1
|
Qiu Y, Gao T, Smith BR. Mechanical deformation and death of circulating tumor cells in the bloodstream. Cancer Metastasis Rev 2024:10.1007/s10555-024-10198-3. [PMID: 38980581 DOI: 10.1007/s10555-024-10198-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024]
Abstract
The circulation of tumor cells through the bloodstream is a significant step in tumor metastasis. To better understand the metastatic process, circulating tumor cell (CTC) survival in the circulation must be explored. While immune interactions with CTCs in recent decades have been examined, research has yet to sufficiently explain some CTC behaviors in blood flow. Studies related to CTC mechanical responses in the bloodstream have recently been conducted to further study conditions under which CTCs might die. While experimental methods can assess the mechanical properties and death of CTCs, increasingly sophisticated computational models are being built to simulate the blood flow and CTC mechanical deformation under fluid shear stresses (FSS) in the bloodstream.Several factors contribute to the mechanical deformation and death of CTCs as they circulate. While FSS can damage CTC structure, diverse interactions between CTCs and blood components may either promote or hinder the next metastatic step-extravasation at a remote site. Overall understanding of how these factors influence the deformation and death of CTCs could serve as a basis for future experiments and simulations, enabling researchers to predict CTC death more accurately. Ultimately, these efforts can lead to improved metastasis-specific therapeutics and diagnostics specific in the future.
Collapse
Affiliation(s)
- Yunxiu Qiu
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
- The Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Tong Gao
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, 48824, USA
- Department of Computational Mathematics, Science, and Engineering, East Lansing, MI, 48824, USA
| | - Bryan Ronain Smith
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA.
- The Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
2
|
Li S, Zhu Z, Chen Z, Guo Z, Wang Y, Li X, Ma K. Network pharmacology-based investigation of the effects of Shenqi Fuzheng injection on glioma proliferation and migration via the SRC/PI3K/AKT signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118128. [PMID: 38561056 DOI: 10.1016/j.jep.2024.118128] [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: 12/28/2023] [Revised: 03/23/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In the clinic, Shenqi Fuzheng Injection (SFI) is used as an adjuvant for cancer chemotherapy. However, the molecular mechanism is unclear. AIM OF THE STUDY We screened potential targets of SFI action on gliomas by network pharmacology and performed experiments to validate possible molecular mechanisms against gliomas. MATERIALS AND METHODS We consulted relevant reports on the SFI and glioma incidence from PubMed and Web of Science and focused on the mechanism through which the SFI inhibits glioma. According to the literature, two primary SFI components-Codonopsis pilosula (Franch.) Nannf. and Astragalus membranaceus (Fisch.) Bunge-have been found. All plant names have been sourced from "The Plant List" (www.theplantlist.org). The cell lines U87, T98G and GL261 were used in this study. The inhibitory effects of SFI on glioma cells U87 and T98G were detected by CCK-8 assay, EdU, plate cloning assay, scratch assay, Transwell assay, immunofluorescence, flow cytometry and Western blot. A subcutaneous tumor model of C57BL/6 mice was constructed using GL261 cells, and the SFI was evaluated by HE staining and immunohistochemistry. The targets of glioma and the SFI were screened using network pharmacology. RESULTS A total of 110 targets were enriched, and a total of 26 major active components in the SFI were investigated. There were a total of 3,343 targets for gliomas, of which 79 targets were shared between the SFI and glioma tissues. SFI successfully prevented proliferation and caused cellular S-phase blockage in U87 and T98G cells, thus decreasing their growth. Furthermore, SFI suppressed cell migration by downregulating EMT marker expression. According to the results of the in vivo tests, the SFI dramatically decreased the development of tumors in a transplanted tumour model. Network pharmacological studies revealed that the SRC/PI3K/AKT signaling pathway may be the pathway through which SFI exerts its anti-glioma effects. CONCLUSIONS The findings revealed that the SRC/PI3K/AKT signaling pathway may be involved in the mechanism through which SFI inhibits the proliferation and migration of glioma cells.
Collapse
Affiliation(s)
- Shuang Li
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Zhenglin Zhu
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Zhijian Chen
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Zhenli Guo
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Physiology, Shihezi University Medical College, Shihezi, 832000, China.
| | - Yan Wang
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China.
| | - Xinzhi Li
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Pathophysiology, School of Medicine, Shihezi University, Shihezi, 832000, China.
| | - Ketao Ma
- The Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University Medical College, Shihezi, 832000, China; NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, Shihezi, 832002, China; Department of Physiology, Shihezi University Medical College, Shihezi, 832000, China.
| |
Collapse
|
3
|
Mares-Quiñones MD, Galán-Vásquez E, Pérez-Rueda E, Pérez-Ishiwara DG, Medel-Flores MO, Gómez-García MDC. Identification of modules and key genes associated with breast cancer subtypes through network analysis. Sci Rep 2024; 14:12350. [PMID: 38811600 PMCID: PMC11137066 DOI: 10.1038/s41598-024-61908-4] [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: 07/13/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Breast cancer is the most common malignancy in women around the world. Intratumor and intertumoral heterogeneity persist in mammary tumors. Therefore, the identification of biomarkers is essential for the treatment of this malignancy. This study analyzed 28,143 genes expressed in 49 breast cancer cell lines using a Weighted Gene Co-expression Network Analysis to determine specific target proteins for Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes. Sixty-five modules were identified, of which five were characterized as having a high correlation with breast cancer subtypes. Genes overexpressed in the tumor were found to participate in the following mechanisms: regulation of the apoptotic process, transcriptional regulation, angiogenesis, signaling, and cellular survival. In particular, we identified the following genes, considered as hubs: IFIT3, an inhibitor of viral and cellular processes; ETS1, a transcription factor involved in cell death and tumorigenesis; ENSG00000259723 lncRNA, expressed in cancers; AL033519.3, a hypothetical gene; and TMEM86A, important for regulating keratinocyte membrane properties, considered as a key in Basal A, Basal B, Luminal A, Luminal B, and HER2 ampl breast cancer subtypes, respectively. The modules and genes identified in this work can be used to identify possible biomarkers or therapeutic targets in different breast cancer subtypes.
Collapse
Affiliation(s)
- María Daniela Mares-Quiñones
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - D Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María Del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Programa de Doctorado en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, Mexico.
| |
Collapse
|
4
|
Hana T, Mukasa A, Nomura M, Nagae G, Yamamoto S, Tatsuno K, Ueda H, Fukuda S, Umeda T, Tanaka S, Nejo T, Kitagawa Y, Yamazawa E, Takahashi S, Koike T, Kushihara Y, Takami H, Takayanagi S, Aburatani H, Saito N. Region-specific DNA hydroxymethylation along the malignant progression of IDH-mutant gliomas. Cancer Sci 2024; 115:1706-1717. [PMID: 38433527 PMCID: PMC11093199 DOI: 10.1111/cas.16127] [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: 08/30/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
The majority of low-grade isocitrate dehydrogenase-mutant (IDHmt) gliomas undergo malignant progression (MP), but their underlying mechanism remains unclear. IDHmt gliomas exhibit global DNA methylation, and our previous report suggested that MP could be partly attributed to passive demethylation caused by accelerated cell cycles. However, during MP, there is also active demethylation mediated by ten-eleven translocation, such as DNA hydroxymethylation. Hydroxymethylation is reported to potentially contribute to gene expression regulation, but its role in MP remains under investigation. Therefore, we conducted a comprehensive analysis of hydroxymethylation during MP of IDHmt astrocytoma. Five primary/malignantly progressed IDHmt astrocytoma pairs were analyzed with oxidative bisulfite and the Infinium EPIC methylation array, detecting 5-hydroxymethyl cytosine at over 850,000 locations for region-specific hydroxymethylation assessment. Notably, we observed significant sharing of hydroxymethylated genomic regions during MP across the samples. Hydroxymethylated CpGs were enriched in open sea and intergenic regions (p < 0.001), and genes undergoing hydroxymethylation were significantly associated with cancer-related signaling pathways. RNA sequencing data integration identified 91 genes with significant positive/negative hydroxymethylation-expression correlations. Functional analysis suggested that positively correlated genes are involved in cell-cycle promotion, while negatively correlated ones are associated with antineoplastic functions. Analyses of The Cancer Genome Atlas clinical data on glioma were in line with these findings. Motif-enrichment analysis suggested the potential involvement of the transcription factor KLF4 in hydroxymethylation-based gene regulation. Our findings shed light on the significance of region-specific DNA hydroxymethylation in glioma MP and suggest its potential role in cancer-related gene expression and IDHmt glioma malignancy.
Collapse
Affiliation(s)
- Taijun Hana
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Genta Nagae
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shogo Yamamoto
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Kenji Tatsuno
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Hiroki Ueda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
- Advanced Data Science Division, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shiro Fukuda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Takayoshi Umeda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Takahide Nejo
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Yosuke Kitagawa
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Satoshi Takahashi
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroyuki Aburatani
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| |
Collapse
|
5
|
Buruiană A, Gheban BA, Gheban-Roșca IA, Georgiu C, Crișan D, Crișan M. The Tumor Stroma of Squamous Cell Carcinoma: A Complex Environment That Fuels Cancer Progression. Cancers (Basel) 2024; 16:1727. [PMID: 38730679 PMCID: PMC11083853 DOI: 10.3390/cancers16091727] [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: 04/08/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
The tumor microenvironment (TME), a complex assembly of cellular and extracellular matrix (ECM) components, plays a crucial role in driving tumor progression, shaping treatment responses, and influencing metastasis. This narrative review focuses on the cutaneous squamous cell carcinoma (cSCC) tumor stroma, highlighting its key constituents and their dynamic contributions. We examine how significant changes within the cSCC ECM-specifically, alterations in fibronectin, hyaluronic acid, laminins, proteoglycans, and collagens-promote cancer progression, metastasis, and drug resistance. The cellular composition of the cSCC TME is also explored, detailing the intricate interplay of cancer-associated fibroblasts (CAFs), mesenchymal stem cells (MSCs), endothelial cells, pericytes, adipocytes, and various immune cell populations. These diverse players modulate tumor development, angiogenesis, and immune responses. Finally, we emphasize the TME's potential as a therapeutic target. Emerging strategies discussed in this review include harnessing the immune system (adoptive cell transfer, checkpoint blockade), hindering tumor angiogenesis, disrupting CAF activity, and manipulating ECM components. These approaches underscore the vital role that deciphering TME interactions plays in advancing cSCC therapy. Further research illuminating these complex relationships will uncover new avenues for developing more effective treatments for cSCC.
