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Liu YJ, Li JP, Han M, Li JX, Ye QW, Lin ST, Zhou JY, Liu SL, Zou X. IFIT1 + neutrophil is a causative factor of immunosuppressive features of poorly cohesive carcinoma (PCC). J Transl Med 2024; 22:580. [PMID: 38898490 DOI: 10.1186/s12967-024-05389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
The importance of the immune microenvironment in poorly cohesive carcinoma (PCC) has been highlighted due to its limited response rate to conventional therapy and emerging treatment resistance. A combination of clinical cohorts, bioinformatics analyses, and functional/molecular experiments revealed that high infiltration of Interferon Induced Protein with Tetratricopeptide Repeats 1 (IFIT1) + tumor-associated neutrophils (TANs) is a distinguishing feature of PCC patients. Upregulation of IFIT1 + TANs promote migration and invasion of gastric cancer (GC) cell lines (MKN45 and MKN74) and stimulates the growth of cell-derived xenograft models. Besides, by promoting macrophage secreted phosphoprotein 1 (SPP1) expression and facilitating cancer-associated fibroblast and endothelial cell recruitment and activation through TANs, IFIT1 promotes a mesenchymal phenotype, which is associated with a poor prognosis. Importantly, compared to non-PCC (NPCC), PCC tumors is more immunosuppressive. Mechanistically, IFIT1 can be stimulated by IFN-γ and contributes to the expression of Programmed Cell Death 1 Ligand (PDL1) in TANs. We demonstrated in mouse models that IFIT1 + PDL1 + TANs can induce acquired resistance to anti-PD-1 immunotherapy, which may be responsible for the difficulty of PCC patients to benefit from immunotherapy. This work highlights the role of IFIT1 + TANs in mediating the remodeling of the tumor immune microenvironment and immunotherapeutic resistance and introduces IFIT1 + TANs as a promising target for precision therapy of PCC.
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Affiliation(s)
- Yuan-Jie Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
- Key Laboratory of Tumor System Biology of Traditional Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Jie-Pin Li
- Key Laboratory of Tumor System Biology of Traditional Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Mei Han
- Department of Pathology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Jing-Xiao Li
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Qian-Wen Ye
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Si-Tian Lin
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jin-Yong Zhou
- Central Laboratory, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Shen-Lin Liu
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China.
| | - Xi Zou
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China.
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing, 210029, Jiangsu, China.
- Key Laboratory of Tumor System Biology of Traditional Chinese Medicine, Nanjing, 210029, Jiangsu, China.
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Angelico G, Attanasio G, Colarossi L, Colarossi C, Montalbano M, Aiello E, Di Vendra F, Mare M, Orsi N, Memeo L. ARID1A Mutations in Gastric Cancer: A Review with Focus on Clinicopathological Features, Molecular Background and Diagnostic Interpretation. Cancers (Basel) 2024; 16:2062. [PMID: 38893181 PMCID: PMC11171396 DOI: 10.3390/cancers16112062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
AT-rich interaction domain 1 (ARID1A) is a pivotal gene with a significant role in gastrointestinal tumors which encodes a protein referred to as BAF250a or SMARCF1, an integral component of the SWI/SNF (SWItch/sucrose non-fermentable) chromatin remodeling complex. This complex is instrumental in regulating gene expression by modifying the structure of chromatin to affect the accessibility of DNA. Mutations in ARID1A have been identified in various gastrointestinal cancers, including colorectal, gastric, and pancreatic cancers. These mutations have the potential to disrupt normal SWI/SNF complex function, resulting in aberrant gene expression and potentially contributing to the initiation and progression of these malignancies. ARID1A mutations are relatively common in gastric cancer, particularly in specific adenocarcinoma subtypes. Moreover, such mutations are more frequently observed in specific molecular subtypes, such as microsatellite stable (MSS) cancers and those with a diffuse histological subtype. Understanding the presence and implications of ARID1A mutations in GC is of paramount importance for tailoring personalized treatment strategies and assessing prognosis, particularly given their potential in predicting patient response to novel treatment strategies including immunotherapy, poly(ADP) ribose polymerase (PARP) inhibitors, mammalian target of rapamycin (mTOR) inhibitors, and enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) inhibitors.
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Affiliation(s)
- Giuseppe Angelico
- Department of Medicine and Surgery, Kore University of Enna, 94100 Enna, Italy;
| | - Giulio Attanasio
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, Anatomic Pathology, University of Catania, 95123 Catania, Italy;
| | - Lorenzo Colarossi
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
| | - Cristina Colarossi
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
| | - Matteo Montalbano
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
- PhD Program in Precision Medicine, University of Palermo, 90144 Palermo, Italy
| | - Eleonora Aiello
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
| | - Federica Di Vendra
- Department of Chemical, Biological and Environmental Chemistry, University of Messina, 98122 Messina, Italy
| | - Marzia Mare
- Medical Oncology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, 95029 Catania, Italy
| | - Nicolas Orsi
- Leeds Institute of Medical Research, St James’s University Hospital, The University of Leeds, Leeds LS9 7TF, UK;
| | - Lorenzo Memeo
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, 95029 Catania, Italy; (L.C.); (C.C.); (E.A.)
