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Jinming Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Julianna G Supplee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Johannes F Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roni Lehmann-Werman
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lauren K Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Maureen Loftus
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ehsan Irajizad
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tal Davidi
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Aviad Zick
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ofer Gal-Rosenberg
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Horn
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Glaser
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Endocrinology and Metabolism, Hadassah Medical Center, Jerusalem, Israel
| | - Natalia Boos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kunal Jajoo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Linda Lee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas E Clancy
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Douglas A Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John A Chabot
- Department of Surgery, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Fay Kastrinos
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Cancer and the Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Michael Kluger
- Department of Surgery, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ben Stanger
- Department of Medicine, Division of Gastroenterology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Mark H O'Hara
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacob Till
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Erica L Carpenter
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea J Bullock
- Division of Hematology and Oncology, Beth-Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Jeanine Genkinger
- Department of epidemiology, Mailman school of public health, Columbia university, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia university Irving Medical Center, New York, New York, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cloud P Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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12
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Eckhoff AM, Kanu E, Fletcher A, Bao M, Aushev VN, Spickard E, Nussbaum DP, Allen PJ. Initial Report: Personalized Circulating Tumor DNA and Survival in Patients with Resectable Pancreatic Cancer. Ann Surg Oncol 2024; 31:1444-1446. [PMID: 38170407 DOI: 10.1245/s10434-023-14751-2] [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: 11/16/2023] [Accepted: 11/25/2023] [Indexed: 01/05/2024]
Abstract
ABSTRACT: BACKGROUND: Pancreatic adenocarcinoma (PDAC) is highly lethal with up to 80% of resected patients experiencing disease recurrence within 2 years (Watanabe, Nakamura, Kimura et al in Int J Mol Sci 23(19):11521, 2022). Cross-sectional imaging and serum tumor markers are used for monitoring post-operative recurrence; however, both have significant limitations (Edland, Tjensvoll, Oltedal et al in Mol Oncol 17:1857-1870, 2023). Circulating tumor DNA (ctDNA) has emerged as a valuable prognostic tool to measure molecular residual disease (MRD) and predict recurrence in solid tumors (Watanabe, Nakamura, Kimura et al in Int J Mol Sci 23(19):11521, 2022). In this study, we evaluated the feasibility of a personalized, tumor-informed ctDNA assay to detect recurrence prior to standard surveillance tools in patients with PDAC. PATIENTS AND METHODS: After Institutional Review Board (IRB) approval (Pro00106870), we assessed serial ctDNA measurements (n = 177) from 35 patients with resectable PDAC treated by either upfront resection or neoadjuvant chemotherapy. Plasma samples (median 4 ml, interquartile range 0.6-5.9 ml) were isolated from blood collected in EDTA tubes and banked at diagnosis, during neoadjuvant therapy if applicable, on the day of surgery, and every 2-3 months postoperatively. A tumor-informed assay (Signatera™, Natera, Inc.) that tracks up to 16 individual-specific, somatic single nucleotide variants in the corresponding patient's plasma samples were used for ctDNA detection. Survival was calculated using Kaplan-Meier curves, and significance was determined with the log-rank test. RESULTS: Personalized ctDNA assays were successfully designed for all patients (with 32/35 patients having 16-plex assays). Median follow-up from initial treatment was 13 months (range 1-26 months; Table 1). ctDNA-positivity at any time point was observed in 40% (14/35) of patients. During the follow-up period, 18 patients (51%) developed radiographic evidence of recurrence after a median of 9 months of follow-up (range 1-26 months). At the time of radiographic recurrence, 50% (9/18) of patients were ctDNA-positive. During the immediate postoperative period (up to 9 weeks post-surgery), RFS and OS were significantly inferior in patients who were ctDNA-positive versus ctDNA-negative (RFS 97 versus 297 days, p < 0.001; OS 110 versus 381 days, p < 0.001; Fig. 1). Table 1 Cohort demographics (N = 35); patient demographics, tumor characteristics, and survival Gender (%) Female 17 (49%) Male 18 (51%) Median age (IQR) 70 years (65-75 years) Neoadjuvant treatment (%) 11 (31%) Median sample plasma volume (IQR) 4.0 mL (0.6-5.9 mL) Median follow-up (range) 13 months (1-26 months) Median initial CA 19-9 in U/mL (IQR) 56 (18-160) Median tumor size in cm (IQR) 2.5 (1.8-3.3) Median number of positive lymph nodes (IQR) 1 (0-3) Median recurrence-free survival 9.4 months Median overall survival N/A (not reached) Fig. 1 a Overview plot showing longitudinal ctDNA status, treatment regimen, and clinical outcomes for each patient (N = 35); median follow-up from the start of the neoadjuvant therapy/surgery was 13 months (range 1-26 months); ctDNA at any time point was 40% (14/35); out of the 35 patients, 18 (51%) developed radiographic evidence of recurrence (median RFS: 9 months), and of these 18 patients with clinical recurrence, 9 (50%) were ctDNA-positive and the remaining ctDNA-negative; notably, all ctDNA-negative patients with recurrence had suboptimal plasma volume available for ctDNA analysis; b, c Kaplan-Meier estimates representing the association of ctDNA status with (b) RFS and (c) OS, at MRD time point (9 weeks post-surgery) DISCUSSION: Our study demonstrates the feasibility of tumor-informed ctDNA-based MRD testing in resectable PDAC and shows that MRD detected by ctDNA within the immediate postoperative period portends a dismal prognosis. This information is valuable for both patients and clinicians in setting prognostic expectations.
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Affiliation(s)
| | - Elishama Kanu
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Matthew Bao
- Department of Surgery, Duke University, Durham, NC, USA
| | | | | | | | - Peter J Allen
- Department of Surgery, Duke University, Durham, NC, USA.
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13
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Macchia E, Torricelli F, Caputo M, Sarcina L, Scandurra C, Bollella P, Catacchio M, Piscitelli M, Di Franco C, Scamarcio G, Torsi L. Point-Of-Care Ultra-Portable Single-Molecule Bioassays for One-Health. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309705. [PMID: 38108547 DOI: 10.1002/adma.202309705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Screening asymptomatic organisms (humans, animals, plants) with a high-diagnostic accuracy using point-of-care-testing (POCT) technologies, though still visionary holds great potential. Convenient surveillance requires easy-to-use, cost-effective, ultra-portable but highly reliable, in-vitro-diagnostic devices that are ready for use wherever they are needed. Currently, there are not yet such devices available on the market, but there are a couple more promising technologies developed at readiness-level 5: the Clustered-Regularly-Interspaced-Short-Palindromic-Repeats (CRISPR) lateral-flow-strip tests and the Single-Molecule-with-a-large-Transistor (SiMoT) bioelectronic palmar devices. They both hold key features delineated by the World-Health-Organization for POCT systems and an occurrence of false-positive and false-negative errors <1-5% resulting in diagnostic-selectivity and sensitivity >95-99%, while limit-of-detections are of few markers. CRISPR-strip is a molecular assay that, can detect down to few copies of DNA/RNA markers in blood while SiMoT immunometric and molecular test can detect down to a single oligonucleotide, protein marker, or pathogens in 0.1mL of blood, saliva, and olive-sap. These technologies can prospectively enable the systematic and reliable surveillance of asymptomatic ones prior to worsening/proliferation of illnesses allowing for timely diagnosis and swift prognosis. This could establish a proactive healthcare ecosystem that results in effective treatments for all living organisms generating diffuse and well-being at efficient costs.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Paolo Bollella
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Michele Catacchio
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Matteo Piscitelli
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | | | - Gaetano Scamarcio
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
- CNR IFN, Bari, 70126, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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14
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Liu X, Jiang H, Wang X. Advances in Cancer Research: Current and Future Diagnostic and Therapeutic Strategies. BIOSENSORS 2024; 14:100. [PMID: 38392019 PMCID: PMC10886776 DOI: 10.3390/bios14020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Cancers of unknown primary (CUP) exhibit significant cellular heterogeneity and malignancy, which poses significant challenges for diagnosis and treatment. Recent years have seen deeper insights into the imaging, pathology, and genetic characteristics of CUP, driven by interdisciplinary collaboration and the evolution of diagnostic and therapeutic strategies. However, due to their insidious onset, lack of evidence-based medicine, and limited clinical understanding, diagnosing and treating CUP remain a significant challenge. To inspire more creative and fantastic research, herein, we report and highlight recent advances in the diagnosis and therapeutic strategies of CUP. Specifically, we discuss advanced diagnostic technologies, including 12-deoxy-2-[fluorine-18]fluoro-D-glucose integrated with computed tomography (18F-FDG PET/CT) or 68Ga-FAPI (fibroblast activation protein inhibitor) PET/CT, liquid biopsy, molecular diagnostics, self-assembling nanotechnology, and artificial intelligence (AI). In particular, the discussion will extend to the effective treatment techniques currently available, such as targeted therapies, immunotherapies, and bio-nanotechnology-based therapeutics. Finally, a novel perspective on the challenges and directions for future CUP diagnostic and therapeutic strategies is discussed.
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Affiliation(s)
- Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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15
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Szczepanski JM, Rudolf MA, Shi J. Clinical Evaluation of the Pancreatic Cancer Microenvironment: Opportunities and Challenges. Cancers (Basel) 2024; 16:794. [PMID: 38398185 PMCID: PMC10887250 DOI: 10.3390/cancers16040794] [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: 01/16/2024] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Advances in our understanding of pancreatic ductal adenocarcinoma (PDAC) and its tumor microenvironment (TME) have the potential to transform treatment for the hundreds of thousands of patients who are diagnosed each year. Whereas the clinical assessment of cancer cell genetics has grown increasingly sophisticated and personalized, current protocols to evaluate the TME have lagged, despite evidence that the TME can be heterogeneous within and between patients. Here, we outline current protocols for PDAC diagnosis and management, review novel biomarkers, and highlight potential opportunities and challenges when evaluating the PDAC TME as we prepare to translate emerging TME-directed therapies to the clinic.
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Affiliation(s)
| | | | - Jiaqi Shi
- Department of Pathology and Clinical Labs, University of Michigan, Ann Arbor, MI 48109, USA; (J.M.S.); (M.A.R.)
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16
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Dai JY, Zhang J, Braun JV, Simon N, Hubbell E, Zhang N. Clinical performance and utility: A microsimulation model to inform the design of screening trials for a multi-cancer early detection test. J Med Screen 2024:9691413241228041. [PMID: 38304990 DOI: 10.1177/09691413241228041] [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: 02/03/2024]
Abstract
OBJECTIVES Designing cancer screening trials for multi-cancer early detection (MCED) tests presents a significant methodology challenge, as natural histories of cell-free DNA-shedding cancers are not yet known. A microsimulation model was developed to project the performance and utility of an MCED test in cancer screening trials. METHODS Individual natural history of preclinical progression through cancer stages for 23 cancer classes was simulated by a stage-transition model under a broad range of cancer latency parameters. Cancer incidences and stage distributions at clinical presentation in simulated trials were set to match the data from Surveillance, Epidemiology, and End Results program. One or multiple rounds of annual screening using a targeted methylation-based MCED test (GalleriⓇ) was conducted to detect preclinical cancers. Mortality benefit of early detection was simulated by a stage-shift model. RESULTS In simulated trials, accounting for healthy volunteer effect and varying test sensitivity, positive predictive value in the prevalence screening round reached 48% to 61% in 6 natural history scenarios. After 3 rounds of annual screening, the cumulative proportions of stage I/II cancers increased by approximately 9% to 14%, the incidence of stage IV cancers was reduced by 37% to 46%, the reduction of stages III and IV cancer incidences was 9% to 24%, and the reduction of mortality reached 13% to 16%. Greater reductions of late-stage cancers and cancer mortality were achieved by five rounds of MCED screening. CONCLUSIONS Simulation results guide trial design and suggest that adding this MCED test to routine screening in the United States may shift cancer detection to earlier stages, and potentially save lives.