Collapse
Affiliation(s)
- Alexandra Buruiană
- Department of Pathology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (A.B.); (C.G.); (D.C.)
| | - Bogdan-Alexandru Gheban
- Department of Histology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
- Emergency Clinical County Hospital, 400347 Cluj-Napoca, Romania
| | - Ioana-Andreea Gheban-Roșca
- Department of Medical Informatics and Biostatistics, Iuliu Hațieganu University of Medicine and Pharmacy, 400129 Cluj-Napoca, Romania;
| | - Carmen Georgiu
- Department of Pathology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (A.B.); (C.G.); (D.C.)
| | - Doința Crișan
- Department of Pathology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (A.B.); (C.G.); (D.C.)
| | - Maria Crișan
- Department of Histology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| |
Collapse
|
6
|
Mogal MR, Jame JA, Sohel M, Mozibullah M, Mahmod MR, Junayed A, Kar N, Arbia L, Al Mamun A, Sikder MA. Integrated bioinformatics analysis reveals upregulated extracellular matrix hub genes in pancreatic cancer: Implications for diagnosis, prognosis, immune infiltration, and therapeutic strategies. Cancer Rep (Hoboken) 2024; 7:e2059. [PMID: 38639039 PMCID: PMC11027013 DOI: 10.1002/cnr2.2059] [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: 08/29/2023] [Revised: 02/20/2024] [Accepted: 03/24/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) stands out as one of the most formidable malignancies and exhibits an exceptionally unfavorable clinical prognosis due to the absence of well-defined diagnostic indicators and its tendency to develop resistance to therapeutic interventions. The primary objective of this present study was to identify extracellular matrix (ECM)-related hub genes (HGs) and their corresponding molecular signatures, with the intent of potentially utilizing them as biomarkers for diagnostic, prognostic, and therapeutic applications. METHODS Three microarray datasets were sourced from the NCBI database to acquire upregulated differentially expressed genes (DEGs), while MatrisomeDB was employed for filtering ECM-related genes. Subsequently, a protein-protein interaction (PPI) network was established using the STRING database. The created network was visually inspected through Cytoscape, and HGs were identified using the CytoHubba plugin tool. Furthermore, enrichment analysis, expression pattern analysis, clinicopathological correlation, survival analysis, immune cell infiltration analysis, and examination of chemical compounds were carried out using Enrichr, GEPIA2, ULCAN, Kaplan Meier plotter, TIMER2.0, and CTD web platforms, respectively. The diagnostic and prognostic significance of HGs was evaluated through the ROC curve analysis. RESULTS Ten genes associated with ECM functions were identified as HGs among 131 DEGs obtained from microarray datasets. Notably, the expression of these HGs exhibited significantly (p < 0.05) higher in PC, demonstrating a clear association with tumor advancement. Remarkably, higher expression levels of these HGs were inversely correlated with the likelihood of patient survival. Moreover, ROC curve analysis revealed that identified HGs are promising biomarkers for both diagnostic (AUC > 0.75) and prognostic (AUC > 0.64) purposes. Furthermore, we observed a positive correlation between immune cell infiltration and the expression of most HGs. Lastly, our study identified nine compounds with significant interaction profiles that could potentially act as effective chemical agents targeting the identified HGs. CONCLUSION Taken together, our findings suggest that COL1A1, KRT19, MMP1, COL11A1, SDC1, ITGA2, COL1A2, POSTN, FN1, and COL5A1 hold promise as innovative biomarkers for both the diagnosis and prognosis of PC, and they present as prospective targets for therapeutic interventions aimed at impeding the progression PC.
Collapse
Affiliation(s)
- Md Roman Mogal
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Jasmin Akter Jame
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular BiologyPrimeasia UniversityDhakaBangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Rashel Mahmod
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Asadullah Junayed
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Newton Kar
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Lubatul Arbia
- Department of Biochemistry and Molecular BiologyPrimeasia UniversityDhakaBangladesh
| | - Abdullah Al Mamun
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Md Asaduzzaman Sikder
- Department of Biochemistry and Molecular BiologyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| |
Collapse
|
7
|
Singh N, Khan IA, Rashid S, Rashid S, Roy S, Kaushik K, Kumar A, Das P, Lalwani S, Gupta D, Gunjan D, Dash NR, Chauhan SS, Gupta S, Saraya A. MicroRNA Signatures for Pancreatic Cancer and Chronic Pancreatitis: Expression Profiling by NGS. Pancreas 2024; 53:e260-e267. [PMID: 38345909 DOI: 10.1097/mpa.0000000000002297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease due to the lack of early detection. Because chronic pancreatitis (CP) patients are a high-risk group for pancreatic cancer, this study aimed to assess the differential miRNA profile in pancreatic tissue of patients with CP and pancreatic cancer. METHODS MiRNAs were isolated from formalin-fixed paraffin-embedded pancreatic tissue of 22 PDAC patients, 18 CP patients, and 10 normal pancreatic tissues from autopsy (C) cases and processed for next-generation sequencing. Known and novel miRNAs were identified and analyzed for differential miRNA expression, target prediction, and pathway enrichment between groups. RESULTS Among the miRNAs identified, 166 known and 17 novel miRNAs were found exclusively in PDAC tissues, while 106 known and 10 novel miRNAs were found specifically in CP tissues. The pathways targeted by PDAC-specific miRNAs and differentially expressed miRNAs between PDAC versus CP tissues and PDAC versus control tissues were the proteoglycans pathway, Hippo signaling pathway, adherens junction, and transforming growth factor-β signaling pathway. CONCLUSIONS This study resulted in a set of exclusive and differentially expressed miRNAs in PDAC and CP can be assessed for their diagnostic value. In addition, studying the role of miRNA-target gene interactions in carcinogenesis may open new therapeutic avenues.
Collapse
Affiliation(s)
- Nidhi Singh
- From the Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences
| | - Imteyaz Ahmad Khan
- From the Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences
| | - Safoora Rashid
- From the Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences
| | - Sumaira Rashid
- From the Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences
| | - Shikha Roy
- International Centre for Genetic Engineering and Biotechnology
| | | | - Amit Kumar
- ICMR AIIMS Computational Genomics Centre
| | | | | | - Dinesh Gupta
- International Centre for Genetic Engineering and Biotechnology
| | - Deepak Gunjan
- From the Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences
| | | | | | - Surabhi Gupta
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - Anoop Saraya
- From the Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences
| |
Collapse
|
8
|
Csonti K, Fazakas C, Molnár K, Wilhelm I, Krizbai IA, Végh AG. Breast adenocarcinoma cells adhere stronger to brain pericytes than to endothelial cells. Colloids Surf B Biointerfaces 2024; 234:113751. [PMID: 38241889 DOI: 10.1016/j.colsurfb.2024.113751] [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: 10/05/2023] [Revised: 12/22/2023] [Accepted: 01/07/2024] [Indexed: 01/21/2024]
Abstract
Most of the malignancies detected within the brain parenchyma are of metastatic origin. As the brain lacks classical lymphatic circulation, the primary way for metastasis relies on hematogenous routes. Dissemination of metastatic cells to the brain implies attachment to the luminal surface of brain endothelial cells, transmigration through the vessel wall, and adhesion to the brain surface of the vasculature. During this process, tumor cells must interact with brain endothelial cells and later on with pericytes. Physical interaction between tumor cells and brain vascular cells might be crucial in the successful extravasation of metastatic cells through blood vessels and later in their survival within the brain environment. Therefore, we applied single-cell force spectroscopy to investigate the nanoscale adhesive properties of living breast adenocarcinoma cells to brain endothelial cells and pericytes. We found target cell type-dependent adhesion characteristics, i.e. increased adhesion of the tumor cells to pericytes in comparison to endothelial cells, which underlines the existence of metastatic potential-related nanomechanical differences relying partly on membrane tether dynamics. Varying adhesion strength of the tumor cells to different cell types of brain vessels presumably reflects the transitory adhesion to endothelial cells before extravasation and the long-lasting strong interaction with pericytes during survival and proliferation in the brain. Our results highlight the importance of specific mechanical interactions between tumor cells and host cells during metastasis formation.
Collapse
Affiliation(s)
- Katalin Csonti
- HUN-REN BRC, Szeged, Institute of Biophysics, Hungary; Doctoral School of Physics, University of Szeged, Szeged, Hungary; Semilab Semiconductor Physics Laboratory Co. Ltd., Budapest, Hungary
| | | | - Kinga Molnár
- HUN-REN BRC, Szeged, Institute of Biophysics, Hungary
| | - Imola Wilhelm
- HUN-REN BRC, Szeged, Institute of Biophysics, Hungary; Institute of Life Sciences, Vasile Goldiş Western University, Arad, Romania
| | - István A Krizbai
- HUN-REN BRC, Szeged, Institute of Biophysics, Hungary; Institute of Life Sciences, Vasile Goldiş Western University, Arad, Romania
| | - Attila G Végh
- HUN-REN BRC, Szeged, Institute of Biophysics, Hungary.
| |
Collapse
|
9
|
Kirikovich SS, Levites EV, Proskurina AS, Ritter GS, Peltek SE, Vasilieva AR, Ruzanova VS, Dolgova EV, Oshihmina SG, Sysoev AV, Koleno DI, Danilenko ED, Taranov OS, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. The Molecular Aspects of Functional Activity of Macrophage-Activating Factor GcMAF. Int J Mol Sci 2023; 24:17396. [PMID: 38139225 PMCID: PMC10743851 DOI: 10.3390/ijms242417396] [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: 10/04/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Group-specific component macrophage-activating factor (GcMAF) is the vitamin D3-binding protein (DBP) deglycosylated at Thr420. The protein is believed to exhibit a wide range of therapeutic properties associated with the activation of macrophagal immunity. An original method for GcMAF production, DBP conversion to GcMAF, and the analysis of the activating potency of GcMAF was developed in this study. Data unveiling the molecular causes of macrophage activation were obtained. GcMAF was found to interact with three CLEC10A derivatives having molecular weights of 29 kDa, 63 kDa, and 65 kDa. GcMAF interacts with high-molecular-weight derivatives via Ca2+-dependent receptor engagement. Binding to the 65 kDa or 63 kDa derivative determines the pro- and anti-inflammatory direction of cytokine mRNA expression: 65 kDa-pro-inflammatory (TNF-α, IL-1β) and 63 kDa-anti-inflammatory (TGF-β, IL-10). No Ca2+ ions are required for the interaction with the canonical 29 kDa CLEC10A. Both forms, DBP protein and GcMAF, bind to the 29 kDa CLEC10A. This interaction is characterized by the stochastic mRNA synthesis of the analyzed cytokines. Ex vivo experiments have demonstrated that when there is an excess of GcMAF ligand, CLEC10A forms aggregate, and the mRNA synthesis of analyzed cytokines is inhibited. A schematic diagram of the presumable mechanism of interaction between the CLEC10A derivatives and GcMAF is provided. The principles and elements of standardizing the GcMAF preparation are elaborated.
Collapse
Affiliation(s)
- Svetlana S. Kirikovich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Evgeniy V. Levites
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Anastasia S. Proskurina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Genrikh S. Ritter
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Sergey E. Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Asya R. Vasilieva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Vera S. Ruzanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Evgeniya V. Dolgova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Sofya G. Oshihmina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Alexandr V. Sysoev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.S.); (D.I.K.)
| | - Danil I. Koleno
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.S.); (D.I.K.)
| | - Elena D. Danilenko
- State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia; (E.D.D.); (O.S.T.)
| | - Oleg S. Taranov
- State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia; (E.D.D.); (O.S.T.)
| | - Alexandr A. Ostanin
- Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia; (A.A.O.); (E.R.C.)
| | - Elena R. Chernykh
- Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia; (A.A.O.); (E.R.C.)
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| | - Sergey S. Bogachev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.V.L.); (A.S.P.); (G.S.R.); (S.E.P.); (A.R.V.); (V.S.R.); (E.V.D.); (S.G.O.); (N.A.K.)
| |
Collapse
|
10
|
Martín-Cruz L, Viñuela M, Kalograiaki I, Angelina A, Oquist-Phillips P, Real-Arévalo I, Cañada FJ, Tudela JI, Moltó L, Moreno-Sierra J, Subiza JL, Palomares O. A tumor-associated heparan sulfate-related glycosaminoglycan promotes the generation of functional regulatory T cells. Cell Mol Immunol 2023; 20:1499-1512. [PMID: 37990034 PMCID: PMC10687014 DOI: 10.1038/s41423-023-01096-9] [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: 04/12/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 11/23/2023] Open
Abstract
Functional Tregs play a key role in tumor development and progression, representing a major barrier to anticancer immunity. The mechanisms by which Tregs are generated in cancer and the influence of the tumor microenvironment on these processes remain incompletely understood. Herein, by using NMR, chemoenzymatic structural assays and a plethora of in vitro and in vivo functional analyses, we demonstrate that the tumoral carbohydrate A10 (Ca10), a cell-surface carbohydrate derived from Ehrlich's tumor (ET) cells, is a heparan sulfate-related proteoglycan that enhances glycolysis and promotes the development of tolerogenic features in human DCs. Ca10-stimulated human DCs generate highly suppressive Tregs by mechanisms partially dependent on metabolic reprogramming, PD-L1, IL-10, and IDO. Ca10 also reprograms the differentiation of human monocytes into DCs with tolerogenic features. In solid ET-bearing mice, we found positive correlations between Ca10 serum levels, tumor size and splenic Treg numbers. Administration of isolated Ca10 also increases the proportion of splenic Tregs in tumor-free mice. Remarkably, we provide evidence supporting the presence of a circulating human Ca10 counterpart (Ca10H) and show, for the first time, that serum levels of Ca10H are increased in patients suffering from different cancer types compared to healthy individuals. Of note, these levels are higher in prostate cancer patients with bone metastases than in prostate cancer patients without metastases. Collectively, we reveal novel molecular mechanisms by which heparan sulfate-related structures associated with tumor cells promote the generation of functional Tregs in cancer. The discovery of this novel structural-functional relationship may open new avenues of research with important clinical implications in cancer treatment.