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Lau DK, Collin JP, Mariadason JM. Clinical Developments and Challenges in Treating FGFR2-Driven Gastric Cancer. Biomedicines 2024; 12:1117. [PMID: 38791079 PMCID: PMC11118914 DOI: 10.3390/biomedicines12051117] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Recent advances in the treatment of gastric cancer (GC) with chemotherapy, immunotherapy, anti-angiogenic therapy and targeted therapies have yielded some improvement in survival outcomes; however, metastatic GC remains a lethal malignancy and amongst the leading causes of cancer-related mortality worldwide. Importantly, the ongoing molecular characterisation of GCs continues to uncover potentially actionable molecular targets. Among these, aberrant FGFR2-driven signalling, predominantly arising from FGFR2 amplification, occurs in approximately 3-11% of GCs. However, whilst several inhibitors of FGFR have been clinically tested to-date, there are currently no approved FGFR-directed therapies for GC. In this review, we summarise the significance of FGFR2 as an actionable therapeutic target in GC, examine the recent pre-clinical and clinical data supporting the use of small-molecule inhibitors, antibody-based therapies, as well as novel approaches such as proteolysis-targeting chimeras (PROTACs) for targeting FGFR2 in these tumours, and discuss the ongoing challenges and opportunities associated with their clinical development.
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Affiliation(s)
- David K. Lau
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Oncology, Monash Health, Clayton, VIC 3168, Australia
| | - Jack P. Collin
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
| | - John M. Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC 3084, Australia
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Ma Y, Li J, Zhao X, Ji C, Hu W, Ma Y, Qu F, Sun Y, Zhang X. Multi-omics cluster defines the subtypes of CRC with distinct prognosis and tumor microenvironment. Eur J Med Res 2024; 29:207. [PMID: 38549156 PMCID: PMC10976740 DOI: 10.1186/s40001-024-01805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a complex malignancy characterized by diverse molecular profiles, clinical outcomes, and limited precision in prognostic markers. Addressing these challenges, this study utilized multi-omics data to define consensus molecular subtypes in CRC and elucidate their association with clinical outcomes and underlying biological processes. METHODS Consensus molecular subtypes were obtained by applying ten integrated multi-omics clustering algorithms to analyze TCGA-CRC multi-omics data, including mRNA, lncRNA, miRNA, DNA methylation CpG sites, and somatic mutation data. The association of subtypes with prognoses, enrichment functions, immune status, and genomic alterations were further analyzed. Next, we conducted univariate Cox and Lasso regression analyses to investigate the potential prognostic application of biomarkers associated with multi-omics subtypes derived from weighted gene co-expression network analysis (WGCNA). The function of one of the biomarkers MID2 was validated in CRC cell lines. RESULTS Two CRC subtypes linked to distinct clinical outcomes were identified in TCGA-CRC cohort and validated with three external datasets. The CS1 subtype exhibited a poor prognosis and was characterized by higher tumor-related Hallmark pathway activity and lower metabolism pathway activity. In addition, the CS1 was predicted to have less immunotherapy responder and exhibited more genomic alteration compared to CS2. Then a prognostic model comprising five genes was established, with patients in the high-risk group showing substantial concordance with the CS1 subtype, and those in the low-risk group with the CS2 subtype. The gene MID2, included in the prognostic model, was found to be correlated with epithelial-mesenchymal transition (EMT) pathway and distinct DNA methylation patterns. Knockdown of MID2 in CRC cells resulted in reduced colony formation, migration, and invasion capacities. CONCLUSION The integrative multi-omics subtypes proposed potential biomarkers for CRC and provided valuable knowledge for precision oncology.
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Affiliation(s)
- Yuan Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Jing Li
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Chao Ji
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Weibin Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - YanFang Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Fengyi Qu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Yuchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
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Alruwaili O, Yousef A, Jumani TA, Armghan A. Response score-based protein structure analysis for cancer prediction aided by the Internet of Things. Sci Rep 2024; 14:2324. [PMID: 38282060 PMCID: PMC10822874 DOI: 10.1038/s41598-024-52634-y] [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: 11/28/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024] Open
Abstract
Medical diagnosis through prediction and analysis is par excellence in integrating modern technologies such as the Internet of Things (IoT). With the aid of such technologies, clinical assessments are eased with protracted computing. Specifically, cancer research through structure prediction and analysis is improved through human and machine interventions sustaining precision improvements. This article, therefore, introduces a Protein Structure Prediction Technique based on Three-Dimensional Sequence. This sequence is modeled using amino acids and their folds observed during the pre-initial cancer stages. The observed sequences and the inflammatory response score of the structure are used to predict the impact of cancer. In this process, ensemble learning is used to identify sequence and folding responses to improve inflammations. This score is correlated with the clinical data for structures and their folds independently for determining the structure changes. Such changes through different sequences are handled using repeated ensemble learning for matching and unmatching response scores. The introduced idea integrated with deep ensemble learning and IoT combination, notably employing stacking method for enhanced cancer prediction precision and interdisciplinary collaboration. The proposed technique improves prediction precision, data correlation, and change detection by 11.83%, 8.48%, and 13.23%, respectively. This technique reduces correlation time and complexity by 10.43% and 12.33%, respectively.
