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Lee JA, Choi HG, Eun HS, Bu J, Jang TM, Lee J, Son CY, Kim MS, Rou WS, Kim SH, Lee BS, Kim HN, Lee TH, Jeon HJ. Programmed Death 1 and Cytotoxic T-Lymphocyte-Associated Protein 4 Gene Expression in Peripheral Blood Mononuclear Cells Can Serve as Prognostic Biomarkers for Hepatocellular Carcinoma. Cancers (Basel) 2024; 16:1493. [PMID: 38672574 PMCID: PMC11048418 DOI: 10.3390/cancers16081493] [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: 02/02/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly aggressive form of liver cancer with poor prognosis. The lack of reliable biomarkers for early detection and accurate diagnosis and prognosis poses a significant challenge to its effective clinical management. In this study, we investigated the diagnostic and prognostic potential of programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) expression in peripheral blood mononuclear cells (PBMCs) in HCC. PD-1 and CTLA-4 gene expression was analyzed comparatively using PBMCs collected from HCC patients and healthy individuals. The results revealed higher PD-1 gene expression levels in patients with multifocal tumors, lymphatic invasion, or distant metastasis than those in their control counterparts. However, conventional serum biomarkers of liver function do not exhibit similar correlations. In conclusion, PD-1 gene expression is associated with OS and PFS and CTLA-4 gene expression is associated with OS, whereas the serum biomarkers analyzed in this study show no significant correlation with survival in HCC. Hence, PD-1 and CTLA-4 expressed in PBMCs are considered potential prognostic biomarkers for patients with HCC that can facilitate prediction of malignancy, response to currently available HCC treatments, and overall survival.
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Affiliation(s)
- Ji Ah Lee
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea; (J.A.L.); (J.B.)
| | - Hei-Gwon Choi
- Department of Medical Science, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (H.-G.C.); (H.S.E.); (H.N.K.)
| | - Hyuk Soo Eun
- Department of Medical Science, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (H.-G.C.); (H.S.E.); (H.N.K.)
- Department of Internal Medicine, College of Medicine, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (W.S.R.); (S.H.K.); (B.S.L.)
- Department of Internal Medicine, Chungnam National University Hospital, 282, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea
| | - Jiyoon Bu
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea; (J.A.L.); (J.B.)
- Department of Biological Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea; (T.M.J.); (C.Y.S.)
| | - Tae Min Jang
- Department of Biological Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea; (T.M.J.); (C.Y.S.)
| | - Jeongdong Lee
- Department of Biomedical Laboratory Science, Daegu Health College, 15 Yeongsong-ro, Buk-gu, Daegu 41453, Republic of Korea; (J.L.); (M.S.K.)
| | - Chae Yeon Son
- Department of Biological Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea; (T.M.J.); (C.Y.S.)
| | - Min Seok Kim
- Department of Biomedical Laboratory Science, Daegu Health College, 15 Yeongsong-ro, Buk-gu, Daegu 41453, Republic of Korea; (J.L.); (M.S.K.)
| | - Woo Sun Rou
- Department of Internal Medicine, College of Medicine, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (W.S.R.); (S.H.K.); (B.S.L.)
- Department of Internal Medicine, Chungnam National University Sejong Hospital, 20, Bodeum 7-ro, Sejong 30099, Republic of Korea
| | - Seok Hyun Kim
- Department of Internal Medicine, College of Medicine, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (W.S.R.); (S.H.K.); (B.S.L.)
- Department of Internal Medicine, Chungnam National University Hospital, 282, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea
| | - Byung Seok Lee
- Department of Internal Medicine, College of Medicine, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (W.S.R.); (S.H.K.); (B.S.L.)
- Department of Internal Medicine, Chungnam National University Hospital, 282, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea
| | - Ha Neul Kim
- Department of Medical Science, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (H.-G.C.); (H.S.E.); (H.N.K.)
| | - Tae Hee Lee
- Department of Biomedical Laboratory Science, Daegu Health College, 15 Yeongsong-ro, Buk-gu, Daegu 41453, Republic of Korea; (J.L.); (M.S.K.)
| | - Hong Jae Jeon
- Department of Internal Medicine, College of Medicine, Chungnam National University, 266, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea; (W.S.R.); (S.H.K.); (B.S.L.)