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Affiliation(s)
| | | | | | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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17
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Sok CP, Polireddy K, Kooby DA. Molecular pathology and protein markers for pancreatic cancer: relevance in staging, in adjuvant therapy, in determination of minimal residual disease, and follow-up. Hepatobiliary Surg Nutr 2024; 13:56-70. [PMID: 38322203 PMCID: PMC10839718 DOI: 10.21037/hbsn-22-628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/10/2023] [Indexed: 02/08/2024]
Abstract
The diagnosis and monitoring of disease through the detection of circulating protein biomarkers is a growing field in the practice of oncology. The search for more effective protein biomarkers to aid in the diagnosis and treatment of patients with pancreatic ductal adenocarcinoma (PDAC) remains a valuable area of study, given the aggressive and often occult nature of this malignancy. Liquid biopsies are attractive, as they offer a minimally invasive and cost-effective approach when compared to traditional biopsy methods and imaging modalities used for diagnosis and surveillance. Carbohydrate antigen (CA) 19-9 is currently the most commonly used serum protein biomarker for the diagnosis and monitoring of patients with PDAC, but due to its sensitivity and specificity, its utility remains limited. In this review, we examine how circulating protein biomarkers are used in the diagnosis, prognostication, and surveillance of PDAC. We also highlight protein biomarkers that are currently under investigation that have the potential to enhance our ability to detect early-stage malignancies, predict response to therapy, and monitor for recurrence, but these markers require larger prospective validation studies before they can be widely implemented. Continued efforts to identify and validate novel biomarkers will be crucial for improving the management and outcomes of patients with this challenging disease.
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Affiliation(s)
- Caitlin P. Sok
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Karunesh Polireddy
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, USA
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18
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Zhou Z, Lin T, Chen S, Zhang G, Xu Y, Zou H, Zhou A, Zhang Y, Weng S, Han X, Liu Z. Omics-based molecular classifications empowering in precision oncology. Cell Oncol (Dordr) 2024:10.1007/s13402-023-00912-8. [PMID: 38294647 DOI: 10.1007/s13402-023-00912-8] [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] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND In the past decades, cancer enigmatical heterogeneity at distinct expression levels could interpret disparities in therapeutic response and prognosis. It built hindrances to precision medicine, a tactic to tailor customized treatment informed by the tumors' molecular profile. Single-omics analysis dissected the biological features associated with carcinogenesis to some extent but still failed to revolutionize cancer treatment as expected. Integrated omics analysis incorporated tumor biological networks from diverse layers and deciphered a holistic overview of cancer behaviors, yielding precise molecular classification to facilitate the evolution and refinement of precision medicine. CONCLUSION This review outlined the biomarkers at multiple expression layers to tutor molecular classification and pinpoint tumor diagnosis, and explored the paradigm shift in precision therapy: from single- to multi-omics-based subtyping to optimize therapeutic regimens. Ultimately, we firmly believe that by parsing molecular characteristics, omics-based typing will be a powerful assistant for precision oncology.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yudi Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Wang F, Li X, Li M, Liu W, Lu L, Li Y, Chen X, Yang S, Liu T, Cheng W, Weng L, Wang H, Lu D, Yao Q, Wang Y, Wu J, Wittkop T, Faham M, Zhou H, Hu H, Jin H, Hu Z, Ma D, Cheng X. Ultra-short cell-free DNA fragments enhance cancer early detection in a multi-analyte blood test combining mutation, protein and fragmentomics. Clin Chem Lab Med 2024; 62:168-177. [PMID: 37678194 DOI: 10.1515/cclm-2023-0541] [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: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVES Cancer morbidity and mortality can be reduced if the cancer is detected early. Cell-free DNA (cfDNA) fragmentomics emerged as a novel epigenetic biomarker for early cancer detection, however, it is still at its infancy and requires technical improvement. We sought to apply a single-strand DNA sequencing technology, for measuring genetic and fragmentomic features of cfDNA and evaluate the performance in detecting multiple cancers. METHODS Blood samples of 364 patients from six cancer types (colorectal, esophageal, gastric, liver, lung, and ovarian cancers) and 675 healthy individuals were included in this study. Circulating tumor DNA mutations, cfDNA fragmentomic features and a set of protein biomarkers were assayed. Sensitivity and specificity were reported by cancer types and stages. RESULTS Circular Ligation Amplification and sequencing (CLAmp-seq), a single-strand DNA sequencing technology, yielded a population of ultra-short fragments (<100 bp) than double-strand DNA preparation protocols and reveals a more significant size difference between cancer and healthy cfDNA fragments (25.84 bp vs. 16.05 bp). Analysis of the subnucleosomal peaks in ultra-short cfDNA fragments indicates that these peaks are regulatory element "footprints" and correlates with gene expression and cancer stages. At 98 % specificity, a prediction model using ctDNA mutations alone showed an overall sensitivity of 46 %; sensitivity reaches 60 % when protein is added, sensitivity further increases to 66 % when fragmentomics is also integrated. More improvements observed for samples representing earlier cancer stages than later ones. CONCLUSIONS These results suggest synergistic properties of protein, genetic and fragmentomics features in the identification of early-stage cancers.
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Affiliation(s)
- Fenfen Wang
- Gynecological Oncology Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, P.R. China
| | - Xinxing Li
- Department of Gastrointestinal Surgery, Tongji Hospital Medical College of Tongji University, Shanghai, P.R. China
| | - Mengxing Li
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Wendi Liu
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Lingjia Lu
- Gynecological Oncology Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, P.R. China
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Hangzhou, P.R. China
| | - Xiaojing Chen
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, P.R. China
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Hangzhou, P.R. China
| | - Siqi Yang
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Hangzhou, P.R. China
| | - Tao Liu
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Wen Cheng
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Li Weng
- Department of Research and Development, AccuraGen Inc., San Jose, CA, USA
| | - Hongyan Wang
- Department of Research and Development, Shanghai Yunsheng Medical Laboratory Co., Ltd., Shanghai, P.R. China
| | - Dongsheng Lu
- Department of Bioinformatics, Shanghai Yunsheng Medical Laboratory Co., Ltd., Shanghai, P.R. China
| | - Qianqian Yao
- Department of Medical Science, Shanghai Yunsheng Medical Laboratory Co., Ltd., Shanghai, P.R. China
| | - Yingyu Wang
- Department of Bioinformatics, AccuraGen Inc., San Jose, CA, USA
| | - Johnny Wu
- Department of Bioinformatics, AccuraGen Inc., San Jose, CA, USA
| | - Tobias Wittkop
- Department of Bioinformatics, AccuraGen Inc., San Jose, CA, USA
| | | | - Huabang Zhou
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Heping Hu
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Hai Jin
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Shanghai, P.R. China
| | - Zhiqian Hu
- Department of Gastrointestinal Surgery, Tongji Hospital Medical College of Tongji University, Shanghai, P.R. China
- Department of General Surgery, Changzheng Hospital Naval Medical University, Shanghai, P.R. China
| | - Ding Ma
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xiaodong Cheng
- Gynecological Oncology Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, P.R. China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, P.R. China
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Jain M, Atayan D, Rakhmatullin T, Dakhtler T, Popov P, Kim P, Viborniy M, Gontareva I, Samokhodskaya L, Egorov V. Cell-Free Tumor DNA Detection-Based Liquid Biopsy of Plasma and Bile in Patients with Various Pancreatic Neoplasms. Biomedicines 2024; 12:220. [PMID: 38255325 PMCID: PMC10813046 DOI: 10.3390/biomedicines12010220] [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: 12/25/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The key challenge of cell-free tumor DNA (cftDNA) analysis in pancreatic ductal adenocarcinoma (PDAC) is overcoming its low detection rate, which is mainly explained by the overall scarcity of this biomarker in plasma. Obstructive jaundice is a frequent event in PDAC, which enables bile collection as a part of routine treatment. The aim of this study was to evaluate the performance of KRAS-mutated cftDNA detection-based liquid biopsy of plasma and bile in patients with pancreatic neoplasms using digital droplet PCR. The study included healthy volunteers (n = 38), patients with PDAC (n = 95, of which 20 had obstructive jaundice) and other pancreatic neoplasms (OPN) (n = 18). The sensitivity and specificity compared to the control group were 61% and 100% (AUC-ROC-0.805), and compared to the OPN group, they were 61% and 94% (AUC-ROC-0.794), respectively. Bile exhibited higher cftDNA levels than plasma (248.6 [6.743; 1068] vs. 3.26 [0; 19.225] copies/mL) and a two-fold higher detection rate (p < 0.01). Plasma cftDNA levels were associated with distant metastases, tumor size, and CA 19-9 (p < 0.05). The probability of survival was worse in patients with higher levels of cftDNA in plasma (hazard ratio-2.4; 95% CI: 1.3-4.6; p = 0.005) but not in bile (p > 0.05). Bile is a promising alternative to plasma in patients with obstructive jaundice, at least for the diagnostic purposes of liquid biopsy.
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Affiliation(s)
- Mark Jain
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - David Atayan
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Tagir Rakhmatullin
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Tatyana Dakhtler
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Pavel Popov
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Pavel Kim
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Mikhail Viborniy
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Iuliia Gontareva
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Larisa Samokhodskaya
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Vyacheslav Egorov
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
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21
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Scandurra C, Björkström K, Caputo M, Sarcina L, Genco E, Modena F, Viola FA, Brunetti C, Kovács-Vajna ZM, Franco CD, Haeberle L, Larizza P, Mancini MT, Österbacka R, Reeves W, Scamarcio G, Wheeler M, Caironi M, Cantatore E, Torricelli F, Esposito I, Macchia E, Torsi L. Analysis of Clinical Samples of Pancreatic Cyst's Lesions with A Multi-Analyte Bioelectronic Simot Array Benchmarked Against Ultrasensitive Chemiluminescent Immunoassay. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308141. [PMID: 38234100 DOI: 10.1002/advs.202308141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/30/2023] [Indexed: 01/19/2024]
Abstract
Pancreatic cancer, ranking as the third factor in cancer-related deaths, necessitates enhanced diagnostic measures through early detection. In response, SiMoT-Single-molecule with a large Transistor multiplexing array, achieving a Technology Readiness Level of 5, is proposed for a timely identification of pancreatic cancer precursor cysts and is benchmarked against the commercially available chemiluminescent immunoassay SIMOA (Single molecule array) SP-X System. A cohort of 39 samples, comprising 33 cyst fluids and 6 blood plasma specimens, undergoes detailed examination with both technologies. The SiMoT array targets oncoproteins MUC1 and CD55, and oncogene KRAS, while the SIMOA SP-X planar technology exclusively focuses on MUC1 and CD55. Employing Principal Component Analysis (PCA) for multivariate data processing, the SiMoT array demonstrates effective discrimination of malignant/pre-invasive high-grade or potentially malignant low-grade pancreatic cysts from benign non-mucinous cysts. Conversely, PCA analysis applied to SIMOA assay reveals less effective differentiation ability among the three cyst classes. Notably, SiMoT unique capability of concurrently analyzing protein and genetic markers with the threshold of one single molecule in 0.1 mL positions it as a comprehensive and reliable diagnostic tool. The electronic response generated by the SiMoT array facilitates direct digital data communication, suggesting potential applications in the development of field-deployable liquid biopsy.