Collapse
Grants
- SAF-2017-84978-R Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- PID2020-114396RB-I00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- PID2021-123781OB-C22 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTC-2015-3805-1 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
Collapse
Affiliation(s)
- Leticia Martín-Cruz
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Marcos Viñuela
- Inmunotek, Alcalá de Henares, Madrid, Spain
- Fundación Investigación Hospital Clínico San Carlos, Martin Lagos s/n, 28040, Madrid, Spain
| | - Ioanna Kalograiaki
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maetzu 9, 28040, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES) Avda, Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Alba Angelina
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Paola Oquist-Phillips
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maetzu 9, 28040, Madrid, Spain
| | | | - Francisco Javier Cañada
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maetzu 9, 28040, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES) Avda, Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | | | - Luis Moltó
- Fundación Investigación Hospital Clínico San Carlos, Martin Lagos s/n, 28040, Madrid, Spain
| | - Jesús Moreno-Sierra
- Servicio de Urología, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Martín Lagos s/n, 28040, Madrid, Spain
| | | | - Oscar Palomares
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain.
| |
Collapse
|
11
|
Sun L, Zhang Y, Li W, Zhang J, Zhang Y. Mucin Glycans: A Target for Cancer Therapy. Molecules 2023; 28:7033. [PMID: 37894512 PMCID: PMC10609567 DOI: 10.3390/molecules28207033] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Mucin glycans are an important component of the mucus barrier and a vital defence against physical and chemical damage as well as pathogens. There are 20 mucins in the human body, which can be classified into secreted mucins and transmembrane mucins according to their distributions. The major difference between them is that secreted mucins do not have transmembrane structural domains, and the expression of each mucin is organ and cell-specific. Under physiological conditions, mucin glycans are involved in the composition of the mucus barrier and thus protect the body from infection and injury. However, abnormal expression of mucin glycans can lead to the occurrence of diseases, especially cancer, through various mechanisms. Therefore, targeting mucin glycans for the diagnosis and treatment of cancer has always been a promising research direction. Here, we first summarize the main types of glycosylation (O-GalNAc glycosylation and N-glycosylation) on mucins and the mechanisms by which abnormal mucin glycans occur. Next, how abnormal mucin glycans contribute to cancer development is described. Finally, we summarize MUC1-based antibodies, vaccines, radio-pharmaceuticals, and CAR-T therapies using the best characterized MUC1 as an example. In this section, we specifically elaborate on the recent new cancer therapy CAR-M, which may bring new hope to cancer patients.
Collapse
Affiliation(s)
- Lingbo Sun
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Yuhan Zhang
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Wenyan Li
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Jing Zhang
- Medical College of Yan'an University, Yan'an University, Yan'an 716000, China
| | - Yuecheng Zhang
- Key Laboratory of Analytical Technology and Detection of Yan'an, College of Chemistry and Chemical Engineering, Yan'an University, Yan'an 716000, China
| |
Collapse
|
12
|
Farrugia BL, Melrose J. The Glycosaminoglycan Side Chains and Modular Core Proteins of Heparan Sulphate Proteoglycans and the Varied Ways They Provide Tissue Protection by Regulating Physiological Processes and Cellular Behaviour. Int J Mol Sci 2023; 24:14101. [PMID: 37762403 PMCID: PMC10531531 DOI: 10.3390/ijms241814101] [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: 07/24/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
This review examines the roles of HS-proteoglycans (HS-PGs) in general, and, in particular, perlecan and syndecan as representative examples and their interactive ligands, which regulate physiological processes and cellular behavior in health and disease. HS-PGs are essential for the functional properties of tissues both in development and in the extracellular matrix (ECM) remodeling that occurs in response to trauma or disease. HS-PGs interact with a biodiverse range of chemokines, chemokine receptors, protease inhibitors, and growth factors in immune regulation, inflammation, ECM stabilization, and tissue protection. Some cell regulatory proteoglycan receptors are dually modified hybrid HS/CS proteoglycans (betaglycan, CD47). Neurexins provide synaptic stabilization, plasticity, and specificity of interaction, promoting neurotransduction, neurogenesis, and differentiation. Ternary complexes of glypican-1 and Robbo-Slit neuroregulatory proteins direct axonogenesis and neural network formation. Specific neurexin-neuroligin complexes stabilize synaptic interactions and neural activity. Disruption in these interactions leads to neurological deficits in disorders of functional cognitive decline. Interactions with HS-PGs also promote or inhibit tumor development. Thus, HS-PGs have complex and diverse regulatory roles in the physiological processes that regulate cellular behavior and the functional properties of normal and pathological tissues. Specialized HS-PGs, such as the neurexins, pikachurin, and Eyes-shut, provide synaptic stabilization and specificity of neural transduction and also stabilize the axenome primary cilium of phototoreceptors and ribbon synapse interactions with bipolar neurons of retinal neural networks, which are essential in ocular vision. Pikachurin and Eyes-Shut interactions with an α-dystroglycan stabilize the photoreceptor synapse. Novel regulatory roles for HS-PGs controlling cell behavior and tissue function are expected to continue to be uncovered in this fascinating class of proteoglycan.
Collapse
Affiliation(s)
- Brooke L. Farrugia
- Department of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, VIC 3010, Australia;
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Raymond Purves Laboratory of Bone and Joint Research, Kolling Institute of Medical Research, Northern Sydney Local Health District, Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
- Sydney Medical School (Northern), University of Sydney at Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
| |
Collapse
|
13
|
Jiang S, Liu Y, Xu Y, Sang X, Lu X. Research on liquid biopsy for cancer: A bibliometric analysis. Heliyon 2023; 9:e14145. [PMID: 36915518 PMCID: PMC10006671 DOI: 10.1016/j.heliyon.2023.e14145] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND In recent years, liquid biopsy has shown great potential for improving cancer diagnosis and treatment. This study aimed to explore the trends and prospects in liquid biopsy for cancer from a bibliometric perspective. METHODS Reviews and articles on liquid biopsy and cancer were collected from the Web of Science Core Collection (WoSCC). Key bibliometric characteristics were analyzed using CiteSpace. Co-occurrence analysis of keywords and co-citation analysis of references was performed. RESULTS A total of 6331 publications from 11 years of scientific research were retrieved. Ninety-five countries and 7004 institutions in liquid biopsy and cancer contributed. The United States (US) and China published the most articles. The institution with the most published articles was the University of Texas MD Anderson Cancer Center. The most published journals were Cancer and Frontiers in Oncology. "Bettegowda (2014)" was the most cited reference with the highest burst strength in the last decade. Cluster analysis revealed that the recent hot topics were "circulating tumor cells," "cancer," and "exosomes." CONCLUSIONS This bibliometric analysis maps the basic knowledge structure of the field of liquid biopsy for cancer. The field is entering a phase of rapid development. The hot spots identified in this study deserve further investigation.
Collapse
Affiliation(s)
- Shitao Jiang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaoge Liu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiyao Xu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Lu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
14
|
Establishment and validation of a plasma oncofetal chondroitin sulfated proteoglycan for pan-cancer detection. Nat Commun 2023; 14:645. [PMID: 36746966 PMCID: PMC9902466 DOI: 10.1038/s41467-023-36374-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Various biomarkers targeting cell-free DNA (cfDNA) and circulating proteins have been tested for pan-cancer detection. Oncofetal chondroitin sulfate (ofCS), which distinctively modifies proteoglycans (PGs) of most cancer cells and binds specifically to the recombinant Plasmodium falciparum VAR2CSA proteins (rVAR2), is explored for its potential as a plasma biomarker in pan-cancer detection. To quantitate the plasma ofCS/ofCSPGs, we optimized an ELISA using different capture/detection pairs (rVAR2/anti-CD44, -SDC1, and -CSPG4) in a case-control study with six cancer types. We show that the plasma levels of ofCS/ofCSPGs are significantly higher in cancer patients (P values, 1.2 × 10-2 to 4.4 × 10-10). Validation studies are performed with two independent cohorts covering 11 malignant tumors. The individuals in the top decile of ofCS-CD44 have more than 27-fold cancer risk (OR = 27.8, 95%CI = 18.8-41.4, P = 2.72 × 10-62) compared with the lowest 20%. Moreover, the elevated plasma ofCS-CD44 could be detected at the early stage of pan-cancer with strong dose-dependent odds risk prediction.
Collapse
|
15
|
Woldmar N, Schwendenwein A, Kuras M, Szeitz B, Boettiger K, Tisza A, László V, Reiniger L, Bagó AG, Szállási Z, Moldvay J, Szász AM, Malm J, Horvatovich P, Pizzatti L, Domont GB, Rényi-Vámos F, Hoetzenecker K, Hoda MA, Marko-Varga G, Schelch K, Megyesfalvi Z, Rezeli M, Döme B. Proteomic analysis of brain metastatic lung adenocarcinoma reveals intertumoral heterogeneity and specific alterations associated with the timing of brain metastases. ESMO Open 2023; 8:100741. [PMID: 36527824 PMCID: PMC10024110 DOI: 10.1016/j.esmoop.2022.100741] [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: 05/25/2022] [Revised: 09/07/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Brain metastases are associated with considerable negative effects on patients' outcome in lung adenocarcinoma (LADC). Here, we investigated the proteomic landscape of primary LADCs and their corresponding brain metastases. MATERIALS AND METHODS Proteomic profiling was conducted on 20 surgically resected primary and brain metastatic LADC samples via label-free shotgun proteomics. After sample processing, peptides were analyzed using an Ultimate 3000 pump coupled to a QExactive HF-X mass spectrometer. Raw data were searched using PD 2.4. Further data analyses were carried out using Perseus, RStudio and GraphPad Prism. Proteomic data were correlated with clinical and histopathological parameters and the timing of brain metastases. Mass spectrometry-based proteomic data are available via ProteomeXchange with identifier PXD027259. RESULTS Out of the 6821 proteins identified and quantified, 1496 proteins were differentially expressed between primary LADCs and corresponding brain metastases. Pathways associated with the immune system, cell-cell/matrix interactions and migration were predominantly activated in the primary tumors, whereas pathways related to metabolism, translation or vesicle formation were overrepresented in the metastatic tumors. When comparing fast- versus slow-progressing patients, we found 454 and 298 differentially expressed proteins in the primary tumors and brain metastases, respectively. Metabolic reprogramming and ribosomal activity were prominently up-regulated in the fast-progressing patients (versus slow-progressing individuals), whereas expression of cell-cell interaction- and immune system-related pathways was reduced in these patients and in those with multiple brain metastases. CONCLUSIONS This is the first comprehensive proteomic analysis of paired primary tumors and brain metastases of LADC patients. Our data suggest a malfunction of cellular attachment and an increase in ribosomal activity in LADC tissue, promoting brain metastasis. The current study provides insights into the biology of LADC brain metastases and, moreover, might contribute to the development of personalized follow-up strategies in LADC.