- Department of Internal Medicine, Chungnam National University Sejong Hospital, 20, Bodeum 7-ro, Sejong 30099, Republic of Korea
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Zhang L, Li S, Zhang D, Yin C, Wang Z, Chen R, Cheng N, Bai Y. Value of GPR, APPRI and FIB-4 in the early diagnosis of hepatocellular carcinoma: a prospective cohort study. Jpn J Clin Oncol 2024; 54:129-136. [PMID: 37869774 DOI: 10.1093/jjco/hyad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
OBJECTIVE There is an urgent need for novel biomarkers that are inexpensive, effective and easily accessible to complement the early diagnosis of hepatocellular carcinoma. This study aimed to analyze the relationship between serum gamma-glutamate-transpeptidase to platelet ratio, alkaline phosphatase-to-platelet ratio index, fibrosis index based on four factors and the risk of hepatocellular carcinoma, and to determine the optimal cut-offs for predicting hepatocellular carcinoma. METHODS Based on a prospective cohort study, 44 215 participants who were cancer-free at baseline (2011-13) were included in the study. Cox proportional hazard models and receiver operating characteristics curves were used to analyze the diagnostic value and optimal cut-off value of gamma-glutamyl-transpeptidase to platelet ratio, alkaline phosphatase-to-platelet ratio index and fibrosis index based on four factors in predicting hepatocellular carcinoma patients. RESULTS Gamma-glutamyl-transpeptidase to platelet ratio, alkaline phosphatase-to-platelet ratio index and fibrosis index based on four factors can be used as early independent predictors of hepatocellular carcinoma risk. The risk of hepatocellular carcinoma in the fourth quantile of gamma-glutamyl-transpeptidase to platelet ratio and alkaline phosphatase-to-platelet ratio index was 4.04 times (hazard ratio = 4.04, 95% confidence interval: 2.09, 7.80) and 2.59 times (hazard ratio = 2.59, 95% confidence interval: 1.45, 4.61), respectively, compared with the first quantile. With fibrosis index based on four factors first quantile as a reference, fibrosis index based on four factors fourth quantile had the highest risk (hazard ratio = 18.58, 95% confidence interval: 7.55, 45.72). Receiver operating characteristic results showed that fibrosis index based on four factors had a stronger ability to predict the risk of hepatocellular carcinoma (area under curve = 0.81, 95% confidence interval: 0.80, 0.81), and similar results were shown for gender stratification. In the total population, the optimal cut-off values of gamma-glutamyl-transpeptidase to platelet ratio, alkaline phosphatase-to-platelet ratio index and fibrosis index based on four factors were 0.208, 0.629 and 1.942, respectively. CONCLUSIONS Gamma-glutamyl-transpeptidase to platelet ratio, alkaline phosphatase-to-platelet ratio index and fibrosis index based on four factors were independent predictors of hepatocellular carcinoma risk. Amongst them, fibrosis index based on four factors shows a stronger predictive ability for hepatocellular carcinoma risk, and gamma-glutamyl-transpeptidase to platelet ratio and alkaline phosphatase-to-platelet ratio index can be used as complementary indicators.
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Affiliation(s)
- Lizhen Zhang
- Department of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, China
| | - Siyu Li
- Department of Epidemiology, Baotou Medical College, Baotou, China
| | - Desheng Zhang
- Jinchuan Group Co., LTD, Jinchuan Company Staff Hospital, Jinchang, China
| | - Chun Yin
- Jinchuan Group Co., LTD, Jinchuan Company Staff Hospital, Jinchang, China
| | - Zhongge Wang
- Department of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, China
| | - Ruirui Chen
- Department of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, China
| | - Ning Cheng
- College of Basic Medicine, Lanzhou University, Lanzhou, China
| | - Yana Bai
- Department of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, China
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Francini E, Nuzzo PV, Fanelli GN. Cell-Free DNA: Unveiling the Future of Cancer Diagnostics and Monitoring. Cancers (Basel) 2024; 16:662. [PMID: 38339412 PMCID: PMC10854618 DOI: 10.3390/cancers16030662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
As we conclude this Special Issue of 21 published articles dedicated to cell-free DNA (cfDNA) as a prognostic and predictive biomarker in solid cancers, we find ourselves gazing at a vibrant landscape of research on cfDNA [...].