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Affiliation(s)
- Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Kim Björkström
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Enrico Genco
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Francesco Modena
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Fabrizio Antonio Viola
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | | | - Zsolt M Kovács-Vajna
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | | | - Lena Haeberle
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Piero Larizza
- Masmec Biomed - Masmec SpA division, Modugno (BA), 70026, Italy
| | | | - Ronald Österbacka
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Gaetano Scamarcio
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
| | - May Wheeler
- FlexEnable Technology Ltd, Cambridge, CB4 0FX, UK
| | - Mario Caironi
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Eugenio Cantatore
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Eleonora Macchia
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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22
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Shi W, Wartmann T, Accuffi S, Al-Madhi S, Perrakis A, Kahlert C, Link A, Venerito M, Keitel-Anselmino V, Bruns C, Croner RS, Zhao Y, Kahlert UD. Integrating a microRNA signature as a liquid biopsy-based tool for the early diagnosis and prediction of potential therapeutic targets in pancreatic cancer. Br J Cancer 2024; 130:125-134. [PMID: 37950093 PMCID: PMC10781694 DOI: 10.1038/s41416-023-02488-4] [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: 06/05/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
INTRODUCTION Pancreatic cancer is a highly aggressive cancer, and early diagnosis significantly improves patient prognosis due to the early implementation of curative-intent surgery. Our study aimed to implement machine-learning algorithms to aid in early pancreatic cancer diagnosis based on minimally invasive liquid biopsies. MATERIALS AND METHODS The analysis data were derived from nine public pancreatic cancer miRNA datasets and two sequencing datasets from 26 pancreatic cancer patients treated in our medical center, featuring small RNAseq data for patient-matched tumor and non-tumor samples and serum. Upon batch-effect removal, systematic analyses for differences between paired tissue and serum samples were performed. The robust rank aggregation (RRA) algorithm was used to reveal feature markers that were co-expressed by both sample types. The repeatability and real-world significance of the enriched markers were then determined by validating their expression in our patients' serum. The top candidate markers were used to assess the accuracy of predicting pancreatic cancer through four machine learning methods. Notably, these markers were also applied for the identification of pancreatic cancer and pancreatitis. Finally, we explored the clinical prognostic value, candidate targets and predict possible regulatory cell biology mechanisms involved. RESULTS Our multicenter analysis identified hsa-miR-1246, hsa-miR-205-5p, and hsa-miR-191-5p as promising candidate serum biomarkers to identify pancreatic cancer. In the test dataset, the accuracy values of the prediction model applied via four methods were 94.4%, 84.9%, 82.3%, and 83.3%, respectively. In the real-world study, the accuracy values of this miRNA signatures were 82.3%, 83.5%, 79.0%, and 82.2. Moreover, elevated levels of these miRNAs were significant indicators of advanced disease stage and allowed the discrimination of pancreatitis from pancreatic cancer with an accuracy rate of 91.5%. Elevated expression of hsa-miR-205-5p, a previously undescribed blood marker for pancreatic cancer, is associated with negative clinical outcomes in patients. CONCLUSION A panel of three miRNAs was developed with satisfactory statistical and computational performance in real-world data. Circulating hsa-miRNA 205-5p serum levels serve as a minimally invasive, early detection tool for pancreatic cancer diagnosis and disease staging and might help monitor therapy success.
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Affiliation(s)
- Wenjie Shi
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany
| | - Thomas Wartmann
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany
| | - Sara Accuffi
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany
| | - Sara Al-Madhi
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany
| | - Aristotelis Perrakis
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany
| | - Christoph Kahlert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Verena Keitel-Anselmino
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital Magdeburg, 39120, Magdeburg, Germany
| | - Christiane Bruns
- Faculty of Medicine and University Hospital Cologne, Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Roland S Croner
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany
| | - Yue Zhao
- Faculty of Medicine and University Hospital Cologne, Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany.
| | - Ulf D Kahlert
- Molecular and Experimental Surgery, Faculty of Medicine and University Hospital Magdeburg, Department of General-, Visceral-, Vascular- and Transplant- Surgery, University of Magdeburg, Magdeburg, Germany.
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23
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Javed AA, Zhu Z, Kinny-Köster B, Habib JR, Kawamoto S, Hruban RH, Fishman EK, Wolfgang CL, He J, Chu LC. Accurate non-invasive grading of nonfunctional pancreatic neuroendocrine tumors with a CT derived radiomics signature. Diagn Interv Imaging 2024; 105:33-39. [PMID: 37598013 PMCID: PMC10873069 DOI: 10.1016/j.diii.2023.08.002] [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: 02/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/21/2023]
Abstract
PURPOSE The purpose of this study was to develop a radiomics-signature using computed tomography (CT) data for the preoperative prediction of grade of nonfunctional pancreatic neuroendocrine tumors (NF-PNETs). MATERIALS AND METHODS A retrospective study was performed on patients undergoing resection for NF-PNETs between 2010 and 2019. A total of 2436 radiomic features were extracted from arterial and venous phases of pancreas-protocol CT examinations. Radiomic features that were associated with final pathologic grade observed in the surgical specimens were subjected to joint mutual information maximization for hierarchical feature selection and the development of the radiomic-signature. Youden-index was used to identify optimal cutoff for determining tumor grade. A random forest prediction model was trained and validated internally. The performance of this tool in predicting tumor grade was compared to that of EUS-FNA sampling that was used as the standard of reference. RESULTS A total of 270 patients were included and a fusion radiomic-signature based on 10 selected features was developed using the development cohort (n = 201). There were 149 men and 121 women with a mean age of 59.4 ± 12.3 (standard deviation) years (range: 23.3-85.0 years). Upon internal validation in a new set of 69 patients, a strong discrimination was observed with an area under the curve (AUC) of 0.80 (95% confidence interval [CI]: 0.71-0.90) with corresponding sensitivity and specificity of 87.5% (95% CI: 79.7-95.3) and 73.3% (95% CI: 62.9-83.8) respectively. Of the study population, 143 patients (52.9%) underwent EUS-FNA. Biopsies were non-diagnostic in 26 patients (18.2%) and could not be graded due to insufficient sample in 42 patients (29.4%). In the cohort of 75 patients (52.4%) in whom biopsies were graded the radiomic-signature demonstrated not different AUC as compared to EUS-FNA (AUC: 0.69 vs. 0.67; P = 0.723), however greater sensitivity (i.e., ability to accurately identify G2/3 lesion was observed (80.8% vs. 42.3%; P < 0.001). CONCLUSION Non-invasive assessment of tumor grade in patients with PNETs using the proposed radiomic-signature demonstrated high accuracy. Prospective validation and optimization could overcome the commonly experienced diagnostic uncertainty in the assessment of tumor grade in patients with PNETs and could facilitate clinical decision-making.
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Affiliation(s)
- Ammar A Javed
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Surgery, New York University Langone Hospital, New York City, New York 10016, USA
| | - Zhuotun Zhu
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Benedict Kinny-Köster
- Department of Surgery, New York University Langone Hospital, New York City, New York 10016, USA
| | - Joseph R Habib
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Satomi Kawamoto
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ralph H Hruban
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elliot K Fishman
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher L Wolfgang
- Department of Surgery, New York University Langone Hospital, New York City, New York 10016, USA
| | - Jin He
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Linda C Chu
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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24
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Cheng C, Hou K, Hsu C, Chiang L. Ultrasensitive and High-Resolution Protein Spatially Decoding Framework for Tumor Extracellular Vesicles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304926. [PMID: 37984870 PMCID: PMC10797477 DOI: 10.1002/advs.202304926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/28/2023] [Indexed: 11/22/2023]
Abstract
Proteins localized on the surface or within the lumen of tumor-derived extracellular vesicles (EVs) play distinct roles in cancer progression. However, quantifying both populations of proteins within EVs has been hampered due to the limited sensitivity of the existing protein detection methods and inefficient EV isolation techniques. In this study, the eSimoa framework, an innovative approach enabling spatial decoding of EV protein biomarkers with unmatched sensitivity and specificity is presented. Using the luminal eSimoa pipeline, the absolute concentration of luminal RAS or KRASG12D proteins is released and measured, uncovering their prevalence in pancreatic tumor-derived EVs. The pulldown eSimoa pipeline measured absolute protein concentrations from low-abundance EV subpopulations. The eSimoa assays detected EVs in both PBS and plasma samples, confirming their applicability across diverse clinical sample types. Overall, the eSimoa framework offers a valuable tool to (1) detect EVs at concentrations as low as 105 EV mL-1 in plasma, (2) quantify absolute EV protein concentrations as low as fM, and (3) decode the spatial distribution of EV proteins. This study highlights the potential of eSimoa in identifying disease-specific EV protein biomarkers in clinical samples with minimal pre-purification, thereby driving advancements in clinical translation.
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Affiliation(s)
- Chi‐An Cheng
- School of PharmacyCollege of MedicineNational Taiwan UniversityTaipei10050Taiwan
| | - Kuan‐Chu Hou
- Department of MedicineCollege of MedicineNational Taiwan UniversityTaipei10050Taiwan
| | - Chen‐Wei Hsu
- School of PharmacyCollege of MedicineNational Taiwan UniversityTaipei10050Taiwan
| | - Li‐Chiao Chiang
- School of PharmacyCollege of MedicineNational Taiwan UniversityTaipei10050Taiwan
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25
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Stosic K, Senar OA, Tarfouss J, Bouchart C, Navez J, Van Laethem JL, Arsenijevic T. A Comprehensive Review of the Potential Role of Liquid Biopsy as a Diagnostic, Prognostic, and Predictive Biomarker in Pancreatic Ductal Adenocarcinoma. Cells 2023; 13:3. [PMID: 38201207 PMCID: PMC10778087 DOI: 10.3390/cells13010003] [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: 10/30/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the most lethal malignant diseases, with a mortality rate being close to incidence. Due to its heterogeneity and plasticity, as well as the lack of distinct symptoms in the early phases, it is very often diagnosed at an advanced stage, resulting in poor prognosis. Traditional tissue biopsies remain the gold standard for making a diagnosis, but have an obvious disadvantage in their inapplicability for frequent sampling. Blood-based biopsies represent a non-invasive method which potentially offers easy and repeated sampling, leading to the early detection and real-time monitoring of the disease and hopefully an accurate prognosis. Given the urgent need for a reliable biomarker that can estimate a patient's condition and response to an assigned treatment, blood-based biopsies are emerging as a potential new tool for improving patients' survival and surveillance. In this article, we discuss the current advances and challenges in using liquid biopsies for pancreatic cancer, focusing on circulating tumour DNA (ctDNA), extracellular vesicles (EVs), and circulating tumour cells (CTCs), and compare the performance and reliability of different biomarkers and combinations of biomarkers.
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Affiliation(s)
- Kosta Stosic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Oier Azurmendi Senar
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Jawad Tarfouss
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
| | - Christelle Bouchart
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Radiation Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Julie Navez
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Hepato-Biliary-Pancreatic Surgery, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Jean-Luc Van Laethem
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Tatjana Arsenijevic
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Brussels, Belgium (O.A.S.); (C.B.)