Collapse
Affiliation(s)
- N Woldmar
- Department of Biomedical Engineering, Lund University, Lund, Sweden; Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A Schwendenwein
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - M Kuras
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - B Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - K Boettiger
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - A Tisza
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - V László
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria; National Korányi Institute of Pulmonology, Budapest, Hungary
| | - L Reiniger
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; Department of Pathology, Forensic and Insurance Medicine, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - A G Bagó
- Department of Neurooncology, National Institute of Clinical Neurosciences, Budapest, Hungary
| | - Z Szállási
- Department of Pathology, Forensic and Insurance Medicine, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary; Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, USA; Danish Cancer Society Research Center, Copenhagen, Denmark
| | - J Moldvay
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Pathology, Forensic and Insurance Medicine, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - A M Szász
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - J Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - P Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - L Pizzatti
- Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G B Domont
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - F Rényi-Vámos
- National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - K Hoetzenecker
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - M A Hoda
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - G Marko-Varga
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - K Schelch
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria
| | - Z Megyesfalvi
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria; National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - M Rezeli
- Department of Biomedical Engineering, Lund University, Lund, Sweden.
| | - B Döme
- Department of Thoracic Surgery, Medical University Vienna, Vienna, Austria; Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden; National Korányi Institute of Pulmonology, Budapest, Hungary; Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary.
| |
Collapse
|
16
|
HS, an Ancient Molecular Recognition and Information Storage Glycosaminoglycan, Equips HS-Proteoglycans with Diverse Matrix and Cell-Interactive Properties Operative in Tissue Development and Tissue Function in Health and Disease. Int J Mol Sci 2023; 24:ijms24021148. [PMID: 36674659 PMCID: PMC9867265 DOI: 10.3390/ijms24021148] [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: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Heparan sulfate is a ubiquitous, variably sulfated interactive glycosaminoglycan that consists of repeating disaccharides of glucuronic acid and glucosamine that are subject to a number of modifications (acetylation, de-acetylation, epimerization, sulfation). Variable heparan sulfate chain lengths and sequences within the heparan sulfate chains provide structural diversity generating interactive oligosaccharide binding motifs with a diverse range of extracellular ligands and cellular receptors providing instructional cues over cellular behaviour and tissue homeostasis through the regulation of essential physiological processes in development, health, and disease. heparan sulfate and heparan sulfate-PGs are integral components of the specialized glycocalyx surrounding cells. Heparan sulfate is the most heterogeneous glycosaminoglycan, in terms of its sequence and biosynthetic modifications making it a difficult molecule to fully characterize, multiple ligands also make an elucidation of heparan sulfate functional properties complicated. Spatio-temporal presentation of heparan sulfate sulfate groups is an important functional determinant in tissue development and in cellular control of wound healing and extracellular remodelling in pathological tissues. The regulatory properties of heparan sulfate are mediated via interactions with chemokines, chemokine receptors, growth factors and morphogens in cell proliferation, differentiation, development, tissue remodelling, wound healing, immune regulation, inflammation, and tumour development. A greater understanding of these HS interactive processes will improve therapeutic procedures and prognoses. Advances in glycosaminoglycan synthesis and sequencing, computational analytical carbohydrate algorithms and advanced software for the evaluation of molecular docking of heparan sulfate with its molecular partners are now available. These advanced analytic techniques and artificial intelligence offer predictive capability in the elucidation of heparan sulfate conformational effects on heparan sulfate-ligand interactions significantly aiding heparan sulfate therapeutics development.
Collapse
|
17
|
Kizhakkeppurath Kumaran A, Sahu A, Singh A, Aynikkattil Ravindran N, Sekhar Chatterjee N, Mathew S, Verma S. Proteoglycans in breast cancer, identification and characterization by LC-MS/MS assisted proteomics approach: A review. Proteomics Clin Appl 2023:e2200046. [PMID: 36598116 DOI: 10.1002/prca.202200046] [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: 06/12/2022] [Revised: 11/24/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
PURPOSE Proteoglycans (PGs) are negatively charged macromolecules containing a core protein and single or several glycosaminoglycan chains attached by covalent bond. They are distributed in all tissues, including extracellular matrix (ECM), cell surface, and basement membrane. They are involved in major pathways and cell signalling cascades which modulate several vital physiological functions of the body. They have also emerged as a target molecule for cancer treatment and as possible biomarkers for early cancer detection. Among cancers, breast cancer is a highly invasive and heterogenous type and has become the major cause of mortality especially among women. So, this review revisits the studies on PGs characterization in breast cancer using LC-MS/MS-based proteomics approach, which will be further helpful for identification of potential PGs-based biomarkers or therapeutic targets. EXPERIMENTAL DESIGN There is a lack of comprehensive knowledge on the use of LC-MS/MS-based proteomics approaches to identify and characterize PGs in breast cancer. RESULTS LC-MS/MS assisted PGs characterization in breast cancer revealed the vital PGs in breast cancer invasion and progression. In addition, comprehensive profiling and characterization of PGs in breast cancer are efficiently carried out by this approach. CONCLUSIONS Proteomics techniques including LC-MS/MS-based identification of proteoglycans is effectively carried out in breast cancer research. Identification of expression at different stages of breast cancer is a major challenge, and LC-MS/MS-based profiling of PGs can boost novel strategies to treat breast cancer, which involve targeting PGs, and also aid early diagnosis using PGs as biomarkers.
Collapse
Affiliation(s)
| | - Ankita Sahu
- Tumor Biology Lab, ICMR-National Institute of Pathology, New Delhi, India
| | - Astha Singh
- Tumor Biology Lab, ICMR-National Institute of Pathology, New Delhi, India
| | - Nisha Aynikkattil Ravindran
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Thrissur, India
| | | | - Suseela Mathew
- Biochemistry and Nutrition Division, ICAR-Central Institute of Fisheries Technology, Kochi, India
| | - Saurabh Verma
- Tumor Biology Lab, ICMR-National Institute of Pathology, New Delhi, India
| |
Collapse
|
18
|
The New General Biological Property of Stem-like Tumor Cells (Part II: Surface Molecules, Which Belongs to Distinctive Groups with Particular Functions, Form a Unique Pattern Characteristic of a Certain Type of Tumor Stem-like Cells). Int J Mol Sci 2022; 23:ijms232415800. [PMID: 36555446 PMCID: PMC9785054 DOI: 10.3390/ijms232415800] [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: 08/25/2022] [Revised: 11/16/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
An ability of poorly differentiated cells of different genesis, including tumor stem-like cells (TSCs), to internalize extracellular double-stranded DNA (dsDNA) fragments was revealed in our studies. Using the models of Krebs-2 murine ascites carcinoma and EBV-induced human B-cell lymphoma culture, we demonstrated that dsDNA internalization into the cell consists of several mechanistically distinct phases. The primary contact with cell membrane factors is determined by electrostatic interactions. Firm contacts with cell envelope proteins are then formed, followed by internalization into the cell of the complex formed between the factor and the dsDNA probe bound to it. The key binding sites were found to be the heparin-binding domains, which are constituents of various cell surface proteins of TSCs-either the C1q domain, the collagen-binding domain, or domains of positively charged amino acids. These results imply that the interaction between extracellular dsDNA fragments and the cell, as well as their internalization, took place with the involvement of glycocalyx components (proteoglycans/glycoproteins (PGs/GPs) and glycosylphosphatidylinositol-anchored proteins (GPI-APs)) and the system of scavenger receptors (SRs), which are characteristic of TSCs and form functional clusters of cell surface proteins in TSCs. The key provisions of the concept characterizing the principle of organization of the "group-specific" cell surface factors of TSCs of various geneses were formulated. These factors belong to three protein clusters: GPs/PGs, GIP-APs, and SRs. For TSCs of different tumors, these clusters were found to be represented by different members with homotypic functions corresponding to the general function of the cluster to which they belong.
Collapse
|
19
|
A stabilized CXCL9(74-103)-derived peptide selectively inhibits proliferation, adhesion and metastasis of tumor cells that express high levels of heparan sulfate. Int J Biol Macromol 2022; 222:2808-2822. [PMID: 36272565 DOI: 10.1016/j.ijbiomac.2022.10.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
|
20
|
Souza DS, Chignalia AZ, Carvalho-de-Souza JL. Modulation of cardiac voltage-activated K + currents by glypican 1 heparan sulfate proteoglycan. Life Sci 2022; 308:120916. [PMID: 36049528 PMCID: PMC11105158 DOI: 10.1016/j.lfs.2022.120916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/15/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Glypican 1 (Gpc1) is a heparan sulfate proteoglycan attached to the cell membrane via a glycosylphosphatidylinositol anchor, where it holds glycosaminoglycans nearby. We have recently shown that Gpc1 knockout (Gpc1-/-) mice feature decreased systemic blood pressure. To date, none has been reported regarding the role of Gpc1 on the electrical properties of the heart and specifically, in regard to a functional interaction between Gpc1 and voltage-gated K+ channels. METHODS We used echocardiography and in vivo (electrocardiographic recordings) and in vitro (patch clamping) electrophysiology to study mechanical and electric properties of mice hearts. We used RT-PCR to probe K+ channels' gene transcription in heart tissue. RESULTS Gpc1-/- hearts featured increased cardiac stroke volume and preserved ejection fraction. Gpc1-/- electrocardiograms showed longer QT intervals, abnormalities in the ST segment, and delayed T waves, corroborated by longer action potentials in isolated ventricular cardiomyocytes. In voltage-clamp, these cells showed decreased Ito and IK voltage-activated K+ current densities. Moreover, IK showed activation at less negative voltages, but a higher level of inactivation at a given membrane potential. Kcnh2 and Kcnq1 voltage-gated K+ channels subunits' transcripts were remarkably more abundant in heart tissues from Gpc1-/- mice, suggesting that Gpc1 may interfere in the steps between transcription and translation in these cases. CONCLUSION Our data reveals an unprecedented connection between Gpc1 and voltage-gated K+ channels expressed in the heart and this knowledge contributes to the understanding of the role of this HSPG in cardiac function which may play a role in the development of cardiovascular disease.
Collapse
Affiliation(s)
- Diego Santos Souza
- Department of Anesthesiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Andreia Zago Chignalia
- Department of Anesthesiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA; Department of Physiology, College of Medicine University of Arizona, Tucson, AZ 85724, USA; Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85724, USA
| | - Joao Luis Carvalho-de-Souza
- Department of Anesthesiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA; Department of Physiology, College of Medicine University of Arizona, Tucson, AZ 85724, USA; Department of Ophthalmology and Visual Sciences, College of Medicine, University of Arizona, Tucson, AZ 85724, USA; BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA.
| |
Collapse
|
21
|
Salavaty A, Shehni SA, Ramialison M, Currie PD. Systematic molecular profiling of acute leukemia cancer stem cells allows identification of druggable targets. Heliyon 2022; 8:e11093. [PMID: 36281397 PMCID: PMC9586918 DOI: 10.1016/j.heliyon.2022.e11093] [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: 08/23/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Acute myeloid leukemia (AML) is one of the most prevalent and acute blood cancers with a poor prognosis and low overall survival rate, especially in the elderly. Although several new AML markers and drug targets have been recently identified, the rate of long-term cancer eradication has not improved significantly due to the presence and drug resistance of AML cancer stem cells (CSCs). Here we develop a novel computational pipeline to analyze the transcriptomic profiles of AML cancer (stem) cells and identify novel candidate AML CSC markers and drug targets. In our novel pipeline we apply a top-down meta-analysis strategy to integrate The Cancer Genome Atlas data with CSC datasets to infer cell stemness features. As a result, a set of genes termed the "AML key CSC genes" along with all the available drugs/compounds that could target them were identified. Overall, our novel computational pipeline could retrieve known cancer drugs (Carfilzomib) and predicted novel drugs such as Zonisamide, Amitriptyline, and their targets amongst the top ranked drugs and drug targets for targeting AML. Additionally, the pipeline applied in this study could be used for the identification of CSC-specific markers, drivers and their respective targeting drugs in other cancer types.