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Affiliation(s)
- Edoardo Francini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Pier Vitale Nuzzo
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Giuseppe Nicolò Fanelli
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
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Manea I, Iacob R, Iacob S, Cerban R, Dima S, Oniscu G, Popescu I, Gheorghe L. Liquid biopsy for early detection of hepatocellular carcinoma. Front Med (Lausanne) 2023; 10:1218705. [PMID: 37809326 PMCID: PMC10556479 DOI: 10.3389/fmed.2023.1218705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly prevalent and lethal cancer globally. Over 90% of HCC cases arise in the context of liver cirrhosis, and the severity of the underlying liver disease or advanced tumor stage at diagnosis significantly limits treatment options. Early diagnosis is crucial, and all guidelines stress the importance of screening protocols for HCC early detection as a public health objective. As serum biomarkers are not optimal for early diagnosis, liquid biopsy has emerged as a promising tool for diagnosis, prognostication, and patients' stratification for personalized therapy in various solid tumors, including HCC. While circulating tumor cells (CTCs) are better suited for personalized therapy and prognosis, cell-free DNA (cfDNA) and extracellular vesicle-based technologies show potential for early diagnosis, HCC screening, and surveillance protocols. Evaluating the added value of liquid biopsy genetic and epigenetic biomarkers for HCC screening is a key goal in translational research. Somatic mutations commonly found in HCC can be investigated in cfDNA and plasma exosomes as genetic biomarkers. Unique methylation patterns in cfDNA or cfDNA fragmentome features have been suggested as innovative tools for early HCC detection. Likewise, extracellular vesicle cargo biomarkers such as miRNAs and long non-coding RNAs may serve as potential biomarkers for early HCC detection. This review will explore recent findings on the utility of liquid biopsy for early HCC diagnosis. Combining liquid biopsy methods with traditional serological biomarkers could improve the overall diagnostic accuracy for early HCC detection.
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Affiliation(s)
- Ioana Manea
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Razvan Iacob
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Speranta Iacob
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Razvan Cerban
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Simona Dima
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Gabriel Oniscu
- Transplant Division, Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden
| | - Irinel Popescu
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Liliana Gheorghe
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [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: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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Mansur A, Vrionis A, Charles JP, Hancel K, Panagides JC, Moloudi F, Iqbal S, Daye D. The Role of Artificial Intelligence in the Detection and Implementation of Biomarkers for Hepatocellular Carcinoma: Outlook and Opportunities. Cancers (Basel) 2023; 15:cancers15112928. [PMID: 37296890 DOI: 10.3390/cancers15112928] [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] [Received: 04/15/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Liver cancer is a leading cause of cancer-related death worldwide, and its early detection and treatment are crucial for improving morbidity and mortality. Biomarkers have the potential to facilitate the early diagnosis and management of liver cancer, but identifying and implementing effective biomarkers remains a major challenge. In recent years, artificial intelligence has emerged as a promising tool in the cancer sphere, and recent literature suggests that it is very promising in facilitating biomarker use in liver cancer. This review provides an overview of the status of AI-based biomarker research in liver cancer, with a focus on the detection and implementation of biomarkers for risk prediction, diagnosis, staging, prognostication, prediction of treatment response, and recurrence of liver cancers.
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Affiliation(s)
| | - Andrea Vrionis
- Morsani College of Medicine, University of South Florida Health, Tampa, FL 33602, USA
| | - Jonathan P Charles
- Morsani College of Medicine, University of South Florida Health, Tampa, FL 33602, USA
| | - Kayesha Hancel
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Farzad Moloudi
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shams Iqbal
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dania Daye
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
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7
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Lee TH, Jeon HJ, Choi JH, Kim YJ, Hwangbo PN, Park HS, Son CY, Choi HG, Kim HN, Chang JW, Bu J, Eun HS. A high-sensitivity cfDNA capture enables to detect the BRAF V600E mutation in papillary thyroid carcinoma. KOREAN J CHEM ENG 2023. [DOI: 10.1007/s11814-022-1348-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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8
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Kumar K, Kim E, Alhammadi M, Umapathi R, Aliya S, Tiwari JN, Park HS, Choi JH, Son CY, Vilian AE, Han YK, Bu J, Huh YS. Recent advances in microfluidic approaches for the isolation and detection of exosomes. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2022.116912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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9
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Xie D, Ying M, Lian J, Li X, Liu F, Yu X, Ni C. Serological indices and ultrasound variables in predicting the staging of hepatitis B liver fibrosis: A comparative study based on random forest algorithm and traditional methods. J Cancer Res Ther 2022; 18:2049-2057. [PMID: 36647969 DOI: 10.4103/jcrt.jcrt_1394_22] [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: 01/13/2023]