- Department of Gastroenterology, Hepatology and Digestive Oncology, Hopital Universitaire de Bruxelles (H.U.B.), Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
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Shao P, Dong D, Huang Y, Wang Y, Pan L, Zhu Q, Wu Z, Jiang F, Wei W. Aptamer-Based Functionalized SERS Biosensor for Rapid and Ultrasensitive Detection of Gastric Cancer-Related Biomarkers. Int J Nanomedicine 2023; 18:7523-7532. [PMID: 38106450 PMCID: PMC10723598 DOI: 10.2147/ijn.s434854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023] Open
Abstract
Background Gastric cancer (GC) as is the second deadliest malignancy still lacks rapid, simple and economical detection and early clinical screening techniques. Surface-enhanced Raman spectroscopy (SERS) is a spectroscopic technique based on the surface plasmon resonance of precious metal nanoparticles, which can effectively detect low-abundance tumor markers. Combining SERS technology with sensors has high potential in the diagnosis and screening of GC. Methods A novel Au/Si nano-umbrella array (Au/SiNUA) was prepared as a SERS substrate and the substrate was functionalized using the corresponding tumor marker aptamers for the detection of clinical biological samples using a one-step recognition release mechanism. Optimization of aptamer and complementary chain concentrations and detection time for optimal sensor preparation. Results Au/SiNUA were tested to have good SERS enhancement activity. The proposed aptamer biosensor has good specificity and stability, with a low detection time of 18 min and a limit of detection (LOD) at the fM level, which is superior to most of the methods reported so far; and the accuracy of the clinical assay is comparable to that of the ELISA method. The expression levels of PDGF-B and thrombin in the serum of GC patients and healthy individuals can be effectively detected and differentiated. Conclusion The ultrasensitive and specific aptamer biosensor is highly feasible for the diagnosis and screening of GC and has good application prospects.
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Affiliation(s)
- Ping Shao
- Department of Spleen and Stomach Diseases, Yixing Traditional Chinese Medicine Hospital, Wuxi, 214200, People’s Republic of China
| | - Danyang Dong
- Department of Spleen and Stomach Diseases, Yixing Traditional Chinese Medicine Hospital, Wuxi, 214200, People’s Republic of China
| | - Yong Huang
- Department of General Surgery, Jiangdu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225200, People’s Republic of China
| | - Yan Wang
- Department of Spleen and Stomach Diseases, Yixing Traditional Chinese Medicine Hospital, Wuxi, 214200, People’s Republic of China
| | - Lian Pan
- Pathology Department, Yixing Traditional Chinese Medicine Hospital, Wuxi, 214200, People’s Republic of China
| | - Qunshan Zhu
- Department of General Surgery, Jiangdu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225200, People’s Republic of China
| | - Zheng Wu
- Department of General Surgery, Jiangdu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225200, People’s Republic of China
| | - Fengjuan Jiang
- Department of Gastroenterology, Jiangdu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225200, People’s Republic of China
| | - Wei Wei
- Department of General Surgery, Jiangdu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225200, People’s Republic of China
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Nie C, Shaw I, Chen C. Application of microfluidic technology based on surface-enhanced Raman scattering in cancer biomarker detection: A review. J Pharm Anal 2023; 13:1429-1451. [PMID: 38223444 PMCID: PMC10785256 DOI: 10.1016/j.jpha.2023.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 01/16/2024] Open
Abstract
With the continuous discovery and research of predictive cancer-related biomarkers, liquid biopsy shows great potential in cancer diagnosis. Surface-enhanced Raman scattering (SERS) and microfluidic technology have received much attention among the various cancer biomarker detection methods. The former has ultrahigh detection sensitivity and can provide a unique fingerprint. In contrast, the latter has the characteristics of miniaturization and integration, which can realize accurate control of the detection samples and high-throughput detection through design. Both have the potential for point-of-care testing (POCT), and their combination (lab-on-a-chip SERS (LoC-SERS)) shows good compatibility. In this paper, the basic situation of circulating proteins, circulating tumor cells, exosomes, circulating tumor DNA (ctDNA), and microRNA (miRNA) in the diagnosis of various cancers is reviewed, and the detection research of these biomarkers by the LoC-SERS platform in recent years is described in detail. At the same time, the challenges and future development of the platform are discussed at the end of the review. Summarizing the current technology is expected to provide a reference for scholars engaged in related work and interested in this field.
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Affiliation(s)
- Changhong Nie
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Ibrahim Shaw
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
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Bu Q, Luo X, He L, Ma J, He S, Lei W, Zhou W, Deng H, Lin Y, Zhang L, Hong X. Septin9 DNA methylation as a promising biomarker for cervical cancer. J OBSTET GYNAECOL 2023; 43:2151356. [PMID: 36476308 DOI: 10.1080/01443615.2022.2151356] [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: 12/13/2022]
Abstract
Aberrant Septin9 methylation in cervical cancer has been rarely studied. We aimed to identify its diagnostic value in cervical cancer using cervical scrapings, and its predictive potential in plasma for pelvic nodal metastasis of cervical cancer. The statuses of methylated Septin9 in fresh cervical lesions and cervical scrapings were first evaluated by using quantitative methylation-specific PCR. Subsequently, the relationship between Septin9 methylation in 113 plasma samples and pelvic nodal metastasis of cervical cancer was evaluated. Methylated Septin9 was detected in all cancerous tissues, but not in cervicitis. The degrees of Septin9 methylation increased with growing severity of cervical lesions in cervical scrapings. The sensitivity of methylated Septin9 was lower than that of cytology, while it yielded a high specificity and area under the curve in detecting high-grade squamous intraepithelial lesion or cervical cancer; and when Septin9 methylation combined with HPV16/18 genotyping, the sensitivity would increase from 70.42% to 82.39%. Plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%. In conclusion, we demonstrated methylated Septin9 to be an innovative diagnostic biomarker for cervical cancer and its non-invasive predictive potential in plasma for pelvic nodal metastasis of cervical cancer.Impact statementWhat is already known on this subject? The occurrence of cervical cancer is related to Septin9 methylation. In fresh specimens and cervical scrapings, we found the degrees of methylated Septin9 increased with growing severity of cervical lesions. Compared with HPV16/18 genotyping and cytological detection, Septin9 methylation had a better specificity and AUC in detecting ≥ HSIL. Furthermore, plasma-based Septin9 methylation also had a high specificity for pelvic lymphatic metastasis prediction.What the results of this study add? Methylation analysis of Septin9 indicated a similar sensitivity, specificity and AUC in detecting ≥ HSIL, relative to HPV16/18 genotyping. Compared with cytological method, Septin9 methylation also yielded a higher specificity and AUC in detecting ≥ HSIL. And we also found plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%; additionally an increasing sensitivity from 50% to nearly 80% was found when combined with SCCAg.What the implications are of these findings for clinical practice and/or further research? This study aimed to evaluate the relationship between Septin9 methylation and cervical cancer, and to explore the value of methylated Septin9 in the detection of cervical (pre)cancerous lesions. Moreover, we would explore plasma-based ctDNA biomarkers for pelvic lymphatic metastasis prediction of cervical cancer, to improve non-invasive predictive accuracy of pelvic nodal metastasis and reduce the complications caused by pelvic lymphadenectomy.
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Affiliation(s)
- Qiaowen Bu
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiping Luo
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lulu He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jian Ma
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shaoyi He
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wen Lei
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Weiping Zhou
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yu Lin
- Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiaoshan Hong
- Department of Gynecology, Guangdong Women and Children Hospital, Guangzhou, China
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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.
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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
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Sikosek T, Horos R, Trudzinski F, Jehn J, Frank M, Rajakumar T, Klotz LV, Mercaldo N, Kahraman M, Heuvelman M, Taha Y, Gerwing J, Skottke J, Daniel-Moreno A, Sanchez-Delgado M, Bender S, Rudolf C, Hinkfoth F, Tikk K, Schenz J, Weigand MA, Feindt P, Schumann C, Christopoulos P, Winter H, Kreuter M, Schneider MA, Muley T, Walterspacher S, Schuler M, Darwiche K, Taube C, Hegedus B, Rabe KF, Rieger-Christ K, Jacobsen FL, Aigner C, Reck M, Bankier AA, Sharma A, Steinkraus BR. Early Detection of Lung Cancer Using Small RNAs. J Thorac Oncol 2023; 18:1504-1523. [PMID: 37437883 DOI: 10.1016/j.jtho.2023.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/20/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
INTRODUCTION Lung cancer remains the deadliest cancer in the world, and lung cancer survival is heavily dependent on tumor stage at the time of detection. Low-dose computed tomography screening can reduce mortality; however, annual screening is limited by low adherence in the United States of America and still not broadly implemented in Europe. As a result, less than 10% of lung cancers are detected through existing programs. Thus, there is a great need for additional screening tests, such as a blood test, that could be deployed in the primary care setting. METHODS We prospectively recruited 1384 individuals meeting the National Lung Screening Trial demographic eligibility criteria for lung cancer and collected stabilized whole blood to enable the pipetting-free collection of material, thus minimizing preanalytical noise. Ultra-deep small RNA sequencing (20 million reads per sample) was performed with the addition of a method to remove highly abundant erythroid RNAs, and thus open bandwidth for the detection of less abundant species originating from the plasma or the immune cellular compartment. We used 100 random data splits to train and evaluate an ensemble of logistic regression classifiers using small RNA expression of 943 individuals, discovered an 18-small RNA feature consensus signature (miLung), and validated this signature in an independent cohort (441 individuals). Blood cell sorting and tumor tissue sequencing were performed to deconvolve small RNAs into their source of origin. RESULTS We generated diagnostic models and report a median receiver-operating characteristic area under the curve of 0.86 (95% confidence interval [CI]: 0.84-0.86) in the discovery cohort and generalized performance of 0.83 in the validation cohort. Diagnostic performance increased in a stage-dependent manner ranging from 0.73 (95% CI: 0.71-0.76) for stage I to 0.90 (95% CI: 0.89-0.90) for stage IV in the discovery cohort and from 0.76 to 0.86 in the validation cohort. We identified a tumor-shed, plasma-bound ribosomal RNA fragment of the L1 stalk as a dominant predictor of lung cancer. The fragment is decreased after surgery with curative intent. In additional experiments, results of dried blood spot collection and sequencing revealed that small RNA analysis could potentially be conducted through home sampling. CONCLUSIONS These data suggest the potential of a small RNA-based blood test as a viable alternative to low-dose computed tomography screening for early detection of smoking-associated lung cancer.
