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Ming L, Tang J, Qin F, Qin Y, Wang D, Huang L, Cao Y, Huang Z, Yin Y. Exosome secretion related gene signature predicts chemoresistance in patients with colorectal cancer. Pathol Res Pract 2024; 257:155313. [PMID: 38642509 DOI: 10.1016/j.prp.2024.155313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/14/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is a highly heterogeneous malignancy, and patients often have different responses to treatment. In this study, the genetic characteristics related to exosome formation and secretion procedure were used to predict chemoresistance and guide the individualized treatment of patients. METHODS Firstly, seven microarray datasets in Gene Expression Omnibus (GEO) and RNA-Seq dataset from the Cancer Genome Atlas (TCGA) were used to analysis the transcriptome profiles and associated characteristics of CRC patients. Then, a predictive model based on gene features linked to exosome formation and secretion was created and validated using Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) machine learning. Finally, we evaluated the model using chemoresistant/chemosensitive cells and tissues by immunofluorescence (IF), western blot (WB), quantitative real-time PCR (qRT-PCR) and immunocytochemistry (IHC) experiments, and the predictive value of integrated model in the clinical validation cohort were performed by Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) curves analyses. RESULTS We established a risk score signature based on three genes related to exosome secretion in CRC. Better Overall Survival (OS) and greater chemosensitivity were seen in the low-risk group, whereas the high-risk group exhibited chemoresistance and a subpar response to immune checkpoint blockade (ICB) therapy. Higher expression of the model genes EXOC2, EXOC3 and STX4 were observed in chemoresistant cells and specimens. The AUC of 5-year disease-free survival (DFS) was 0.804. Compared with that in the low-risk group, patients' DFS was found to be significantly worse in the high-risk group. CONCLUSIONS In summary, the gene signature related to exosome formation and secretion could reliably predict patients' chemosensitivity and ICB treatment response, which providing new independent biomarkers for the treatment of CRC.
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Affiliation(s)
- Liang Ming
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junhui Tang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Feiyu Qin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Qin
- Department of Pathology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China
| | - Duo Wang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Liuying Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Costa A, Gozzellino L, Nannini M, Astolfi A, Pantaleo MA, Pasquinelli G. Preclinical Models of Visceral Sarcomas. Biomolecules 2023; 13:1624. [PMID: 38002306 PMCID: PMC10669128 DOI: 10.3390/biom13111624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Visceral sarcomas are a rare malignant subgroup of soft tissue sarcomas (STSs). STSs, accounting for 1% of all adult tumors, are derived from mesenchymal tissues and exhibit a wide heterogeneity. Their rarity and the high number of histotypes hinder the understanding of tumor development mechanisms and negatively influence clinical outcomes and treatment approaches. Although some STSs (~20%) have identifiable genetic markers, as specific mutations or translocations, most are characterized by complex genomic profiles. Thus, identification of new therapeutic targets and development of personalized therapies are urgent clinical needs. Although cell lines are useful for preclinical investigations, more reliable preclinical models are required to develop and test new potential therapies. Here, we provide an overview of the available in vitro and in vivo models of visceral sarcomas, whose gene signatures are still not well characterized, to highlight current challenges and provide insights for future studies.
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Affiliation(s)
- Alice Costa
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Livia Gozzellino
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Margherita Nannini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Annalisa Astolfi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Maria Abbondanza Pantaleo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Gianandrea Pasquinelli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Division of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
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Mukherjee S, Mukherjee SB, Frenkel-Morgenstern M. Functional and regulatory impact of chimeric RNAs in human normal and cancer cells. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1777. [PMID: 36633099 DOI: 10.1002/wrna.1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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Macioszek S, Dudzik D, Biesemans M, Wozniak A, Schöffski P, Markuszewski MJ. A multiplatform metabolomics approach for comprehensive analysis of GIST xenografts with various KIT mutations. Analyst 2023; 148:3883-3891. [PMID: 37458061 DOI: 10.1039/d3an00599b] [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: 07/18/2023]
Abstract
Metabolites in biological matrices belong to diverse chemical groups, ranging from non-polar long-chain fatty acids to small polar molecules. The goal of untargeted metabolomic analysis is to measure the highest number of metabolites in the sample. Nevertheless, from an analytical point of view, no single technique can measure such a broad spectrum of analytes. Therefore, we selected a method based on GC-MS and LC-MS with two types of stationary phases for the untargeted profiling of gastrointestinal stromal tumours. The procedure was applied to GIST xenograft samples (n = 71) representing four different mutation models, half of which were treated with imatinib. We aimed to verify the method coverage and advantages of applying each technique. RP-LC-MS measured most metabolites due to a significant fraction of lipid components of the tumour tissue. What is unique and worth noting is that all applied techniques were able to distinguish between different mutation models. However, for detecting imatinib-induced alterations in the GIST metabolome, RP-LC-MS and GC-MS proved to be more relevant than HILIC-LC-MS, resulting in a higher number of significantly changed metabolites in four treated models. Undoubtedly, the inclusion of all mentioned techniques makes the method more comprehensive. Nonetheless, for green chemistry and time and labour saving, we assume that RP-LC-MS and GC-MS analyses are sufficient to cover the global GIST metabolome.