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Affiliation(s)
- Omar Alruwaili
- Department of Computer Engineering and Networks, College of Computer and Information Science, Jouf University, 72388, Sakaka, Saudi Arabia
| | - Amr Yousef
- Electrical Engineering Department, University of Business and Technology, 23435, Ar Rawdah, Jeddah, Saudi Arabia
- Engineering Mathematics Department, Alexandria University, Lotfy El-Sied St. Off Gamal Abd El-Naser, Alexandria, 11432, Egypt
| | - Touqeer A Jumani
- Department of Electrical Engineering, Mehran University of Engineering and Technology, SZAB Campus, Khairpur Mirs, 66020, Pakistan
| | - Ammar Armghan
- Department of Electrical Engineering. College of Engineering, Jouf University, 72388, Sakaka, Saudi Arabia.
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Zadeh Shirazi A, Tofighi M, Gharavi A, Gomez GA. The Application of Artificial Intelligence to Cancer Research: A Comprehensive Guide. Technol Cancer Res Treat 2024; 23:15330338241250324. [PMID: 38775067 PMCID: PMC11113055 DOI: 10.1177/15330338241250324] [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: 10/29/2023] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Advancements in AI have notably changed cancer research, improving patient care by enhancing detection, survival prediction, and treatment efficacy. This review covers the role of Machine Learning, Soft Computing, and Deep Learning in oncology, explaining key concepts and algorithms (like SVM, Naïve Bayes, and CNN) in a clear, accessible manner. It aims to make AI advancements understandable to a broad audience, focusing on their application in diagnosing, classifying, and predicting various cancer types, thereby underlining AI's potential to better patient outcomes. Moreover, we present a tabular summary of the most significant advances from the literature, offering a time-saving resource for readers to grasp each study's main contributions. The remarkable benefits of AI-powered algorithms in cancer care underscore their potential for advancing cancer research and clinical practice. This review is a valuable resource for researchers and clinicians interested in the transformative implications of AI in cancer care.
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Affiliation(s)
- Amin Zadeh Shirazi
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Morteza Tofighi
- Department of Electrical Engineering, Faculty of Engineering, Bu-Ali Sina University, Hamedan, Iran
| | - Alireza Gharavi
- Department of Computer Science, Azad University, Mashhad Branch, Mashhad, Iran
| | - Guillermo A. Gomez
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
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Ke X, Cai X, Bian B, Shen Y, Zhou Y, Liu W, Wang X, Shen L, Yang J. Predicting early gastric cancer risk using machine learning: A population-based retrospective study. Digit Health 2024; 10:20552076241240905. [PMID: 38559579 PMCID: PMC10979538 DOI: 10.1177/20552076241240905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Background Early detection and treatment are crucial for reducing gastrointestinal tumour-related mortality. The diagnostic efficiency of the most commonly used diagnostic markers for gastric cancer (GC) is not very high. A single laboratory test cannot meet the requirements of early screening, and machine learning methods are needed to aid the early diagnosis of GC by combining multiple indicators. Methods Based on the XGBoost algorithm, a new model was developed to distinguish between GC and precancerous lesions in newly admitted patients between 2018 and 2023 using multiple laboratory tests. We evaluated the ability of the prediction score derived from this model to predict early GC. In addition, we investigated the efficacy of the model in correctly screening for GC given negative protein tumour marker results. Results The XHGC20 model constructed using the XGBoost algorithm could distinguish GC from precancerous disease well (area under the receiver operating characteristic curve [AUC] = 0.901), with a sensitivity, specificity and cut-off value of 0.830, 0.806 and 0.265, respectively. The prediction score was very effective in the diagnosis of early GC. When the cut-off value was 0.27, and the AUC was 0.888, the sensitivity and specificity were 0.797 and 0.807, respectively. The model was also effective at evaluating GC given negative conventional markers (AUC = 0.970), with the sensitivity and specificity of 0.941 and 0.906, respectively, which helped to reduce the rate of missed diagnoses. Conclusions The XHGC20 model established by the XGBoost algorithm integrates information from 20 clinical laboratory tests and can aid in the early screening of GC, providing a useful new method for auxiliary laboratory diagnosis.