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Affiliation(s)
| | | | - Franziska Trudzinski
- Center for Interstitial and Rare Lung Diseases, Department of Pneumology and Critical Care Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Julia Jehn
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | | | | | - Laura V Klotz
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany; Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Nathaniel Mercaldo
- Institute for Technology Assessment, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Yasser Taha
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | | | | | | | | | | | | | | | - Kaja Tikk
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | - Judith Schenz
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Feindt
- Klinik für Thoraxchirurgie, Clemenshospital Münster, Münster, Germany
| | - Christian Schumann
- Klinik für Pneumologie, Thoraxonkologie, Schlaf- und Beatmungsmedizin, Klinikum Kempten und Klinik Immenstadt, Klinikverbund Allgäu, Kempten, Germany
| | - Petros Christopoulos
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany; Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany; Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Kreuter
- Mainz Center for Pulmonary Medicine, Departments of Pneumology, Mainz University Medical Center and of Pulmonary, Critical Care & Sleep Medicine, Marienhaus Clinic Mainz, Mainz, Germany
| | - Marc A Schneider
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany; Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany; Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Stephan Walterspacher
- Lungenzentrum Bodensee, II. Medizinische Klinik, Klinikum Konstanz, Konstanz, Germany; Faculty of Health/School of Medicine, Witten/Herdecke University, Witten, Germany
| | - Martin Schuler
- West German Cancer Center, Department of Medical Oncology, University Hospital Essen, Essen, Germany
| | - Kaid Darwiche
- Klinik für Pneumologie, Universitätsmedizin Essen - Ruhrlandklinik, Essen, Germany
| | - Christian Taube
- Klinik für Pneumologie, Universitätsmedizin Essen - Ruhrlandklinik, Essen, Germany
| | - Balazs Hegedus
- Department of Thoracic Surgery, University Medicine Essen, Ruhrlandklinik, Essen, Germany
| | - Klaus F Rabe
- LungenClinic Grosshansdorf, Airway Research Center North, German Center for Lung Research (DZL), Grosshansdorf, Germany; Department of Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Kimberly Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Francine L Jacobsen
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Clemens Aigner
- Department of Thoracic Surgery, University Medicine Essen, Ruhrlandklinik, Essen, Germany
| | - Martin Reck
- LungenClinic Grosshansdorf, Airway Research Center North, German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Alexander A Bankier
- Department of Radiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Amita Sharma
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
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Dbouk M, Abe T, Koi C, Ando Y, Saba H, Abou Diwan E, MacGregor-Das A, Blackford AL, Mocci E, Beierl K, Dbouk A, He J, Burkhart R, Lennon AM, Sokoll L, Canto MI, Eshleman JR, Goggins M. Diagnostic Performance of a Tumor Marker Gene Test to Personalize Serum CA19-9 Reference Ranges. Clin Cancer Res 2023; 29:4178-4185. [PMID: 37566230 PMCID: PMC10570677 DOI: 10.1158/1078-0432.ccr-23-0655] [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: 03/07/2023] [Revised: 05/25/2023] [Accepted: 08/08/2023] [Indexed: 08/12/2023]
Abstract
PURPOSE CA19-9 synthesis is influenced by common variants in the fucosyltransferase (FUT) enzymes FUT3 and FUT2. We developed a clinical test to detect FUT variants, and evaluated its diagnostic performance for pancreatic ductal adenocarcinoma (PDAC). EXPERIMENTAL DESIGN A representative set of controls from the Cancer of the Pancreas Screening study was identified for each FUT functional group. Diagnostic sensitivity was determined first in a testing set of 234 PDAC cases, followed by a 134-case validation set, all of whom had undergone resection with curative intent without neoadjuvant therapy. Tumor marker gene testing was performed in the Johns Hopkins Molecular Diagnostics Laboratory. CA19-9 levels were measured in the Hopkins Clinical Chemistry lab. Receiver operating characteristic (ROC) curve analysis was used to evaluate the discriminative ability of CA19-9 alone versus with the gene test. RESULTS Applying the CA19-9 standard cutoff (<36 U/mL) to all 716 subjects yielded a 68.8% sensitivity in the test set of cases, 67.2% in the validation set, at 91.4% specificity. Applying 99th percentile cutoffs according to each individual's FUT group (3, 34.9, 41.8, and 89.2, for the FUT3-null, FUT-low, FUT-intermediate, and FUT-high groups, respectively) yielded a diagnostic sensitivity for CA19-9 in the first set of cases of 66.7%, 65.7% in the validation set, at 98.9% specificity. ROC analysis for CA19-9 alone yielded an AUC of 0.84; with the tumor marker gene test, AUC improved to 0.92 (P < 0.001). CONCLUSIONS Using a tumor marker gene test to personalize an individual's CA19-9 reference range significantly improves diagnostic accuracy.
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Affiliation(s)
- Mohamad Dbouk
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Toshiya Abe
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Chiho Koi
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Yohei Ando
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Helena Saba
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Elizabeth Abou Diwan
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Anne MacGregor-Das
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Amanda L. Blackford
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Evelina Mocci
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Katie Beierl
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ali Dbouk
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jin He
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Richard Burkhart
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Anne Marie Lennon
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Lori Sokoll
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Marcia Irene Canto
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - James R. Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
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Wang K, Wang X, Pan Q, Zhao B. Liquid biopsy techniques and pancreatic cancer: diagnosis, monitoring, and evaluation. Mol Cancer 2023; 22:167. [PMID: 37803304 PMCID: PMC10557192 DOI: 10.1186/s12943-023-01870-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Pancreatic cancer (PC) is one of the most common malignancies. Surgical resection is a potential curative approach for PC, but most patients are unsuitable for operations when at the time of diagnosis. Even with surgery, some patients may still experience tumour metastasis during the operation or shortly after surgery, as precise prognosis evaluation is not always possible. If patients miss the opportunity for surgery and resort to chemotherapy, they may face the challenging issue of chemotherapy resistance. In recent years, liquid biopsy has shown promising prospects in disease diagnosis, treatment monitoring, and prognosis assessment. As a noninvasive detection method, liquid biopsy offers advantages over traditional diagnostic procedures, such as tissue biopsy, in terms of both cost-effectiveness and convenience. The information provided by liquid biopsy helps clinical practitioners understand the molecular mechanisms underlying tumour occurrence and development, enabling the formulation of more precise and personalized treatment decisions for each patient. This review introduces molecular biomarkers and detection methods in liquid biopsy for PC, including circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), noncoding RNAs (ncRNAs), and extracellular vesicles (EVs) or exosomes. Additionally, we summarize the applications of liquid biopsy in the early diagnosis, treatment response, resistance assessment, and prognostic evaluation of PC.
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Affiliation(s)
- Kangchun Wang
- Department of Organ Transplantation and Hepatobiliary, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Xin Wang
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qi Pan
- Department of Organ Transplantation and Hepatobiliary, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.
| | - Bei Zhao
- Department of Ultrasound, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Wei L, Niraula D, Gates EDH, Fu J, Luo Y, Nyflot MJ, Bowen SR, El Naqa IM, Cui S. Artificial intelligence (AI) and machine learning (ML) in precision oncology: a review on enhancing discoverability through multiomics integration. Br J Radiol 2023; 96:20230211. [PMID: 37660402 PMCID: PMC10546458 DOI: 10.1259/bjr.20230211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/15/2023] [Accepted: 06/27/2023] [Indexed: 09/05/2023] Open
Abstract
Multiomics data including imaging radiomics and various types of molecular biomarkers have been increasingly investigated for better diagnosis and therapy in the era of precision oncology. Artificial intelligence (AI) including machine learning (ML) and deep learning (DL) techniques combined with the exponential growth of multiomics data may have great potential to revolutionize cancer subtyping, risk stratification, prognostication, prediction and clinical decision-making. In this article, we first present different categories of multiomics data and their roles in diagnosis and therapy. Second, AI-based data fusion methods and modeling methods as well as different validation schemes are illustrated. Third, the applications and examples of multiomics research in oncology are demonstrated. Finally, the challenges regarding the heterogeneity data set, availability of omics data, and validation of the research are discussed. The transition of multiomics research to real clinics still requires consistent efforts in standardizing omics data collection and analysis, building computational infrastructure for data sharing and storing, developing advanced methods to improve data fusion and interpretability, and ultimately, conducting large-scale prospective clinical trials to fill the gap between study findings and clinical benefits.
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Affiliation(s)
- Lise Wei
- Department of Radiation Oncology, University of Michigan, Michigan, United States
| | - Dipesh Niraula
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, United States
| | - Evan D. H. Gates
- Department of Radiation Oncology, University of Washington, Washington, United States
| | - Jie Fu
- Department of Radiation Oncology, Stanford University, Stanford, California, United States
| | - Yi Luo
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, United States
| | - Matthew J. Nyflot
- Department of Radiation Oncology, University of Washington, Washington, United States
| | - Stephen R. Bowen
- Department of Radiation Oncology, University of Washington, Washington, United States
| | - Issam M El Naqa
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, United States
| | - Sunan Cui
- Department of Radiation Oncology, University of Washington, Washington, United States
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Genco E, Modena F, Sarcina L, Björkström K, Brunetti C, Caironi M, Caputo M, Demartis VM, Di Franco C, Frusconi G, Haeberle L, Larizza P, Mancini MT, Österbacka R, Reeves W, Scamarcio G, Scandurra C, Wheeler M, Cantatore E, Esposito I, Macchia E, Torricelli F, Viola FA, Torsi L. A Single-Molecule Bioelectronic Portable Array for Early Diagnosis of Pancreatic Cancer Precursors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304102. [PMID: 37452695 DOI: 10.1002/adma.202304102] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
A cohort of 47 patients is screened for pancreatic cancer precursors with a portable 96-well bioelectronic sensing-array for single-molecule assay in cysts fluid and blood plasma, deployable at point-of-care (POC). Pancreatic cancer precursors are mucinous cysts diagnosed with a sensitivity of at most 80% by state-of-the-art cytopathological molecular analyses (e.g., KRASmut DNA). Adding the simultaneous assay of proteins related to malignant transformation (e.g., MUC1 and CD55) is deemed essential to enhance diagnostic accuracy. The bioelectronic array proposed here, based on single-molecule-with-a-large-transistor (SiMoT) technology, can assay both nucleic acids and proteins at the single-molecule limit-of-identification (LOI) (1% of false-positives and false-negatives). It comprises an enzyme-linked immunosorbent assay (ELISA)-like 8 × 12-array organic-electronics disposable cartridge with an electrolyte-gated organic transistor sensor array, and a reusable reader, integrating a custom Si-IC chip, operating via software installed on a USB-connected smart device. The cartridge is complemented by a 3D-printed sensing gate cover plate. KRASmut , MUC1, and CD55 biomarkers either in plasma or cysts-fluid from 5 to 6 patients at a time, are multiplexed at single-molecule LOI in 1.5 h. The pancreatic cancer precursors are classified via a machine-learning analysis resulting in at least 96% diagnostic-sensitivity and 100% diagnostic-specificity. This preliminary study opens the way to POC liquid-biopsy-based early diagnosis of pancreatic-cancer precursors in plasma.