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Affiliation(s)
- Szymon Macioszek
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | - Danuta Dudzik
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | - Margot Biesemans
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | - Agnieszka Wozniak
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, and Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Patrick Schöffski
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, and Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Michal J Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
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Kim SH, Bae IS, Lee HU, Moon JY, Lee YC. A Bioactive Compound-Loaded Zinc-Aminoclay Encapsulated, Pickering Emulsion System for Treating Acne-Inducing Microbes. Int J Mol Sci 2023; 24:9669. [PMID: 37298619 PMCID: PMC10253637 DOI: 10.3390/ijms24119669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Acne is a common skin condition caused by the growth of certain bacteria. Many plant extracts have been investigated for their potential to combat acne-inducing microbes, and one such plant extract is microwave-assisted Opuntia humifusa extract (MA-OHE). The MA-OHE was loaded onto zinc-aminoclay (ZnAC) and encapsulated in a Pickering emulsion system (MA-OHE/ZnAC PE) to evaluate its therapeutic potential against acne-inducing microbes. Dynamic light scattering and scanning electron microscopy were used to characterize MA-OHE/ZnAC PE with a mean particle diameter of 353.97 nm and a PDI of 0.629. The antimicrobial effect of MA-OHE/ZnAC was evaluated against Staphylococcus aureus (S. aureus) and Cutibacterium acnes (C. acnes), which contribute to acne inflammation. The antibacterial activity of MA-OHE/ZnAC was 0.1 and 0.025 mg/mL to S. aureus and C. acnes, respectively, which were close to naturally derived antibiotics. Additionally, the cytotoxicity of MA-OHE, ZnAC, and MA-OHE/ZnAC was tested, and the results showed that they had no cytotoxic effects on cultured human keratinocytes in a range of 10-100 μg/mL. Thus, MA-OHE/ZnAC is suggested to be a promising antimicrobial agent for treating acne-inducing microbes, while MA-OHE/ZnAC PE is a potentially advantageous dermal delivery system.
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Affiliation(s)
- Seong-Hyeon Kim
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea;
| | - In-Sun Bae
- Swsonaki Inc., Gwangyang Frontier-Valley 3rd, 30 Gaseok-ro, Incheon 22827, Republic of Korea;
| | - Hyun Uk Lee
- Research Center for Materials Analysis, Korea Basic Science Institute, Daejeon 34133, Republic of Korea;
| | - Ju-Young Moon
- Department of Beauty Design Management, Hansung University, 116, Samseongyo-ro 16gil, Seoul 02876, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea;
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Mohan B, Kumar S, Xi H, Ma S, Tao Z, Xing T, You H, Zhang Y, Ren P. Fabricated Metal-Organic Frameworks (MOFs) as luminescent and electrochemical biosensors for cancer biomarkers detection. Biosens Bioelectron 2022; 197:113738. [PMID: 34740120 DOI: 10.1016/j.bios.2021.113738] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023]
Abstract
In the health domain, a major challenge is the detection of diseases using rapid and cost-effective techniques. Most of the existing cancer detection methods show poor sensitivity and selectivity and are time consuming with high cost. To overcome this challenge, we analyzed porous fabricated metal-organic frameworks (MOFs) that have better structures and porosities for enhanced biomarker sensing. Here, we summarize the use of fabricated MOF luminescence and electrochemical sensors in devices for cancer biomarker detection. Various strategies of fabrication and the role of fabricated materials in sensing cancer biomarkers have been studied and described. The structural properties, sensing mechanisms, roles of noncovalent interactions, limits of detection, modeling, advantages, and limitations of MOF sensors have been well-discussed. The study presents an innovative technique to detect the cancer biomarkers by the use of luminescence and electrochemical MOF sensors. In addition, the potential association studies have been opening the way for personalized patient treatments and the development of new cancer-detecting devices.
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Affiliation(s)
- Brij Mohan
- Laboratory of Coordination Chemistry and Functional Materials, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China; School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Sandeep Kumar
- Laboratory of Coordination Chemistry and Functional Materials, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China; School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Hui Xi
- School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Shixuan Ma
- Laboratory of Coordination Chemistry and Functional Materials, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China; School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Zhiyu Tao
- Laboratory of Coordination Chemistry and Functional Materials, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China; School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Tiantian Xing
- Laboratory of Coordination Chemistry and Functional Materials, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China; School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Hengzhi You
- School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China
| | - Yang Zhang
- School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China.
| | - Peng Ren
- Laboratory of Coordination Chemistry and Functional Materials, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China; School of Science, Harbin Institute of Technology (Shezhen), Shenzhen 518055, China.
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Honda K. Development of biomarkers for predicting recurrence by determining the metastatic ability of cancer cells. J NIPPON MED SCH 2021; 89:24-32. [PMID: 34526453 DOI: 10.1272/jnms.jnms.2022_89-118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Adjuvant chemotherapy has been carried out for patients with cancer who underwent curative resection, but it is basically not needed for patients without micro-metastatic lesions who undergo a perfectly curative surgical operation. The patients who need adjuvant chemotherapy are defined as those whose micro-metastases cannot be detected by imaging modalities in the other sites of the resective areas, despite curative resection for the primary sites. If biomarkers to efficiently evaluate the metastatic potential of each patient could be developed, we may be able to provide personalized adjuvant chemotherapy in the clinical setting. Actinin-4 (ACTN4, gene name ACTN4) is an actin-bundling protein that we identified in 1998 as a novel molecule involved in cancer invasion and metastasis. Protein overexpression of actinin-4 in cancer cells leads to the invasive phenotype, and patients with gene amplification of ACTN4 have a worse prognosis than patients with a normal copy number in some cancers, including pancreas, lung, and salivary gland cancers. In this review, the biological roles of actinin-4 for cancer invasion and metastasis are summarized, and the potential usefulness of actinin-4 as a biomarker for evaluation of metastatic ability is examined.
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Affiliation(s)
- Kazufumi Honda
- Department of Bioregulation, Institution for Advanced Medical Science, Nippon Medical School
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