Collapse
Affiliation(s)
- Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia
| | - Sara Alaei Shehni
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
- Department of Pediatrics, The Royal Children's Hospital, University of Melbourne Parkville, VIC, 3052, Australia
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
22
|
Taherkhani A, Dehto SS, Jamshidi S, Shojaei S. Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach. Genomics Inform 2022; 20:e27. [PMID: 36239104 PMCID: PMC9576470 DOI: 10.5808/gi.22038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck malignancy, with frequent cervical lymph-node metastasis, leading to a poor prognosis in OSCC patients. The present study aimed to identify potential markers, including microRNAs (miRNAs) and genes, significantly involved in the etiology of early-stage OSCC. Additionally, the main OSCC's dysregulated Gene Ontology annotations and significant signaling pathways were identified. The dataset GSE45238 underwent multivariate statistical analysis in order to distinguish primary OSCC tissues from healthy oral epithelium. Differentially expressed miRNAs (DEMs) with the criteria of p-value < 0.001 and |Log2 fold change| > 1.585 were identified in the two groups, and subsequently, validated targets of DEMs were identified. A protein interaction map was constructed, hub genes were identified, significant modules within the network were illustrated, and significant pathways and biological processes associated with the clusters were demonstrated. Using the GEPI2 database, the hub genes' predictive function was assessed. Compared to the healthy controls, main OSCC had a total of 23 DEMs. In patients with head and neck squamous cell carcinoma (HNSCC), upregulation of CALM1, CYCS, THBS1, MYC, GATA6, and SPRED3 was strongly associated with a poor prognosis. In HNSCC patients, overexpression of PIK3R3, GIGYF1, and BCL2L11 was substantially correlated with a good prognosis. Besides, “proteoglycans in cancer” was the most significant pathway enriched in the primary OSCC. The present study results revealed more possible mechanisms mediating primary OSCC and may be useful in the prognosis of the patients with early-stage OSCC.
Collapse
Affiliation(s)
- Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahab Shahmoradi Dehto
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shokoofeh Jamshidi
- Dental Research Center, Department of Oral and Maxillofacial Pathology, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Setareh Shojaei
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
- Corresponding author E-mail:
| |
Collapse
|
23
|
Palshikar MG, Palli R, Tyrell A, Maggirwar S, Schifitto G, Singh MV, Thakar J. Executable models of immune signaling pathways in HIV-associated atherosclerosis. NPJ Syst Biol Appl 2022; 8:35. [PMID: 36131068 PMCID: PMC9492768 DOI: 10.1038/s41540-022-00246-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
Atherosclerosis (AS)-associated cardiovascular disease is an important cause of mortality in an aging population of people living with HIV (PLWH). This elevated risk has been attributed to viral infection, anti-retroviral therapy, chronic inflammation, and lifestyle factors. However, the rates at which PLWH develop AS vary even after controlling for length of infection, treatment duration, and for lifestyle factors. To investigate the molecular signaling underlying this variation, we sequenced 9368 peripheral blood mononuclear cells (PBMCs) from eight PLWH, four of whom have atherosclerosis (AS+). Additionally, a publicly available dataset of PBMCs from persons before and after HIV infection was used to investigate the effect of acute HIV infection. To characterize dysregulation of pathways rather than just measuring enrichment, we developed the single-cell Boolean Omics Network Invariant Time Analysis (scBONITA) algorithm. scBONITA infers executable dynamic pathway models and performs a perturbation analysis to identify high impact genes. These dynamic models are used for pathway analysis and to map sequenced cells to characteristic signaling states (attractor analysis). scBONITA revealed that lipid signaling regulates cell migration into the vascular endothelium in AS+ PLWH. Pathways implicated included AGE-RAGE and PI3K-AKT signaling in CD8+ T cells, and glucagon and cAMP signaling pathways in monocytes. Attractor analysis with scBONITA facilitated the pathway-based characterization of cellular states in CD8+ T cells and monocytes. In this manner, we identify critical cell-type specific molecular mechanisms underlying HIV-associated atherosclerosis using a novel computational method.
Collapse
Affiliation(s)
- Mukta G Palshikar
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Rohith Palli
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Alicia Tyrell
- University of Rochester Clinical & Translational Science Institute, Rochester, USA
| | - Sanjay Maggirwar
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Giovanni Schifitto
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, USA
- Department of Imaging Sciences, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Meera V Singh
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, USA
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Juilee Thakar
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA.
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, USA.
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, USA.
| |
Collapse
|
24
|
Ritter GS, Dolgova EV, Petrova DD, Efremov YR, Proskurina AS, Potter EA, Ruzanova VS, Kirikovich SS, Levites EV, Taranov OS, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. The new general biological property of stem-like tumor cells Part I. Peculiarities of the process of the double-stranded DNA fragments internalization into stem-like tumor cells. Front Genet 2022; 13:954395. [PMID: 36159968 PMCID: PMC9492886 DOI: 10.3389/fgene.2022.954395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
Stem-like tumor cells of ascites carcinoma Krebs-2 and Epstein-Barr virus–induced B-lymphoma were shown to possess the innate capability of binding and internalizing the TAMRA-labeled double-stranded DNA (dsDNA) probe. The process of binding and internalizing is rather complicated and composed of the following successive stages: 1) initiating electrostatic interaction and contact of a negatively charged dsDNA molecule with a positively charged molecule(s) on the surface of a stem-like tumor cell; 2) binding of the dsDNA probe to a tumor stem cell surface protein(s) via the formation of a strong chemical/molecular bond; and 3) the very internalization of dsDNA into the cell. Binding of DNA to cell surface proteins is determined by the presence of heparin/polyanion-binding sites within the protein structure, which can be competitively blocked by heparin and/or dextran sulfate, wherein heparin blocks only the binding, while dextran sulfate abrogates both binding and internalization. The abrogation of internalization by dextran sulfate implies the role of scavenger receptors in this process. Cells were shown to uptake DNA in amounts constituting ∼0.008% of the haploid genome. Inhibitors of caveolae-dependent internalization abrogate the DNA uptake in Krebs-2 cells, and inhibitors of the clathrin/caveolar mechanism block the internalization in B-lymphoma cells. In the present report, it is shown for the first time that in contrast to the majority of committed tumor cells, stem-like tumor cells of Krebs-2 and B-lymphoma carry a general positive charge on their surface.
Collapse
Affiliation(s)
- Genrikh S. Ritter
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniya V. Dolgova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daria D. Petrova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yaroslav R. Efremov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk National Research State University, Novosibirsk, Russia
| | - Anastasia S. Proskurina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina A. Potter
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Vera S. Ruzanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk National Research State University, Novosibirsk, Russia
| | - Svetlana S. Kirikovich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniy V. Levites
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg S. Taranov
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Alexandr A. Ostanin
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Elena R. Chernykh
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey S. Bogachev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Correspondence: Sergey S. Bogachev,
| |
Collapse
|
25
|
Santi MD, Zhang M, Salvo E, Asam K, Viet C, Xie T, Amit M, Aouizerat B, Ye Y. Schwann Cells Induce Phenotypic Changes in Oral Cancer Cells. Adv Biol (Weinh) 2022; 6:e2200187. [PMID: 35925609 PMCID: PMC9474679 DOI: 10.1002/adbi.202200187] [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: 07/04/2022] [Revised: 07/18/2022] [Indexed: 01/28/2023]
Abstract
Head and neck cancer (HNC) is the seventh most common cancer worldwide, the majority being oral squamous cell carcinoma. Despite advances in cancer diagnosis and treatment, the survival rate of patients with HNC remains stagnant. The cancer-nerve interaction has been recognized as an important driver of cancer progression. Schwann cells, a type of peripheral glia, have been implicated in promoting cancer cell growth, migration, dispersion, and invasion into the nerve in many cancers. Here, it is demonstrated that the presence of Schwann cells makes oral cancer cells more aggressive by promoting their proliferation, extracellular matrix breakdown, and altering cell metabolism. Furthermore, oral cancer cells became larger, more circular, with more projections and nuclei following co-culturing with Schwann cells. RNA-sequencing analysis in oral cancer cells following exposure to Schwann cells shows corresponding changes in genes involved in the hallmarks of cancer and cell metabolism; the enriched KEGG pathways are spliceosome, RNA transport, cell cycle, axon guidance, signaling pathways regulating pluripotency of stem cells, cAMP signaling, WNT signaling, proteoglycans in cancer and PI3K-Akt signaling. Taken together, these results suggest a significant role for Schwann cells in facilitating oral cancer progression, highlighting their potential as a target to treat oral cancer progression.
Collapse
Affiliation(s)
- Maria Daniela Santi
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Morgan Zhang
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Elizabeth Salvo
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Kesava Asam
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Chi Viet
- Loma Linda University School of Dentistry, Loma Linda, CA92350
| | - Tongxin Xie
- Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Moran Amit
- Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Bradley Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| | - Yi Ye
- Bluestone Center for Clinical Research, College of Dentistry, New York University
- Department of Oral Maxillofacial Surgery, College of Dentistry, New York University
| |
Collapse
|
26
|
Khan SA, Lee TKW. Investigations of nitazoxanide molecular targets and pathways for the treatment of hepatocellular carcinoma using network pharmacology and molecular docking. Front Pharmacol 2022; 13:968148. [PMID: 35959427 PMCID: PMC9358010 DOI: 10.3389/fphar.2022.968148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Nitazoxanide has been investigated for colorectal cancer and breast cancer. However, its molecular targets and pathways have not yet been explored for hepatocellular carcinoma (HCC) treatment. Utilizing a network pharmacology approach, nitazoxanide’s potential targets and molecular pathways for HCC treatment were investigated. HCC targets were extracted from the GeneCards database. Potential targets of nitazoxanide were predicted using Swiss Target Prediction and Super Pred. Intersecting targets were analyzed with VENNY online tool. Using Cytoscape, a protein-protein interaction (PPI), cluster, and core targets-pathways networks were constructed. Using the Database for Annotation, Visualization and Integrated Discovery (DAVID), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. The nitazoxanide was molecularly docked with anti-HCC core targets by employing Auto Dock Vina. A total of 168 potential targets of nitazoxanide, 13,415 HCC-related targets, and 153 intersecting targets were identified. The top eight anti-HCC core targets were identified: SRC, EGFR, CASP3, MMP9, mTOR, HIF1A, ERBB2, and PPARG. GO enrichment analysis showed that nitazoxanide might have anti-HCC effects by affecting gene targets involved in multiple biological processes (BP) (protein phosphorylation, transmembrane receptor protein tyrosine kinase (RTKs) signaling pathway, positive regulation of MAP kinase activity, etc.). KEGG pathways and core targets-pathways network analysis indicated that pathways in cancer and proteoglycans in cancer are two key pathways that significantly contribute to the anti-HCC effects of nitazoxanide. Results of molecular docking demonstrated the potential for active interaction between the top eight anti-HCC core targets and nitazoxanide. Our research offers a theoretical basis for the notion that nitazoxanide may have distinct therapeutic effects in HCC, and the identified pharmacological targets and pathways might function as biomarkers for HCC therapy.
Collapse
Affiliation(s)
- Shakeel Ahmad Khan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- *Correspondence: Shakeel Ahmad Khan, ; Terence Kin Wah Lee,
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- *Correspondence: Shakeel Ahmad Khan, ; Terence Kin Wah Lee,
| |
Collapse
|
27
|
Molecular Targets and Mechanisms of Hedyotis diffusa- Scutellaria barbata Herb Pair for the Treatment of Colorectal Cancer Based on Network Pharmacology and Molecular Docking. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6186662. [PMID: 35707465 PMCID: PMC9192289 DOI: 10.1155/2022/6186662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
Abstract
Objective: Hedyotis diffusa-Scutellaria barbata herb pair (HS) has therapeutic effects on a variety of cancers, and this study aims to systematically explore the multiple mechanisms of HS in the treatment of colorectal cancer (CRC). Methods. The active ingredients of HS were obtained from TCMSP, and the potential targets related to these ingredients were screened from the STITCH, SuperPred, and Swiss TargetPrediction databases. Targets associated with CRC were retrieved by Drugbank, TTD, DisGeNET, and GeneCards. We used a Venn diagram to screen the intersection targets and used Cytoscape to construct the herb-ingredient-target-disease network, and the core targets were selected. The Go analysis and KEGG pathway annotation were performed by R language software. We used PyMol and Autodock Vina to achieve molecular docking of core ingredients and targets. Results: A total of 33 active ingredients were obtained from the HS, and 762 CRC-related targets were reserved from the four databases. We got 170 intersection targets to construct the network and found that the four ingredients with the most targets were quercetin, luteolin, baicalein, and dinatin, which were the core ingredients. The PPI analysis showed that the core targets were STAT3, TP53, MAPK3, AKT1, JUN, EGFR, MYC, VEGFA, EGF, and CTNNB1. Molecular docking results showed that these core ingredients had good binding potential with core targets, especially the docking of each component with MAPK obtained the lowest binding energy. HS acts simultaneously on various signaling pathways related to CRC, including the PI3K-Akt signaling pathway, proteoglycans in cancer, and the MAPK signaling pathway. Conclusions: This study systematically analyzed the active ingredients, core targets, and central mechanisms of HS in the treatment of CRC. It reveals the role of HS targeting PI3K-Akt signaling and MAPK signaling pathways in the treatment of CRC. We hope that our research could bring a new perspective to the therapy of CRC and find new anticancer drugs.