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Affiliation(s)
- Enrico Genco
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Francesco Modena
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milan, 20133, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Kim Björkström
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Mario Caironi
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Virginia Maria Demartis
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | | | - Giulia Frusconi
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Lena Haeberle
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Piero Larizza
- Masmec Biomed - Masmec SpA division, Modugno (BA), 70026, Italy
| | | | - Ronald Österbacka
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Gaetano Scamarcio
- CNR IFN, Bari, 70126, Italy
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - May Wheeler
- FlexEnable Technology Ltd, Cambridge, CB4 0FX, UK
| | - Eugenio Cantatore
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Eleonora Macchia
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Fabrizio Antonio Viola
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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Schröder L, Mallmann MR, Domroese CM, Wefers N, Dolscheid-Pommerich R, Stoffel-Wagner B, Trulson I, Vahldiek K, Klawonn F, Holdenrieder S. Method Comparison and Clinical Performance of Breast Cancer Tumor Markers on Novel Multiplex Immunoassay and Automatized LOCI Technology Platforms. Diagnostics (Basel) 2023; 13:3101. [PMID: 37835844 PMCID: PMC10572608 DOI: 10.3390/diagnostics13193101] [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: 08/08/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Tumor marker determinations are valuable tools for the guidance of breast cancer patients during the course of disease. They are assessed on diverse analytical platforms that may be associated with differences according to the methods applied and the clinical performance. To investigate the method dependency and clinical significance of breast cancer protein tumor markers, CEA, CA 15-3, CA 125, CA 19-9 and AFP were measured in a total of 154 biobanked samples from 77 patients with breast cancer, 10 with DCIS, 31 with benign breast diseases and 36 healthy controls using a Millipore multiplex biomarker panel (MP) and an automized version of the routinely used Vista LOCI technology. The markers were compared between methods and investigated for diagnostic performance. CEA, CA 15-3 and AFP showed good correlations between both platforms with correlation coefficients of R = 0.85, 0.85 and 0.92, respectively, in all samples, but similarly also in the various subgroups. CA 125 and CA 19-9 showed only moderate correlations (R = 0.71 and 0.56, respectively). Absolute values were significantly higher for CEA, CA 15-3, CA 125 and AFP in the Vista LOCI as compared with the MP method and vice versa for CA 19-9. The diagnostic performance for discrimination of breast cancer from healthy controls was similar for both methods with AUCs in ROC curves for CEA (MP 0.81, 95% CI 0.72-0.91; LOCI 0.81; 95% CI 0.72-0.91) and CA-15-3 (MP 0.75, 95% CI 0.65-0.86; LOCI 0.67, 95% CI 0.54-0.79). Similar results were obtained for the comparison of breast cancer with benign breast diseases regarding CEA (AUC MP 0.62, 95% CI 0.51-0.73; LOCI 0.64, 95% CI 0.53-0.74) and CA-15-3 (MP 0.70, 95% CI 0.6-0.81; LOCI 0.66, 95% CI 0.54-0.77). Both platforms show moderate to good method comparability for tumor markers with similar clinical performance. However, absolute levels in individual patients should be interpreted with care.
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Affiliation(s)
- Lars Schröder
- Department of Gynecology, Ketteler-Hospital Offenbach, 63071 Offenbach, Germany
- Department of Gynecology, University Hospital Bonn, 53127 Bonn, Germany
- Department of Obstetrics and Gynecology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Michael R Mallmann
- Department of Gynecology, University Hospital Bonn, 53127 Bonn, Germany
- Department of Obstetrics and Gynecology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christian M Domroese
- Department of Gynecology, University Hospital Bonn, 53127 Bonn, Germany
- Department of Obstetrics and Gynecology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Natalie Wefers
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Ramona Dolscheid-Pommerich
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Birgit Stoffel-Wagner
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Inga Trulson
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany
| | - Kai Vahldiek
- Department of Computer Science, Ostfalia University, 38302 Wolfenbüttel, Germany
| | - Frank Klawonn
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany
- Department of Computer Science, Ostfalia University, 38302 Wolfenbüttel, Germany
- Helmholtz Centre for Infection Research, Biostatistics, 38124 Braunschweig, Germany
| | - Stefan Holdenrieder
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center, Technical University Munich, 80636 Munich, Germany
- Center for the Evaluation of Biomarkers, 81679 Munich, Germany
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Koltai T. Earlier Diagnosis of Pancreatic Cancer: Is It Possible? Cancers (Basel) 2023; 15:4430. [PMID: 37760400 PMCID: PMC10526520 DOI: 10.3390/cancers15184430] [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: 06/07/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 09/29/2023] Open
Abstract
Pancreatic ductal adenocarcinoma has a very high mortality rate which has been only minimally improved in the last 30 years. This high mortality is closely related to late diagnosis, which is usually made when the tumor is large and has extensively infiltrated neighboring tissues or distant metastases are already present. This is a paradoxical situation for a tumor that requires nearly 15 years to develop since the first founding mutation. Response to chemotherapy under such late circumstances is poor, resistance is frequent, and prolongation of survival is almost negligible. Early surgery has been, and still is, the only approach with a slightly better outcome. Unfortunately, the relapse percentage after surgery is still very high. In fact, early surgery clearly requires early diagnosis. Despite all the advances in diagnostic methods, the available tools for improving these results are scarce. Serum tumor markers permit a late diagnosis, but their contribution to an improved therapeutic result is very limited. On the other hand, effective screening methods for high-risk populations have not been fully developed as yet. This paper discusses the difficulties of early diagnosis, evaluates whether the available diagnostic tools are adequate, and proposes some simple and not-so-simple measures to improve it.
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Affiliation(s)
- Tomas Koltai
- Hospital del Centro Gallego de Buenos Aires, Buenos Aires C1094, Argentina
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Zhang M, Yang H, Fu T, Meng M, Feng Y, Qu C, Li Z, Xing X, Li W, Ye M, Li S, Bu Z, Jia S. Liquid biopsy: circulating tumor DNA monitors neoadjuvant chemotherapy response and prognosis in stage II/III gastric cancer. Mol Oncol 2023; 17:1930-1942. [PMID: 37356061 PMCID: PMC10483607 DOI: 10.1002/1878-0261.13481] [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: 10/06/2022] [Revised: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023] Open
Abstract
A good response to neoadjuvant chemotherapy (NACT) is strongly associated with a higher curative resection rate and favorable outcomes for patients with gastric cancer (GC). We examined the utility of serial circulating tumor DNA (ctDNA) testing for monitoring NACT response and prognosis in stage II-III GC. Seventy-nine patients were enrolled to receive two cycles of NACT following gastrectomy with D2-lymphadenectomy. Plasma at baseline, post-NACT, and after surgery, and tissue at pretreatment and surgery were collected. We used a 425-gene panel to detect genomic alterations (GAs). Results show that the mean cell-free DNA concentration of patients with clinical stage III was significantly higher than patients with stage II (15.43 ng·mL-1 vs 14.40 ng·mL-1 ). After receiving NACT and surgery, the overall detection rate of ctDNA gradually reduced (59.5%, 50.8%, and 47.4% for baseline, post-NACT, and postsurgery). The maximum variant allele frequency (max-VAF) and the number of GAs decreased from 0.50% to 0.08% and from 2.9 to 1.7 after NACT. For patients with a partial response after NACT, the max-VAF and the number of GAs declined significantly, but they increased for patients with progressive disease. Patients with detectable ctDNA at baseline, after NACT, or after surgery have a worse overall survival (OS) than patients with undetectable ctDNA. The estimated 3-year OS was 73% for the post-NACT ctDNA-negative patients and 34% for ctDNA-positive. Patients with perpetual negative ctDNA before and after NACT have the best prognosis. In conclusion, ctDNA was proposed as a potential biomarker to predict prognosis and monitor the NACT response for stage II-III GC patients.
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Affiliation(s)
- Meng Zhang
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Heli Yang
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Tao Fu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Meizhu Meng
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Yi Feng
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Changda Qu
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhongwu Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Xiaofang Xing
- Department of Gastrointestinal Translational Research, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Wenmei Li
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Meiying Ye
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Sisi Li
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhaode Bu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
| | - Shuqin Jia
- Center for Molecular Diagnosis, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Peking University Cancer Hospital & InstituteBeijingChina
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Akshintala S, Sundby RT, Bernstein D, Glod JW, Kaplan RN, Yohe ME, Gross AM, Derdak J, Lei H, Pan A, Dombi E, Palacio-Yance I, Herrera KR, Miettinen MM, Chen HX, Steinberg SM, Helman LJ, Mascarenhas L, Widemann BC, Navid F, Shern JF, Heske CM. Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma. Clin Cancer Res 2023; 29:3329-3339. [PMID: 37398992 PMCID: PMC10529967 DOI: 10.1158/1078-0432.ccr-23-0709] [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: 03/24/2023] [Revised: 05/05/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
PURPOSE Antibodies against insulin-like growth factor (IGF) type 1 receptor have shown meaningful but transient tumor responses in patients with rhabdomyosarcoma (RMS). The SRC family member YES has been shown to mediate IGF type 1 receptor (IGF-1R) antibody acquired resistance, and cotargeting IGF-1R and YES resulted in sustained responses in murine RMS models. We conducted a phase I trial of the anti-IGF-1R antibody ganitumab combined with dasatinib, a multi-kinase inhibitor targeting YES, in patients with RMS (NCT03041701). PATIENTS AND METHODS Patients with relapsed/refractory alveolar or embryonal RMS and measurable disease were eligible. All patients received ganitumab 18 mg/kg intravenously every 2 weeks. Dasatinib dose was 60 mg/m2/dose (max 100 mg) oral once daily [dose level (DL)1] or 60 mg/m2/dose (max 70 mg) twice daily (DL2). A 3+3 dose escalation design was used, and maximum tolerated dose (MTD) was determined on the basis of cycle 1 dose-limiting toxicities (DLT). RESULTS Thirteen eligible patients, median age 18 years (range 8-29) enrolled. Median number of prior systemic therapies was 3; all had received prior radiation. Of 11 toxicity-evaluable patients, 1/6 had a DLT at DL1 (diarrhea) and 2/5 had a DLT at DL2 (pneumonitis, hematuria) confirming DL1 as MTD. Of nine response-evaluable patients, one had a confirmed partial response for four cycles, and one had stable disease for six cycles. Genomic studies from cell-free DNA correlated with disease response. CONCLUSIONS The combination of dasatinib 60 mg/m2/dose daily and ganitumab 18 mg/kg every 2 weeks was safe and tolerable. This combination had a disease control rate of 22% at 5 months.
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Affiliation(s)
- Srivandana Akshintala
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Donna Bernstein
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - John W. Glod
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Rosandra N. Kaplan
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, Maryland
| | - Andrea M. Gross
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Joanne Derdak
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Haiyan Lei
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Alexander Pan
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Isabel Palacio-Yance
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Kailey R. Herrera
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Markku M. Miettinen
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Helen X. Chen
- Cancer Therapy Evaluation Program (CTEP), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Seth M. Steinberg
- Biostatistics and Data Management, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Lee J. Helman
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles (CHLA), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
- The Osteosarcoma Institute, Dallas, Texas
| | - Leo Mascarenhas
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles (CHLA), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Brigitte C. Widemann
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Fariba Navid
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles (CHLA), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Christine M. Heske
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
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Dao J, Conway PJ, Subramani B, Meyyappan D, Russell S, Mahadevan D. Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation. Int J Mol Sci 2023; 24:13219. [PMID: 37686024 PMCID: PMC10487653 DOI: 10.3390/ijms241713219] [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: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management.
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Affiliation(s)
- Jonathan Dao
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick J. Conway
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Baskaran Subramani
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Devi Meyyappan
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
| | - Sammy Russell
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Daruka Mahadevan
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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40
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Zhu L, Xu R, Yang L, Shi W, Zhang Y, Liu J, Li X, Zhou J, Bing P. Minimal residual disease (MRD) detection in solid tumors using circulating tumor DNA: a systematic review. Front Genet 2023; 14:1172108. [PMID: 37636270 PMCID: PMC10448395 DOI: 10.3389/fgene.2023.1172108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/20/2023] [Indexed: 08/29/2023] Open
Abstract
Minimal residual disease (MRD) refers to a very small number of residual tumor cells in the body during or after treatment, representing the persistence of the tumor and the possibility of clinical progress. Circulating tumor DNA (ctDNA) is a DNA fragment actively secreted by tumor cells or released into the circulatory system during the process of apoptosis or necrosis of tumor cells, which emerging as a non-invasive biomarker to dynamically monitor the therapeutic effect and prediction of recurrence. The feasibility of ctDNA as MRD detection and the revolution in ctDNA-based liquid biopsies provides a potential method for cancer monitoring. In this review, we summarized the main methods of ctDNA detection (PCR-based Sequencing and Next-Generation Sequencing) and their advantages and disadvantages. Additionally, we reviewed the significance of ctDNA analysis to guide the adjuvant therapy and predict the relapse of lung, breast and colon cancer et al. Finally, there are still many challenges of MRD detection, such as lack of standardization, false-negatives or false-positives results make misleading, and the requirement of validation using large independent cohorts to improve clinical outcomes.