Abstract
Objective To compare the diagnostic efficacy of serological indices and ultrasound (US) variables in hepatitis B virus (HBV) liver fibrosis staging using random forest algorithm (RFA) and traditional methods. Methods The demographic and serological indices and US variables of patients with HBV liver fibrosis were retrospectively collected and divided into serology group, US group, and serology + US group according to the research content. RFA was used for training and validation. The diagnostic efficacy was compared to logistic regression analysis (LRA) and APRI and FIB-4 indices. Results For the serology group, the diagnostic performance of RFA was significantly higher than that of APRI and FIB-4 indices. The diagnostic accuracy of RFA in the four classifications (S0S1/S2/S3/S4) of the hepatic fibrosis stage was 79.17%. The diagnostic accuracy for significant fibrosis (≥S2), advanced fibrosis (≥S3), and cirrhosis (S4) was 87.99%, 90.69%, and 92.40%, respectively. The area under the curve (AUC) values were 0.945, 0.959, and 0.951, respectively. For the US group, there was no significant difference in diagnostic performance between RFA and LRA. The diagnostic performance of RFA in the serology + US group was significantly better than that of LRA. The diagnostic accuracy of the four classifications (S0S1/S2/S3/S4) of the hepatic fibrosis stage was 77.21%. The diagnostic accuracy for significant fibrosis (≥S2), advanced fibrosis (≥S3), and cirrhosis (S4) was 87.50%, 90.93%, and 93.38%, respectively. The AUC values were 0.948, 0.959, and 0.962, respectively. Conclusion RFA can significantly improve the diagnostic performance of HBV liver fibrosis staging. RFA based on serological indices has a good ability to predict liver fibrosis staging. RFA can help clinicians accurately judge liver fibrosis staging and reduce unnecessary biopsies.
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Affiliation(s)
- Daolin Xie
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou; Department of Interventional Ultrasound, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Minghua Ying
- Department of Interventional Ultrasound, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jingru Lian
- Department of Interventional Ultrasound, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xin Li
- Department of Interventional Ultrasound, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fangyi Liu
- Department of Interventional Ultrasound, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaoling Yu
- Department of Interventional Ultrasound, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Caifang Ni
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou, China
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10
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Screening of Hub Genes in Hepatocellular Carcinoma Based on Network Analysis and Machine Learning. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7300788. [PMID: 36479313 PMCID: PMC9722289 DOI: 10.1155/2022/7300788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022]
Abstract
Hepatocellular carcinoma (LIHC) is the fifth common cancer worldwide, and it requires effective diagnosis and treatment to prevent aggressive metastasis. The purpose of this study was to construct a machine learning-based diagnostic model for the diagnosis of liver cancer. Using weighted correlation network analysis (WGCNA), univariate analysis, and Lasso-Cox regression analysis, protein-protein interactions network analysis is used to construct gene networks from transcriptome data of hepatocellular carcinoma patients and find hub genes for machine learning. The five models, including gradient boosting, random forest, support vector machine, logistic regression, and integrated learning, were to identify a multigene prediction model of patients. Immunological assessment, TP53 gene mutation and promoter methylation level analysis, and KEGG pathway analysis were performed on these groups. Potential drug molecular targets for the corresponding hepatocellular carcinomas were obtained by molecular docking for analysis, resulting in the screening of 2 modules that may be relevant to the survival of hepatocellular carcinoma patients, and the construction of 5 diagnostic models and multiple interaction networks. The modes of action of drug-molecule interactions that may be effective against hepatocellular carcinoma core genes CCNA2, CCNB1, and CDK1 were investigated. This study is expected to provide research ideas for early diagnosis of hepatocellular carcinoma.
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11
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Liu S, Wang J. Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy. Curr Issues Mol Biol 2022; 44:2695-2709. [PMID: 35735625 PMCID: PMC9222159 DOI: 10.3390/cimb44060184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
A liquid biopsy is a minimally invasive or non-invasive method to analyze a range of tumor material in blood or other body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), messenger RNA (mRNA), microRNA (miRNA), and exosomes, which is a very promising technology. Among these cancer biomarkers, plasma cfDNA is the most widely used in clinical practice. Compared with a tissue biopsy of traditional cancer diagnosis, in assessing tumor heterogeneity, a liquid biopsy is more reliable because all tumor sites release cfDNA into the blood. Therefore, a cfDNA liquid biopsy is less invasive and comprehensive. Moreover, the development of next-generation sequencing technology makes cfDNA sequencing more sensitive than a tissue biopsy, with higher clinical applicability and wider application. In this publication, we aim to review the latest perspectives of cfDNA liquid biopsy clinical significance and application in cancer diagnosis, treatment, and prognosis. We introduce the sequencing techniques and challenges of cfDNA detection, analysis, and clinical applications, and discuss future research directions.