Collapse
|
28
|
Khan SA, Lee TKW. Network-Pharmacology-Based Study on Active Phytochemicals and Molecular Mechanism of Cnidium monnieri in Treating Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:5400. [PMID: 35628212 PMCID: PMC9140548 DOI: 10.3390/ijms23105400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignancy with a high mortality rate globally. For thousands of years, Cnidium monnieri has been used to treat human ailments and is regarded as a veritable treasure trove for drug discovery. This study has investigated the key active phytochemicals and molecular mechanisms of Cnidium monnieri implicated in curing HCC. We utilized the TCMSP database to collect data on the phytochemicals of Cnidium monnieri. The SwissTargetPrediction website tool was used to predict the targets of phytochemicals of Cnidium monnieri. HCC-related genes were retrieved from OncoDB.HCC and Liverome, two liver-cancer-related databases. Using the DAVID bioinformatic website tool, Gene Ontology (GO) and KEGG enrichment analysis were performed on the intersecting targets of HCC-related genes and active phytochemicals in Cnidium monnieri. A network of active phytochemicals and anti-HCC targets was constructed and analyzed using Cytoscape software. Molecular docking of key active phytochemicals was performed with anti-HCC targets using AutoDock Vina (version 1.2.0.). We identified 19 active phytochemicals in Cnidium monnieri, 532 potential targets of these phytochemicals, and 566 HCC-related genes. Results of GO enrichment indicated that Cnidium monnieri might be implicated in affecting gene targets involved in multiple biological processes, such as protein phosphorylation, negative regulation of the apoptotic process, which could be attributed to its anti-HCC effects. KEGG pathway analyses indicated that the PI3K-AKT signaling pathway, pathways in cancer, proteoglycans in cancer, the TNF signaling pathway, VEGF signaling pathway, ErbB signaling pathway, and EGFR tyrosine kinase inhibitor resistance are the main pathways implicated in the anti-HCC effects of Cnidium monnieri. Molecular docking analyses showed that key active phytochemicals of Cnidium monnieri, such as ar-curcumene, diosmetin, and (E)-2,3-bis(2-keto-7-methoxy-chromen-8-yl)acrolein, can bind to core therapeutic targets EGFR, CASP3, ESR1, MAPK3, CCND1, and ERBB2. The results of the present study offer clues for further investigation of the anti-HCC phytochemicals and mechanisms of Cnidium monnieri and provide a basis for developing modern anti-HCC drugs based on phytochemicals in Cnidium monnieri.
Collapse
Affiliation(s)
- Shakeel Ahmad Khan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Rd., Hung Hom, Kowloon 999077, Hong Kong
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, 11 Yuk Choi Rd., Hung Hom, Kowloon 999077, Hong Kong
| |
Collapse
|
29
|
Genome-Scale Metabolic Model Analysis of Metabolic Differences between Lauren Diffuse and Intestinal Subtypes in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14092340. [PMID: 35565469 PMCID: PMC9104812 DOI: 10.3390/cancers14092340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 01/01/2023] Open
Abstract
Gastric cancer (GC) is one of the most lethal cancers worldwide; it has a high mortality rate, particularly in East Asia. Recently, genetic events (e.g., mutations and copy number alterations) and molecular signaling associated with histologically different GC subtypes (diffuse and intestinal) have been elucidated. However, metabolic differences among the histological GC subtypes have not been studied systematically. In this study, we utilized transcriptome-based genome-scale metabolic models (GEMs) to identify differential metabolic pathways between Lauren diffuse and intestinal subtypes. We found that diverse metabolic pathways, including cholesterol homeostasis, xenobiotic metabolism, fatty acid metabolism, the MTORC1 pathway, and glycolysis, were dysregulated between the diffuse and intestinal subtypes. Our study provides an overview of the metabolic differences between the two subtypes, possibly leading to an understanding of metabolism in GC heterogeneity.
Collapse
|
30
|
Aziz S, Rasheed F, Zahra R, König S. Gastric Cancer Pre-Stage Detection and Early Diagnosis of Gastritis Using Serum Protein Signatures. Molecules 2022; 27:molecules27092857. [PMID: 35566209 PMCID: PMC9099457 DOI: 10.3390/molecules27092857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Background: A gastric cancer (GC) diagnosis relies on histopathology. Endoscopy rates are increasing. Helicobacter pylori infection is a major GC risk factor. In an effort to elucidate abundant blood biomarkers, and potentially reduce the number of diagnostic surgical interventions, we investigated sera and biopsies from a cohort of 219 H. pylori positive and negative patients diagnosed with GC, gastritis, and ulcers. This allowed the comparative investigation of the different gastroduodenal diseases, and the exclusion of protein changes resulting from bacterial infection or inflammation of the gastric mucosa when searching for GC-dependent proteins. Methods: High-definition mass spectrometry-based expression analysis of tryptically digested proteins was performed, followed by multivariate statistical and network analyses for the different disease groups, with respect to H. pylori infection status. Significantly regulated proteins differing more than two-fold between groups were shortlisted, and their role in gastritis and GC discussed. Results: We present data of comparative protein analyses of biopsies and sera from patients suffering from mild to advanced gastritis, ulcers, and early to advanced GC, in conjunction with a wealth of metadata, clinical information, histopathological evaluation, and H. pylori infection status. We used samples from pre-malignant stages to extract prospective serum markers for early-stage GC, and present a 29-protein marker panel containing, amongst others, integrin β-6 and glutathione peroxidase. Furthermore, ten serum markers specific for advanced GC, independent of H. pylori infection, are provided. They include CRP, protein S100A9, and kallistatin. The majority of these proteins were previously discussed in the context of cancer or GC. In addition, we detected hypoalbuminemia and increased fibrinogen serum levels in gastritis. Conclusion: Two protein panels were suggested for the development of multiplex tests for GC serum diagnostics. For most of the elements contained in these panels, individual commercial tests are available. Thus, we envision the design of multi-protein assays, incorporating several to all of the panel members, in order to gain a level of specificity that cannot be achieved by testing a single protein alone. As their development and validation will take time, gastritis diagnosis based on the fibrinogen to albumin serum ratio may be a quick way forward. Its determination at the primary/secondary care level for early diagnosis could significantly reduce the number of referrals to endoscopy. Preventive measures are in high demand. The protein marker panels presented in this work will contribute to improved GC diagnostics, once they have been transferred from a research result to a practical tool.
Collapse
Affiliation(s)
- Shahid Aziz
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
| | - Faisal Rasheed
- BreathMAT Lab, Pakistan Institute of Nuclear Science and Technology (PINSTEC), Islamabad 44000, Pakistan; (S.A.); (F.R.)
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Simone König
- IZKF Core Unit Proteomics, University of Münster, 48149 Münster, Germany
- Correspondence:
| |
Collapse
|
31
|
Detroja TS, Gil-Henn H, Samson AO. Text-Mining Approach to Identify Hub Genes of Cancer Metastasis and Potential Drug Repurposing to Target Them. J Clin Med 2022; 11:jcm11082130. [PMID: 35456223 PMCID: PMC9029557 DOI: 10.3390/jcm11082130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 12/11/2022] Open
Abstract
Metastasis accounts for the majority of cancer-related deaths. Despite decades of research, the prevention and suppression of metastasis remain an elusive goal, and to date, only a few metastasis-related genes have been targeted therapeutically. Thus, there is a strong need to find potential genes involved in key driver traits of metastasis and their available drugs. In this study, we identified genes associated with metastasis and repurposable drugs that potentially target them. First, we use text mining of PubMed citations to identify candidate genes associated with metastatic processes, such as invadopodia, motility, movement, metastasis, invasion, wound healing, EMT (epithelial to mesenchymal transition), and podosome. Next, we annotated the top genes involved in each process as a driver, tumor suppressor, or oncogene. Then, a total of 185 unique cancer genes involved in metastasis-related processes were used for hub gene analysis using bioinformatics tools. Notably, a total of 77 hub genes were identified. Further, we used virtual screening data of druggable candidate hub genes involved in metastasis and identified potential drugs that can be repurposed as anti-metastatic drugs. Remarkably, we found a total of 50 approved drugs that have the potential to be repurposed against 19 hub genes involved in metastasis-related processes. These 50 drugs were also found to be validated in different cancer cell lines, such as dasatinib, captopril, leflunomide, and dextromethorphan targeting SRC, MMP2, PTK2B, and RAC1 hub genes, respectively. These repurposed drugs potentially target metastasis, provide pharmacodynamic insight, and offer a window of opportunity for the development of much-needed antimetastatic drugs.
Collapse
Affiliation(s)
- Trishna Saha Detroja
- Cell Migration and Invasion Lab, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Drug Discovery Lab, Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel;
- Correspondence: (T.S.D.); (H.G.-H.)
| | - Hava Gil-Henn
- Cell Migration and Invasion Lab, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Correspondence: (T.S.D.); (H.G.-H.)
| | - Abraham O. Samson
- Drug Discovery Lab, Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel;
| |
Collapse
|
32
|
Abstract
Glycosaminoglycans (GAGs) are an important component of the tumor microenvironment (TME). GAGs can interact with a variety of binding partners and thereby influence cancer progression on multiple levels. GAGs can modulate growth factor and chemokine signaling, invasion and metastasis formation. Moreover, GAGs are able to change the physical property of the extracellular matrix (ECM). Abnormalities in GAG abundance and structure (e.g., sulfation patterns and molecular weight) are found across various cancer types and show biomarker potential. Targeting GAGs, as well as the usage of GAGs and their mimetics, are promising approaches to interfere with cancer progression. In addition, GAGs can be used as drug and cytokine carriers to induce an anti-tumor response. In this review, we summarize the role of GAGs in cancer and the potential use of GAGs and GAG derivatives to target cancer.