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Affiliation(s)
- Lemei Zhu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Ran Xu
- Geneis Beijing Co., Ltd., Beijing, China
| | | | - Wei Shi
- Geneis Beijing Co., Ltd., Beijing, China
| | - Yuan Zhang
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Juan Liu
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
- School of Public Health, Changsha Medical University, Changsha, China
| | - Xi Li
- Department of Orthopedics, Xiangya Hospital Central South University, Changsha, China
| | - Jun Zhou
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Pingping Bing
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha, China
- Academician Workstation, Changsha Medical University, Changsha, China
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41
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Su X, Xie Y, Liu X, Chen M, Zheng C, Zhong H, Li M. Absolute Quantification of Serum Exosomes in Patients with an SERS-Lateral Flow Strip Biosensor for Noninvasive Clinical Cancer Diagnosis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:37130-37142. [PMID: 37525365 DOI: 10.1021/acsami.3c05039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Exosomes (exos) widely existing in body fluids show great potential for noninvasive cancer diagnosis. Quantitative analysis of exos is traditionally performed by targeting specific exosomal surface proteins, but it is often imprecise due to the common expression of exosomal proteins and subtle expression differences between different cancer subtypes. Herein, we report quantitative surface-enhanced Raman spectroscopy (SERS) of serum exos through a combination of a paper-based lateral flow strip (LFS) biosensor with multivariate spectral unmixing analysis rather than simply quantifying exosomal proteins. Our SERS-LFS biosensor enables absolute quantification of two different serum exos with a limit of detection down to ∼106 particles/mL for both exos. We further exemplify the application of this strategy in quantitative dual-plex detection of serum exos from breast cancer patients. We find that human epidermal growth factor receptor 2+ (HER2+) and luminal A breast cancer patients undergoing no surgery are enriched in serum exos derived from SKBR-3 cells and MCF-7 cells (denoted as SKBR and MCF exos), respectively. The surgical treatment of these breast cancer patients accompanies an obvious decrease of either SKBR or MCF exos in the serum. These results suggest the great potential of the combination of the SERS-LFS biosensor and multivariate spectral unmixing for breast cancer subtyping and therapeutic surveillance with the powerful quantitative capability of exos in clinical samples.
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Affiliation(s)
- Xiaoming Su
- School of Materials Science and Engineering, Central South University, Changsha 410083, Hunan, China
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Yangcenzi Xie
- School of Materials Science and Engineering, Central South University, Changsha 410083, Hunan, China
| | - Xinyu Liu
- School of Materials Science and Engineering, Central South University, Changsha 410083, Hunan, China
| | - Mingyang Chen
- School of Materials Science and Engineering, Central South University, Changsha 410083, Hunan, China
| | - Chao Zheng
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, Shandong, China
| | - Hong Zhong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Ming Li
- School of Materials Science and Engineering, Central South University, Changsha 410083, Hunan, China
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Yin T, Xu L, Gil B, Merali N, Sokolikova MS, Gaboriau DCA, Liu DSK, Muhammad Mustafa AN, Alodan S, Chen M, Txoperena O, Arrastua M, Gomez JM, Ontoso N, Elicegui M, Torres E, Li D, Mattevi C, Frampton AE, Jiao LR, Ramadan S, Klein N. Graphene Sensor Arrays for Rapid and Accurate Detection of Pancreatic Cancer Exosomes in Patients' Blood Plasma Samples. ACS NANO 2023; 17:14619-14631. [PMID: 37470391 PMCID: PMC10416564 DOI: 10.1021/acsnano.3c01812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
Biosensors based on graphene field effect transistors (GFETs) have the potential to enable the development of point-of-care diagnostic tools for early stage disease detection. However, issues with reproducibility and manufacturing yields of graphene sensors, but also with Debye screening and unwanted detection of nonspecific species, have prevented the wider clinical use of graphene technology. Here, we demonstrate that our wafer-scalable GFETs array platform enables meaningful clinical results. As a case study of high clinical relevance, we demonstrate an accurate and robust portable GFET array biosensor platform for the detection of pancreatic ductal adenocarcinoma (PDAC) in patients' plasma through specific exosomes (GPC-1 expression) within 45 min. In order to facilitate reproducible detection in blood plasma, we optimized the analytical performance of GFET biosensors via the application of an internal control channel and the development of an optimized test protocol. Based on samples from 18 PDAC patients and 8 healthy controls, the GFET biosensor arrays could accurately discriminate between the two groups while being able to detect early cancer stages including stages 1 and 2. Furthermore, we confirmed the higher expression of GPC-1 and found that the concentration in PDAC plasma was on average more than 1 order of magnitude higher than in healthy samples. We found that these characteristics of GPC-1 cancerous exosomes are responsible for an increase in the number of target exosomes on the surface of graphene, leading to an improved signal response of the GFET biosensors. This GFET biosensor platform holds great promise for the development of an accurate tool for the rapid diagnosis of pancreatic cancer.
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Affiliation(s)
- Tianyi Yin
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Lizhou Xu
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Bruno Gil
- Hamlyn
Centre, Imperial College London, London SW7 2AZ, U.K.
| | - Nabeel Merali
- Oncology
Section, Surrey Cancer Research Institute, Department of Clinical
and Experimental Medicine, FHMS, University
of Surrey, The Leggett Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
- HPB
Surgical Unit, Royal Surrey NHS Foundation Trust, Guildford, Surrey GU2 7XX, U.K.
- Minimal Access
Therapy Training Unit (MATTU), University
of Surrey, The Leggett
Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
| | | | - David C. A. Gaboriau
- Facility
for Imaging By Light Microscopy, Imperial
College London, London SW7 2AZ, U.K.
| | - Daniel S. K. Liu
- Department
of Surgery & Cancer, Imperial College
London, Hammersmith Hospital
Campus, London W12 0NN, U.K.
- HPB
Surgical Unit, Imperial College Healthcare NHS Trust, Hammersmith
Hospital, London W12 0HS, U.K.
| | - Ahmad Nizamuddin Muhammad Mustafa
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
- FTKEE,
Universiti Teknikal Malaysia Melaka, 76100 Durian Tunggal, Melaka, Malaysia
| | - Sarah Alodan
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Michael Chen
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Oihana Txoperena
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - María Arrastua
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Juan Manuel Gomez
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Nerea Ontoso
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Marta Elicegui
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Elias Torres
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián ES 20009, Spain
| | - Danyang Li
- Research
Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
| | - Cecilia Mattevi
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Adam E. Frampton
- Oncology
Section, Surrey Cancer Research Institute, Department of Clinical
and Experimental Medicine, FHMS, University
of Surrey, The Leggett Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
- HPB
Surgical Unit, Royal Surrey NHS Foundation Trust, Guildford, Surrey GU2 7XX, U.K.
- Minimal Access
Therapy Training Unit (MATTU), University
of Surrey, The Leggett
Building, Daphne Jackson Road, Guildford GU2 7WG, U.K.
- Department
of Surgery & Cancer, Imperial College
London, Hammersmith Hospital
Campus, London W12 0NN, U.K.
| | - Long R. Jiao
- Department
of Surgery & Cancer, Imperial College
London, Hammersmith Hospital
Campus, London W12 0NN, U.K.
| | - Sami Ramadan
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
| | - Norbert Klein
- Department
of Materials, Imperial College London, London SW7 2AZ, U.K.
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Schlick K, Gantschnigg A, Seymer A, Huemer F, Greil R, Weiss L. Comparison of gemcitabine plus oxaliplatin versus gemcitabine plus nab-paclitaxel as first-line chemotherapy for advanced pancreatic adenocarcinoma: A single-center retrospective analysis. Cancer Med 2023; 12:16997-17004. [PMID: 37537780 PMCID: PMC10501299 DOI: 10.1002/cam4.6334] [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: 03/23/2023] [Revised: 06/13/2023] [Accepted: 07/02/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Pancreatic cancer is mostly diagnosed in an advanced stage and treated with systemic therapy with palliative intent. Nowadays, the doublet chemotherapy of Gemcitabine and nab-paclitaxel (Gem-Nab) is one of the most frequently used regimens worldwide, but is not ubiquitarily available or reimbursed. Therefore, we compared the clinical efficacy of Gem-Nab to a historical control of patients treated with gemcitabine and oxaliplatin (Gem-Ox) at our tertiary cancer center, which was the standard treatment prior to the introduction of FOLFIRINOX. METHODS This single-center retrospective real world study includes 121 patients diagnosed with locally advanced or primary metastatic pancreatic adenocarcinoma who were treated with chemotherapy doublet, with either Gem-Nab or Gem-Ox in palliative first-line. Survival rates were analyzed using the Kaplan-Meier method, and comparisons were made with log-rank tests. Gem-Ox was considered as standard first line therapy at our institution for patients who were deemed fit for doublet chemotherapy between the years 2006 to 2012. These patients were compared to a cohort of patients treated with the new standard first-line therapy of Gem-Nab between 2013 and 2020. RESULTS A total of 554 patients with pancreatic cancer of all stages were screened, and 73 patients treated with Gem-Nab and 48 patients treated with Gem-Ox in the palliative first-line setting were identified and included in this analysis. Patients receiving Gem-Ox had a statistically significantly better performance score (ECOG PS) when compared to the Gem-Nab group (Odds ratio (OR) 0.28, 95% CI 0.12-0.65, p = 0.005), more often suffered from locally advanced than metastatic disease (OR 3.10, 95% CI 1.27-7.91, p = 0.019) and were younger in age (OR 0.95, 95% CI 0.91-0.99, p = 0.013). Median overall survival (OS) of the whole study cohort was 10.3 months (95% CI 8.5-11.6). No statistically significant difference in OS could be observed between the Gem-Nab and the Gem-Ox cohort (median OS: 8.9 months (95% CI 6.4-13.5) versus 10.9 months (95% CI 9.5-13.87, p = 0.794, HR 1.27, 95% CI 0.85-1.91)). Median progression-free survival (PFS) was 6.8 months in the entire cohort (95% CI 4.9-8.4). No statistically significant difference in PFS could be observed between the Gem-Nab and the Gem-Ox cohort (median PFS: 5.8 months (95% CI 4.3-8.2) versus 7.9 months (95% CI 5.4-9.5) p = 0.536, HR 1.11, 95% CI 0.74-1.67). Zero-truncated negative binomial regressions on OS and PFS adjusting for gender, age, performance status (ECOG PS), and CA19-9 levels yielded no significant difference between Gem-Nab or Gem-Ox. CONCLUSION From our analysis, we could evidence no difference in outcome parameters in this retrospective analysis despite the worse prognostic pattern for GemOX. Therefore, we suggest Gem-Ox as potential first line treatment option for inoperable locally advanced or metastatic pancreatic cancer, especially if Gem-Nab is not available.