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Affiliation(s)
- Xing Ke
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Artificial Intelligence Medicine, Shanghai Academy of Experimental Medicine, Shanghai, China
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyu Cai
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingxian Bian
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanheng Shen
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunlan Zhou
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Liu
- Department of Research Collaboration, R&D Center, Beijing Deepwise & League of PHD Technology Co., Ltd, Beijing, China
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lisong Shen
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Artificial Intelligence Medicine, Shanghai Academy of Experimental Medicine, Shanghai, China
| | - Junyao Yang
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Artificial Intelligence Medicine, Shanghai Academy of Experimental Medicine, Shanghai, China
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Li X, Li S, Wu Q. Non-Invasive Detection of Biomolecular Abundance from Fermentative Microorganisms via Raman Spectra Combined with Target Extraction and Multimodel Fitting. Molecules 2023; 29:157. [PMID: 38202740 PMCID: PMC10780171 DOI: 10.3390/molecules29010157] [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: 11/13/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Biomolecular abundance detection of fermentation microorganisms is significant for the accurate regulation of fermentation, which is conducive to reducing fermentation costs and improving the yield of target products. However, the development of an accurate analytical method for the detection of biomolecular abundance still faces important challenges. Herein, we present a non-invasive biomolecular abundance detection method based on Raman spectra combined with target extraction and multimodel fitting. The high gain of the eXtreme Gradient Boosting (XGBoost) algorithm was used to extract the characteristic Raman peaks of metabolically active proteins and nucleic acids within E. coli and yeast. The test accuracy for different culture times and cell cycles of E. coli was 94.4% and 98.2%, respectively. Simultaneously, the Gaussian multi-peak fitting algorithm was exploited to calculate peak intensity from mixed peaks, which can improve the accuracy of biomolecular abundance calculations. The accuracy of Gaussian multi-peak fitting was above 0.9, and the results of the analysis of variance (ANOVA) measurements for the lag phase, log phase, and stationary phase of E. coli growth demonstrated highly significant levels, indicating that the intracellular biomolecular abundance detection was consistent with the classical cell growth law. These results suggest the great potential of the combination of microbial intracellular abundance, Raman spectra analysis, target extraction, and multimodel fitting as a method for microbial fermentation engineering.
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Affiliation(s)
- Xinli Li
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun 130061, China
| | - Suyi Li
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun 130061, China
| | - Qingyi Wu
- Changchun Institute of Optics, Fine Mechanics and Physics, Changchun 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Zhang S, Li X, Zheng Y, Liu J, Hu H, Zhang S, Kuang W. Single cell and bulk transcriptome analysis identified oxidative stress response-related features of Hepatocellular Carcinoma. Front Cell Dev Biol 2023; 11:1191074. [PMID: 37842089 PMCID: PMC10568628 DOI: 10.3389/fcell.2023.1191074] [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: 03/21/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Background: Hepatocellular Carcinoma (HCC) is a common lethal digestive system tumor. The oxidative stress mechanism is crucial in the HCC genesis and progression. Methods: Our study analyzed single-cell and bulk sequencing data to compare the microenvironment of non-tumor liver tissues and HCC tissues. Through these analyses, we aimed to investigate the effect of oxidative stress on cells in the HCC microenvironment and identify critical oxidative stress response-related genes that impact the survival of HCC patients. Results: Our results showed increased oxidative stress in HCC tissue compared to non-tumor tissue. Immune cells in the HCC microenvironment exhibited higher oxidative detoxification capacity, and oxidative stress-induced cell death of dendritic cells was attenuated. HCC cells demonstrated enhanced communication with immune cells through the MIF pathway in a highly oxidative hepatoma microenvironment. Meanwhile, using machine learning and Cox regression screening, we identified PRDX1 as a predictor of early occurrence and prognosis in patients with HCC. The expression level of PRDX1 in HCC was related to dysregulated ribosome biogenesis and positively correlated with the expression of immunological checkpoints (PDCD1LG2, CTLA4, TIGIT, LAIR1). High PRDX1 expression in HCC patients correlated with better sensitivity to immunotherapy agents such as sorafenib, IGF-1R inhibitor, and JAK inhibitor. Conclusion: In conclusion, our study unveiled variations in oxidative stress levels between non-tumor liver and HCC tissues. And we identified oxidative stress gene markers associated with hepatocarcinogenesis development, offering novel insights into the oxidative stress response mechanism in HCC.
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Affiliation(s)
- Shuqiao Zhang
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xinyu Li
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yilu Zheng
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiahui Liu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hao Hu
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shijun Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weihong Kuang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Chronic Inflammatory Diseases, School of Pharmacy, The First Dongguan Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Dongguan, Guangdong, China
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