Collapse
Affiliation(s)
- Ronja Wieboldt
- Laboratories for Cancer Immunotherapy and Immunology, Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland
| | - Heinz Läubli
- Laboratories for Cancer Immunotherapy and Immunology, Department of Biomedicine, University Hospital and University of Basel, Switzerland; Division of Oncology, Department of Theragnostics, University Hospital Basel, Basel, Switzerland
| |
Collapse
|
33
|
Folic Acid Treatment Directly Influences the Genetic and Epigenetic Regulation along with the Associated Cellular Maintenance Processes of HT-29 and SW480 Colorectal Cancer Cell Lines. Cancers (Basel) 2022; 14:cancers14071820. [PMID: 35406592 PMCID: PMC8997840 DOI: 10.3390/cancers14071820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Folic acid (FA) participates in DNA synthesis and in DNA methylation; hence, it has a dual role in established neoplasms. We aimed to observe this phenomenon on FA-treated colorectal cancer cell lines (HT-29, SW480). Our results demonstrated that the maintenance processes, namely cell proliferation, cell viability, and DNA repair, were altered in HT-29 cells for short-term FA supplementation, while genetic and epigenetic regulations of SW480 cells were also affected. Despite the fact that FA is a precursor molecule in methyl donor formation, DNA methylation alterations were observed in both directions, primarily influencing the pathways of carcinogenesis. Moreover, behind the great number of differentially expressed genes, other FA-related effects than promoter methylation were suspected. All of our results point beyond the attributes related to FA so far. The different response of the two cell lines is worth considering in clinical practice to facilitate the effectiveness of therapy in the case of tumor heterogeneity. Abstract Folic acid (FA) is a synthetic form of vitamin B9, generally used as a nutritional supplement and an adjunctive medication in cancer therapy. FA is involved in genetic and epigenetic regulation; therefore, it has a dual modulatory role in established neoplasms. We aimed to investigate the effect of short-term (72 h) FA supplementation on colorectal cancer; hence, HT-29 and SW480 cells were exposed to different FA concentrations (0, 100, 10,000 ng/mL). HT-29 cell proliferation and viability levels elevated after 100 ng/mL but decreased for 10,000 ng/mL FA. Additionally, a significant (p ≤ 0.05) improvement of genomic stability was detected in HT-29 cells with micronucleus scoring and comet assay. Conversely, the FA treatment did not alter these parameters in SW480 samples. RRBS results highlighted that DNA methylation changes were bidirectional in both cells, mainly affecting carcinogenesis-related pathways. Based on the microarray analysis, promoter methylation status was in accordance with FA-induced expression alterations of 27 genes. Our study demonstrates that the FA effect was highly dependent on the cell type, which can be attributed to the distinct molecular background and the different expression of proliferation- and DNA-repair-associated genes (YWHAZ, HES1, STAT3, CCL2). Moreover, new aspects of FA-regulated DNA methylation and consecutive gene expression were revealed.
Collapse
|
34
|
Kanyo N, Kovács K, Kovács S, Béres B, Peter B, Székács I, Horvath R. Single-cell adhesivity distribution of glycocalyx digested cancer cells from high spatial resolution label-free biosensor measurements. Matrix Biol Plus 2022; 14:100103. [PMID: 35243300 PMCID: PMC8857652 DOI: 10.1016/j.mbplus.2022.100103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 12/01/2022] Open
Abstract
A high spatial resolution label-free biosensor monitors the adhesivity of cancer cells. Chondroitinase ABC was added to the adhering cells to digest their glycocalyx. Population level distributions of single-cell adhesivity were first recorded and analyzed. At relatively low and high concentration subpopulations were identified. The found subpopulations have remarkably large and weak adhesivities.
The glycocalyx is a cell surface sugar layer of most cell types that greatly influences the interaction of cells with their environment. Its components are glycolipids, glycoproteins, and oligosaccharides. Interestingly, cancer cells have a thicker glycocalyx layer compared to healthy cells, but to date, there has been no consensus in the literature on the exact role of cell surface polysaccharides and their derivatives in cellular adhesion and signaling. In our previous work we discovered that specific glycocalyx components of cancer cells regulate the kinetics and strength of adhesion on RGD (arginine-glycine-aspartic acid) peptide-coated surfaces [1]. Depending on the employed enzyme concentration digesting specific components both adhesion strengthening and weakening could be observed by monitoring the averaged behavior of thousands of cells. The enzyme chondroitinase ABC (ChrABC) was used to digest the chondroitin-4-sulfate, chondroitin-6-sulfate, and dermatan sulfate components in the glycocalyx of cancer cells. In the present work, a high spatial resolution label-free optical biosensor was employed to monitor the adhesivity of cancer cells both at the single-cell and population level. Population-level distributions of single-cell adhesivity were first recorded and analyzed when ChrABC was added to the adhering cells. At relatively low and high ChrABC concentrations subpopulations with remarkably large and weak adhesivity were identified. The changes in the adhesivity distribution due to the enzyme treatment were analyzed and the subpopulations most affected by the enzyme treatment were highlighted. The presented results open up new directions in glycocalyx related cell adhesion research and in the development of more meaningful targeted cancer treatments affecting adhesion.
Collapse
Affiliation(s)
- N. Kanyo
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
| | - K.D. Kovács
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
- ELTE Eötvös Loránd University, Department of Biological Physics, Budapest, Hungary
| | - S.V. Kovács
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
| | - B. Béres
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
| | - B. Peter
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
| | - I. Székács
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
| | - R. Horvath
- Nanobiosensorics Laboratory, ELKH EK MFA, Budapest, Hungary
- Corresponding author.
| |
Collapse
|
35
|
Kaur B, Mukhlis Y, Natesh J, Penta D, Musthapa Meeran S. Identification of hub genes associated with EMT-induced chemoresistance in breast cancer using integrated bioinformatics analysis. Gene 2022; 809:146016. [PMID: 34655723 DOI: 10.1016/j.gene.2021.146016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/17/2021] [Accepted: 10/11/2021] [Indexed: 02/07/2023]
Abstract
Chemoresistance is one of the major challenges in the treatment of breast cancer. Recent evidence suggests that epithelial-to-mesenchymal transition (EMT) plays a critical role in not only metastasis but also in chemoresistance, hence causing tumor relapse. This study aimed to identify the hub genes associated with EMT and chemoresistance in breast cancer affecting patient/clinical survival. Commonly differentially expressed genes (DEGs) during EMT and chemoresistance in breast cancer cells were identified using publicly available datasets, GSE23655, GSE39359, GSE33146 and GSE76540. Hierarchical clustering analysis was utilized to determine the commonly DEGs expression pattern in chemoresistant (CR) breast cancer cells. GSEA revealed that EMT-related genes sets were enriched in the CR samples. Further, we found that EMT-induced breast cancer cells showed overexpression of drug efflux transporters along with resistance to chemotherapeutic drug. Pathway enrichment analysis revealed that the commonly DEGs were enriched in immunological pathways, early endosome, protein dimerization, and proteoglycans in cancer. Further, we identified eight hub genes from the protein-protein interaction (PPI) network. We validated the gene expression levels of the hub genes among TCGA breast cancer samples using UALCAN. Survival analysis for the hub genes was performed using KM plotter, which showed a worse relapse-free survival (RFS) of the hub genes among breast cancer patients. In conclusion, this study identified eight hub genes that play an important role in the pathways underlying EMT-induced chemoresistance in breast cancer and can be used as therapeutic targets after clinical validation.
Collapse
Affiliation(s)
- Bhavjot Kaur
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
| | - Yahya Mukhlis
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jagadish Natesh
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dhanamjai Penta
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed Musthapa Meeran
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
36
|
Indications of Persistent Glycocalyx Damage in Convalescent COVID-19 Patients: A Prospective Multicenter Study and Hypothesis. Viruses 2021; 13:v13112324. [PMID: 34835130 PMCID: PMC8619155 DOI: 10.3390/v13112324] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/24/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022] Open
Abstract
The COVID-19 pandemic is caused by the SARS CoV-2 virus and can lead to severe lung damage and hyperinflammation. In the context of COVID-19 infection, inflammation-induced degradation of the glycocalyx layer in endothelial cells has been demonstrated. Syndecan-1 (SDC-1) is an established parameter for measuring glycocalyx injury. This prospective, multicenter, observational, cross-sectional study analyzed SDC-1 levels in 24 convalescent patients that had been infected with SARS-CoV-2 with mild disease course without need of hospitalization. We included 13 age-matched healthy individuals and 10 age-matched hospitalized COVID-19 patients with acute mild disease course as controls. In convalescent COVID-19 patients, significantly elevated SDC-1 levels were detected after a median of 88 days after symptom onset compared to healthy controls, whereas no difference was found when compared to SDC-1 levels of hospitalized patients undergoing acute disease. This study is the first to demonstrate signs of endothelial damage in non-pre-diseased, convalescent COVID-19 patients after mild disease progression without hospitalization. The data are consistent with studies showing evidence of persistent endothelial damage after severe or critical disease progression. Further work to investigate endothelial damage in convalescent COVID-19 patients should follow.
Collapse
|
37
|
Bertok T, Pinkova Gajdosova V, Bertokova A, Svecova N, Kasak P, Tkac J. Breast cancer glycan biomarkers: their link to tumour cell metabolism and their perspectives in clinical practice. Expert Rev Proteomics 2021; 18:881-910. [PMID: 34711108 DOI: 10.1080/14789450.2021.1996231] [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: 10/20/2022]
Abstract
INTRODUCTION Breast cancer (BCa) is the most common cancer type diagnosed in women and 5th most common cause of deaths among all cancer deaths despite the fact that screening program is at place. This is why novel diagnostics approaches are needed in order to decrease number of BCa cases and disease mortality. AREAS COVERED In this review paper, we aim to cover some basic aspects regarding cellular metabolism and signalling in BCa behind altered glycosylation. We also discuss novel exciting discoveries regarding glycan-based analysis, which can provide useful information for better understanding of the disease. The final part deals with clinical usefulness of glycan-based biomarkers and the clinical performance of such biomarkers is compared to already approved BCa biomarkers and diagnostic tools based on imaging. EXPERT OPINION Recent discoveries suggest that glycan-based biomarkers offer high accuracy for possible BCa diagnostics in blood, but also for better monitoring and management of BCa patients. The review article was written using Web of Science search engine to include articles published between 2019 and 2021.
Collapse
Affiliation(s)
- Tomas Bertok
- Glycanostics Ltd., Bratislava, Slovak Republic.,Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Veronika Pinkova Gajdosova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | | | - Natalia Svecova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kasak
- Center for Advanced Materials, Qatar University, Doha, Qatar
| | - Jan Tkac
- Glycanostics Ltd., Bratislava, Slovak Republic.,Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| |
Collapse
|
38
|
Liang ZQ, Gao L, Chen JH, Dai WB, Su YS, Chen G. Downregulation of the Coiled-Coil Domain Containing 80 and Its Perspective Mechanisms in Ovarian Carcinoma: A Comprehensive Study. Int J Genomics 2021; 2021:3752871. [PMID: 34820451 PMCID: PMC8608537 DOI: 10.1155/2021/3752871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/21/2021] [Accepted: 10/23/2021] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION We aimed to explore the downregulation of the coiled-coil domain containing 80 (CCDC80) and its underlying molecular mechanisms in ovarian carcinoma (OVCA). Materials/Methods. Immunohistochemical staining was performed to confirm the expression status of CCDC80 protein. Combining the data from in-house tissue microarrays and high-throughput datasets, we identified the expression level of CCDC80 in OVCA. We utilized cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm and single-sample gene set enrichment analysis (ssGSEA) to explore the relationship between CCDC80 and the tumor microenvironment (TME) landscape in OVCA. Pathway enrichment, function annotation, and transcription factor (TFs) exploration were conducted to study the latent molecular mechanisms. Moreover, the cell line data in the Genomics of Drug Sensitivity in Cancer (GDSC) database was used to discover the relationship between CCDC80 and drug sensitivity. RESULTS An integrated standard mean difference (SMD) of -0.919 (95% CI: -1.515-0.324, P = 0.002) identified the downregulation of CCDC80 in OVCA based on 1048 samples, and the sROC (AUC = 0.76) showed a moderate discriminatory ability of CCDC80 in OVCA. The fraction of infiltrating naive B cells showed significant differences between the high- and low-CCDC80 expression groups. Also, CCDC80-related genes are enriched in the Ras signaling pathway and metabolic of lipid. Nuclear receptor subfamily three group C member 1 (NR3C1) may be an upstream TF of CCDC80, and CCDC80 may be related to the sensitivity of mitocycin C and nilotinib. CONCLUSION CCDC80 was downregulated in OVCA and may play a role as a tumor suppressor in OVCA.