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Affiliation(s)
- Konstantin Schlick
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic CenterParacelsus Medical UniversitySalzburgAustria
- Salzburg Cancer Research Institute, Center for Clinical Cancer and Immunology TrialsSalzburgAustria
| | | | - Alexander Seymer
- Department of Sociology and Human Geography, Division of SociologyParis Lodron University Salzburg (PLUS)SalzburgAustria
| | - Florian Huemer
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic CenterParacelsus Medical UniversitySalzburgAustria
- Salzburg Cancer Research Institute, Center for Clinical Cancer and Immunology TrialsSalzburgAustria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic CenterParacelsus Medical UniversitySalzburgAustria
- Salzburg Cancer Research Institute, Center for Clinical Cancer and Immunology TrialsSalzburgAustria
- Cancer Cluster SalzburgSalzburgAustria
| | - Lukas Weiss
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic CenterParacelsus Medical UniversitySalzburgAustria
- Salzburg Cancer Research Institute, Center for Clinical Cancer and Immunology TrialsSalzburgAustria
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Earland N, Chen K, Semenkovich NP, Chauhan PS, Zevallos JP, Chaudhuri AA. Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology. Semin Radiat Oncol 2023; 33:262-278. [PMID: 37331781 DOI: 10.1016/j.semradonc.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate . Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease.
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Affiliation(s)
- Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Pradeep S Chauhan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Jose P Zevallos
- Department of Otolaryngology, University of Pittsburgh Medical School, Pittsburgh, PA
| | - Aadel A Chaudhuri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO; Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO; Department of Genetics, Washington University School of Medicine, St. Louis, MO; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO; Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO.
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45
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Tornel-Avelar AI, Velarde Ruiz-Velasco JA, Pelaez-Luna M. Pancreatic cancer, autoimmune or chronic pancreatitis, beyond tissue diagnosis: Collateral imaging and clinical characteristics may differentiate them. World J Gastrointest Oncol 2023; 15:925-942. [PMID: 37389107 PMCID: PMC10302998 DOI: 10.4251/wjgo.v15.i6.925] [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: 02/20/2023] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/14/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is developing into the 2nd leading cause of cancer-related death. Often, the clinical and radiological presentation of PDAC may be mirrored by other inflammatory pancreatic masses, such as autoimmune pancreatitis (AIP) and mass-forming chronic pancreatitis (MFCP), making its diagnosis challenging. Differentiating AIP and MFCP from PDAC is vital due to significant therapeutic and prognostic implications. Current diagnostic criteria and tools allow the precise differentiation of benign from malignant masses; however, the diagnostic accuracy is imperfect. Major pancreatic resections have been performed in AIP cases under initial suspicion of PDAC after a diagnostic approach failed to provide an accurate diagnosis. It is not unusual that after a thorough diagnostic evaluation, the clinician is confronted with a pancreatic mass with uncertain diagnosis. In those cases, a re-evaluation must be entertained, preferably by an experienced multispecialty team including radiologists, pathologists, gastroenterologists, and surgeons, looking for disease-specific clinical, imaging, and histological hallmarks or collateral evidence that could favor a specific diagnosis. Our aim is to describe current diagnostic limitations that hinder our ability to reach an accurate diagnosis among AIP, PDAC, and MFCP and to highlight those disease-specific clinical, radiological, serological, and histological characteristics that could support the presence of any of these three disorders when facing a pancreatic mass with uncertain diagnosis after an initial diagnostic approach has been unsuccessful.
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Affiliation(s)
- Ana I Tornel-Avelar
- Department of Gastroenterology, Hospital Civil of Guadalajara “Fray Antonio Alcalde”, Guadalajara 44340, Jalisco, Mexico
| | | | - Mario Pelaez-Luna
- Research Division School of Medicine/Department of Gastroenterology, Universidad Nacional Autonoma de México/National Institute of Medical Sciences and Nutrition “Salvador Zubiran”, Tlalpan 14000, Mexico City, Mexico
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Pan HJ, Gong YC, Cao WQ, Zhang ZH, Jia LP, Zhang W, Shang L, Li XJ, Xue QW, Wang HS, Ma RN. Fascinating Immobilization-Free Electrochemical Immunosensing Strategy Based on the Cooperation of Buoyancy and Magnetism. Anal Chem 2023; 95:7336-7343. [PMID: 37129510 DOI: 10.1021/acs.analchem.3c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Rapid and accurate detection of biomolecules is of vital importance for the diagnosis of disease and for performing timely treatments. The point-of-care analysis of cancer biomarkers in the blood with low cost and easy processing is still challenging. Herein, an advanced and robust strategy, which integrates the buoyant recognition probe with the magnetic reporter probe in one solution, was first proposed for immobilization-free electrochemical immunosensing. The tumor marker of alpha fetoprotein (AFP) can be captured immune-buoyantly, and then a multifunctional magnetic reporter probe in pseudo-homogeneous solution was further captured to fulfill a sandwich-type immunoreaction. The residual magnetic reporter probe can be firmly and efficiently attracted on a magnetic glassy carbon electrode to fulfill the conversion of the target AFP amount into the residual magnetic electrochemical signal indicator. As a result, the electrochemical signal of methylene blue can accurately reflect the original level of target antigen AFP concentration. By integrating buoyancy-driven quasi-homogenous biorecognition with magnetism-mediated amplification and signal output, the proposed immobilization-free electrochemical immunosensing strategy displayed a wide range of linear response (100 fg mL-1 to 10 ng mL-1), low detection limit (14.52 fg mL-1), and good reproducibility, selectivity, and stability. The designed strategy manifests remarkable advantages including assay simplicity, rapidness, and high sensitivity owing to the in-solution instead of on-electrode biorecognition that could accelerate and improve the biorecognition efficiency. To the best of our knowledge, this is the first cooperation of buoyancy-driven biorecognition with magnetism-mediated signal output in bioanalysis, which would be attractive for rapid clinic biomedical application. Thus, this work provides a fresh perspective for convenient and favorable immobilization-free electrochemical biosensing of universal biomolecules.
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Affiliation(s)
- Hui-Jing Pan
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Ying-Chao Gong
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Wen-Qi Cao
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Zhi-Heng Zhang
- Oncology Department, Hospital of Traditional Chinese Medicine of Liaocheng City, Liaocheng, Shandong 252000, P.R. China
| | - Li-Ping Jia
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Wei Zhang
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Lei Shang
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Xiao-Jian Li
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Qing-Wang Xue
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Huai-Sheng Wang
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
| | - Rong-Na Ma
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory/Collaborative Innovation Center of Chemical Energy Storage, Liaocheng University, Liaocheng, Shandong 252059, P.R. China
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Liou GY, Byrd CJ. Diagnostic Bioliquid Markers for Pancreatic Cancer: What We Have vs. What We Need. Cancers (Basel) 2023; 15:2446. [PMID: 37173913 PMCID: PMC10177101 DOI: 10.3390/cancers15092446] [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: 02/15/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer, currently has a dismal five-year survival rate of approximately 10% due to late diagnosis and a lack of efficient treatment options such as surgery. Furthermore, the majority of PDAC patients have surgically unresectable cancer, meaning cancer cells have either reached the surrounding blood vessels or metastasized to other organs distant from the pancreas area, resulting in low survival rates as compared to other types of cancers. In contrast, the five-year survival rate of surgically resectable PDAC patients is currently 44%. The late diagnosis of PDAC is a result of little or no symptoms in its early stage of development and a lack of specific biomarkers that may be utilized in routine examinations in the clinic. Although healthcare professionals understand the importance of early detection of PDAC, the research on the subject has lagged and no significant changes in the death toll of PDAC patients has been observed. This review is focused on understanding potential biomarkers that may increase the early diagnosis of PDAC patients at its surgically resectable stage. Here, we summarize the currently available biomarkers used in the clinic as well as those being developed with the hope of providing insight into the future of liquid biomarkers to be used in routine examinations for the early diagnosis of PDAC.
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Affiliation(s)
- Geou-Yarh Liou
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA 30314, USA
- Department of Biological Sciences, Clark Atlanta University, Atlanta, GA 30314, USA
| | - Crystal J. Byrd
- Department of Biological Sciences, Clark Atlanta University, Atlanta, GA 30314, USA
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Reilly L, Seddighi S, Singleton AB, Cookson MR, Ward ME, Qi YA. Variant biomarker discovery using mass spectrometry-based proteogenomics. FRONTIERS IN AGING 2023; 4:1191993. [PMID: 37168844 PMCID: PMC10165118 DOI: 10.3389/fragi.2023.1191993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Genomic diversity plays critical roles in risk of disease pathogenesis and diagnosis. While genomic variants-including single nucleotide variants, frameshift variants, and mis-splicing isoforms-are commonly detected at the DNA or RNA level, their translated variant protein or polypeptide products are ultimately the functional units of the associated disease. These products are often released in biofluids and could be leveraged for clinical diagnosis and patient stratification. Recent emergence of integrated analysis of genomics with mass spectrometry-based proteomics for biomarker discovery, also known as proteogenomics, have significantly advanced the understanding disease risk variants, precise medicine, and biomarker discovery. In this review, we discuss variant proteins in the context of cancers and neurodegenerative diseases, outline current and emerging proteogenomic approaches for biomarker discovery, and provide a comprehensive proteogenomic strategy for detection of putative biomarker candidates in human biospecimens. This strategy can be implemented for proteogenomic studies in any field of enquiry. Our review timely addresses the need of biomarkers for aging related diseases.
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Affiliation(s)
- Luke Reilly
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Yue A. Qi
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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Bararia A, Chakraborty P, Roy P, Chattopadhay BK, Das A, Chatterjee A, Sikdar N. Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer. World J Gastroenterol 2023; 29:2241-2260. [PMID: 37124888 PMCID: PMC10134423 DOI: 10.3748/wjg.v29.i15.2241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.
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Affiliation(s)
- Akash Bararia
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Prosenjeet Chakraborty
- Department of Molecular Biosciences, SVYASA School of Yoga and Naturopathy, Bangalore 560105, India
| | - Paromita Roy
- Department of Pathology, Tata Medical Center, Kolkata 700160, India
| | | | - Amlan Das
- Department of Biochemistry, Royal Global University, Assam 781035, India
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9061, New Zealand
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Nilabja Sikdar
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
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Ko SW, Yoon SB. Clinical implications and perspectives of portal venous circulating tumor cells in pancreatic cancer. World J Gastrointest Oncol 2023; 15:632-643. [PMID: 37123055 PMCID: PMC10134213 DOI: 10.4251/wjgo.v15.i4.632] [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: 12/24/2022] [Revised: 02/10/2023] [Accepted: 03/16/2023] [Indexed: 04/12/2023] Open
Abstract
Despite recent improvements in the diagnosis and treatment of pancreatic cancer (PC), clinical outcomes remain dismal. Moreover, there are no effective prognostic or predictive biomarkers or options beyond carbohydrate antigen 19-9 for personalized and precise treatment. Circulating tumor cells (CTCs), as a member of the liquid biopsy family, could be a promising biomarker; however, the rarity of CTCs in peripheral venous blood limits their clinical use. Because the first venous drainage of PC is portal circulation, the portal vein can be a more suitable location for the detection of CTCs. Endoscopic ultrasound-guided portal venous sampling of CTCs is both feasible and safe. Several studies have suggested that the detection rate and number of CTCs may be higher in the portal blood than in the peripheral blood. CTC counts in the portal blood are highly associated with hepatic metastasis, recurrence after surgery, and survival. The phenotypic and genotypic properties measured in the captured portal CTCs can help us to understand tumor heterogeneity and predict the prognosis of PC. Small sample sizes and heterogeneous CTC detection methods limit the studies to date. Therefore, a large number of prospective studies are needed to corroborate portal CTCs as a valid biomarker in PC.
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Affiliation(s)
- Sung Woo Ko
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, South Korea
| | - Seung Bae Yoon
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, South Korea
- Department of Internal Medicine, Eunpyeong St. Mary’s Hospital, Seoul 03312, South Korea
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