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Bu J, Jeong WJ, Jafari R, Kubiatowicz LJ, Nair A, Poellmann MJ, Hong RS, Liu EW, Owen RH, Rawding PA, Hopkins CM, Kim D, George DJ, Armstrong AJ, Král P, Wang AZ, Bruce J, Zhang T, Kimple RJ, Hong S. Bimodal liquid biopsy for cancer immunotherapy based on peptide engineering and nanoscale analysis. Biosens Bioelectron 2022; 213:114445. [PMID: 35679646 DOI: 10.1016/j.bios.2022.114445] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 11/02/2022]
Abstract
Despite its high potential, PD-L1 expressed by tumors has not been successfully utilized as a biomarker for estimating treatment responses to immunotherapy. Circulating tumor cells (CTCs) and tumor-derived exosomes that express PD-L1 can potentially be used as biomarkers; however, currently available assays lack clinically significant sensitivity and specificity. Here, a novel peptide-based capture surface is developed to effectively isolate PD-L1-expressing CTCs and exosomes from human blood. For the effective targeting of PD-L1, this study integrates peptide engineering strategies to enhance the binding strength and specificity of a β-hairpin peptide derived from PD-1 (pPD-1). Specifically, this study examines the effect of poly(ethylene glycol) spacers, the secondary peptide structure, and modification of peptide sequences (e.g., removal of biologically redundant amino acid residues) on capture efficiency. The optimized pPD-1 configuration captures PD-L1-expressing tumor cells and tumor-derived exosomes with 1.5-fold (p = 0.016) and 1.2-fold (p = 0.037) higher efficiencies, respectively, than their whole antibody counterpart (aPD-L1). This enhanced efficiency is translated into more clinically significant detection of CTCs (1.9-fold increase; p = 0.035) and exosomes (1.5-fold increase; p = 0.047) from patients' baseline samples, demonstrating stronger correlation with patients' treatment responses. Additionally, we confirmed that the clinical accuracy of our system can be further improved by co-analyzing the two biomarkers (bimodal CTC/exosome analysis). These data demonstrate that pPD-1-based capture is a promising approach for capturing PD-L1-expressing CTCs and exosomes, which can be used as a reliable biomarker for cancer immunotherapy.
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Affiliation(s)
- Jiyoon Bu
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA; Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Woo-Jin Jeong
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA; Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, USA
| | - Luke J Kubiatowicz
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Ashita Nair
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Michael J Poellmann
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Rachel S Hong
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Elizabeth W Liu
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Randall H Owen
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Piper A Rawding
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Caroline M Hopkins
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - DaWon Kim
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Daniel J George
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, 10 Bryan Searle Drive, Durham, NC, 27710, USA; Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, 20 Duke Medicine Cir, Durham, NC, 27710, USA
| | - Andrew J Armstrong
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, 10 Bryan Searle Drive, Durham, NC, 27710, USA; Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, 20 Duke Medicine Cir, Durham, NC, 27710, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, USA; Department of Physics, Department of Pharmaceutical Sciences, University of Illinois at Chicago, 845 W Taylar St, Chicage, IL, 60607, USA
| | - Andrew Z Wang
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Radiation Oncology and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Justine Bruce
- Department of Human Oncology, University of Wisconsin-Madison, Madison, 600 Highland Ave, WI, 53792, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, 600 Highland Ave, WI, 53792, USA
| | - Tian Zhang
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, 10 Bryan Searle Drive, Durham, NC, 27710, USA; Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, 20 Duke Medicine Cir, Durham, NC, 27710, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin-Madison, Madison, 600 Highland Ave, WI, 53792, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, 600 Highland Ave, WI, 53792, USA
| | - Seungpyo Hong
- Pharmaceutical Sciences Division and Wisconsin Center for NanoBioSystems (WisCNano), School of Pharmacy, University of Wisconsin - Madison, 777 Highland Ave, Madison, WI, 53705, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, 600 Highland Ave, WI, 53792, USA; Department of Biomedical Engineering, The University of Wisconsin-Madison, 1550 Engineering Dr., Madison, WI, 53705, USA; Yonsei Frontier Lab, Department of Pharmacy, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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