Collapse
Affiliation(s)
- Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Li Gao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| | - Jun-Hong Chen
- Department of Pathology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59. Xiangzhu Rd, Nanning, Guangxi Zhuang Autonomous Region 530003, China
| | - Wen-Bin Dai
- Department of Pathology, Liuzhou People's Hospital, NO.8, Wenchang Road, Chengzhong District, Liuzhou, Guangxi Zhuang Autonomous Region 545006, China
| | - Ya-Si Su
- Department of Pathology, Liuzhou People's Hospital, NO.8, Wenchang Road, Chengzhong District, Liuzhou, Guangxi Zhuang Autonomous Region 545006, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Rd, Nanning, Guangxi Zhuang Autonomous Region 530021, China
| |
Collapse
|
39
|
Schmitt M, Sinnberg T, Bratl K, Zittlau K, Garbe C, Macek B, Nalpas NC. Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. Mol Cell Proteomics 2021; 20:100163. [PMID: 34673281 PMCID: PMC8603206 DOI: 10.1016/j.mcpro.2021.100163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/04/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Analysis of nucleotide variants is a cornerstone of cancer medicine. Although only 2% of the genomic sequence is protein coding, mutations occurring in these regions have the potential to influence protein structure or modification status and may have severe impact on disease aetiology. Proteogenomics enables the analysis of sample-specific nonsynonymous nucleotide variants with regard to their effect at the proteome and phosphoproteome levels. Here, we developed a proof-of-concept proteogenomics workflow and applied it to the malignant melanoma cell line A375. Initially, we studied the resistance to serine/threonine-protein kinase B-raf (BRAF) inhibitor (BRAFi) vemurafenib in A375 cells. This allowed identification of several oncogenic nonsynonymous nucleotide variants, including a gain-of-function variant on aurora kinase A (AURKA) at F31I. We also detected significant changes in abundance among (phospho)proteins, which led to reactivation of the MAPK signaling pathway in BRAFi-resistant A375 cells. Upon reconstruction of the multiomic integrated signaling networks, we predicted drug therapies with the potential to disrupt BRAFi resistance mechanism in A375 cells. Notably, we showed that AURKA inhibition is effective and specific against BRAFi-resistant A375 cells. Subsequently, we investigated amino acid variants that interfere with protein posttranslational modification (PTM) status and potentially influence A375 cell signaling irrespective of BRAFi resistance. Mass spectrometry (MS) measurements confirmed variant-driven PTM changes in 12 proteins. Among them was the runt-related transcription factor 1 (RUNX1) displaying a variant on a known phosphorylation site S(Ph)276L. We confirmed the loss of phosphorylation site by MS and demonstrated the impact of this variant on RUNX1 interactome.
Collapse
Affiliation(s)
- Marisa Schmitt
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Tobias Sinnberg
- Division of Dermatooncology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany
| | - Katrin Bratl
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Katharina Zittlau
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Claus Garbe
- Division of Dermatooncology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany
| | - Boris Macek
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany.
| | - Nicolas C Nalpas
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany.
| |
Collapse
|
40
|
Integrated mRNA and miRNA Transcriptomic Analyses Reveals Divergent Mechanisms of Sunitinib Resistance in Clear Cell Renal Cell Carcinoma (ccRCC). Cancers (Basel) 2021; 13:cancers13174401. [PMID: 34503211 PMCID: PMC8430814 DOI: 10.3390/cancers13174401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Clear cell renal cell carcinoma (ccRCC) is a frequent cancer that causes more than 100,000 deaths every year. Treatment with drugs that target enzymes that help tumours grow such as sunitinib have greatly improved the prospects for ccRCC patients, however a large proportion of patients become resistant. We created sunitinib resistant cell lines and identified consequent changes in gene (and miRNA) expression by microarray analyses. Using this approach, we identified different pathways of resistance suggesting that tumour cells have many ways to overcome sunitinib treatment. We were able to overcome resistance in cells by inhibiting a protein, PD-L1, that is targeted by many immunotherapeutics currently in use for ccRCC patients suggesting a combination of immunotherapy and sunitinib may benefit patients. In addition, we identified miRNAs that are common to multiple resistance mechanisms suggesting they may be useful targets for future studies. Abstract The anti-angiogenic therapy sunitinib remains the standard first-line treatment for meta static clear cell renal cell carcinoma (ccRCC). However, acquired resistance develops in nearly all responsive patients and represents a major source of treatment failure. We used an integrated miRNA and mRNA transcriptomic approach to identify miRNA:target gene interactions involved in sunitinib resistance. Through the generation of stably resistant clones in three ccRCC cell lines (786-O, A498 and Caki-1), we identified non-overlapping miRNA:target gene networks, suggesting divergent mechanisms of sunitinib resistance. Surprisingly, even though the genes involved in these networks were different, they shared targeting by multiple members of the miR-17~92 cluster. In 786-O cells, targeted genes were related to hypoxia/angiogenic pathways, whereas, in Caki-1 cells, they were related to inflammatory/proliferation pathways. The immunotherapy target PD-L1 was consistently up-regulated in resistant cells, and we demonstrated that the silencing of this gene resulted in an increase in sensitivity to sunitinib treatment only in 786-O-resistant cells, suggesting that some ccRCC patients might benefit from combination therapy with PD-L1 checkpoint inhibitors. In summary, we demonstrate that, although there are clearly divergent mechanisms of sunitinib resistance in ccRCC subtypes, the commonality of miRNAs in multiple pathways could be targeted to overcome sunitinib resistance.
Collapse
|
41
|
Combinatorial therapy in tumor microenvironment: Where do we stand? Biochim Biophys Acta Rev Cancer 2021; 1876:188585. [PMID: 34224836 DOI: 10.1016/j.bbcan.2021.188585] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/28/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023]
Abstract
The tumor microenvironment plays a pivotal role in tumor initiation and progression by creating a dynamic interaction with cancer cells. The tumor microenvironment consists of various cellular components, including endothelial cells, fibroblasts, pericytes, adipocytes, immune cells, cancer stem cells and vasculature, which provide a sustained environment for cancer cell proliferation. Currently, targeting tumor microenvironment is increasingly being explored as a novel approach to improve cancer therapeutics, as it influences the growth and expansion of malignant cells in various ways. Despite continuous advancements in targeted therapies for cancer treatment, drug resistance, toxicity and immune escape mechanisms are the basis of treatment failure and cancer escape. Targeting tumor microenvironment efficiently with approved drugs and combination therapy is the solution to this enduring challenge that involves combining more than one treatment modality such as chemotherapy, surgery, radiotherapy, immunotherapy and nanotherapy that can effectively and synergistically target the critical pathways associated with disease pathogenesis. This review shed light on the composition of the tumor microenvironment, interaction of different components within tumor microenvironment with tumor cells and associated hallmarks, the current status of combinatorial therapies being developed, and various growing advancements. Furthermore, computational tools can also be used to monitor the significance and outcome of therapies being developed. We addressed the perceived barriers and regulatory hurdles in developing a combinatorial regimen and evaluated the present status of these therapies in the clinic. The accumulating depth of knowledge about the tumor microenvironment in cancer may facilitate further development of effective treatment modalities. This review presents the tumor microenvironment as a sweeping landscape for developing novel cancer therapies.
Collapse
|
42
|
ECM Remodeling in Squamous Cell Carcinoma of the Aerodigestive Tract: Pathways for Cancer Dissemination and Emerging Biomarkers. Cancers (Basel) 2021. [DOI: 10.3390/cancers13112759
expr 955442319 + 839973387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Squamous cell carcinomas (SCC) include a number of different types of tumors developing in the skin, in hollow organs, as well as the upper aerodigestive tract (UADT) including the head and neck region and the esophagus which will be dealt with in this review. These tumors are often refractory to current therapeutic approaches with poor patient outcome. The most important prognostic determinant of SCC tumors is the presence of distant metastasis, significantly correlating with low patient survival rates. Rapidly emerging evidence indicate that the extracellular matrix (ECM) composition and remodeling profoundly affect SSC metastatic dissemination. In this review, we will summarize the current knowledge on the role of ECM and its remodeling enzymes in affecting the growth and dissemination of UADT SCC. Taken together, these published evidence suggest that a thorough analysis of the ECM composition in the UADT SCC microenvironment may help disclosing the mechanism of resistance to the treatments and help defining possible targets for clinical intervention.
Collapse
|
43
|
ECM Remodeling in Squamous Cell Carcinoma of the Aerodigestive Tract: Pathways for Cancer Dissemination and Emerging Biomarkers. Cancers (Basel) 2021; 13:cancers13112759. [PMID: 34199373 PMCID: PMC8199582 DOI: 10.3390/cancers13112759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Local and distant metastasis of patients affected by squamous cell carcinoma of the upper aerodigestive tract predicts poor prognosis. In the latest years, the introduction of new therapeutic approaches, including targeted and immune therapies, has improved the overall survival. However, a large number of these patients do not benefit from these treatments. Thus, the identification of suitable prognostic and predictive biomarkers, as well as the discovery of new therapeutic targets have emerged as a crucial clinical need. In this context, the extracellular matrix represents a suitable target for the development of such therapeutic tools. In fact, the extracellular matrix is composed by complex molecules able to interact with a plethora of receptors and growth factors, thus modulating the dynamic crosstalk between cancer cells and the tumor microenvironment. In this review, we summarize the current knowledge of the role of the extracellular matrix in affecting squamous cell carcinoma growth and dissemination. Despite extracellular matrix is known to affect the development of many cancer types, only a restricted number of these molecules have been recognized to impact on squamous cell carcinoma progression. Thus, we consider that a thorough analysis of these molecules may be key to develop new potential therapeutic targets/biomarkers. Abstract Squamous cell carcinomas (SCC) include a number of different types of tumors developing in the skin, in hollow organs, as well as the upper aerodigestive tract (UADT) including the head and neck region and the esophagus which will be dealt with in this review. These tumors are often refractory to current therapeutic approaches with poor patient outcome. The most important prognostic determinant of SCC tumors is the presence of distant metastasis, significantly correlating with low patient survival rates. Rapidly emerging evidence indicate that the extracellular matrix (ECM) composition and remodeling profoundly affect SSC metastatic dissemination. In this review, we will summarize the current knowledge on the role of ECM and its remodeling enzymes in affecting the growth and dissemination of UADT SCC. Taken together, these published evidence suggest that a thorough analysis of the ECM composition in the UADT SCC microenvironment may help disclosing the mechanism of resistance to the treatments and help defining possible targets for clinical intervention.
Collapse
|
44
|
Karampoor S, Zahednasab H, Farahmand M, Mirzaei R, Zamani F, Tabibzadeh A, Bouzari B, Ajdarkosh H, Nikkhah M, Hashemi MR, Laali A, Keyvani H. A possible pathogenic role of Syndecan-1 in the pathogenesis of coronavirus disease 2019 (COVID-19). Int Immunopharmacol 2021; 97:107684. [PMID: 33932696 PMCID: PMC8052477 DOI: 10.1016/j.intimp.2021.107684] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023]
Abstract
A cell-surface heparan proteoglycan called Syndecan-1 (SDC-1) has multiple roles in healthy and pathogenic conditions, including respiratory viral infection. In this study, we explore the dynamic alternation in the levels of SDC-1 in cases with COVID-19. A total of 120 cases definitely diagnosed with COVID-19 were admitted to the Firoozgar Hospital, Tehran, Iran, from December 1, 2020, to January 29, 2021, and included in our study. Also, 58 healthy subjects (HS) were chosen as the control group. Patients were classified into two groups: 1) ICU patients and (63 cases) 2) non-ICU patients (57 cases). The dynamic changes of serum SCD-1, CRP, IL-6, IL-10, IL-18, and Vit D levels a well as the disease activity were investigated in three-time points (T1-T3). Our results indicated that the COVID-19 patients had significantly increased SCD-1, CRP, IL-6, IL-10, and IL-18 levels than in HS, while the Vit D levels in COVID-19 patients were significantly lower than HS. Further analysis demonstrated that the SCD-1, CRP, IL-6, IL-10, and IL-18 levels in ICU patients were significantly higher than in non-ICU patients. Tracking dynamic changes in the above markers indicated that on the day of admission, the SCD-1, CRP, IL-6, IL-10, and IL-18 levels were gradually increased on day 5 (T2) and then gradually decreased on day 10 (T3). ROC curve analysis suggests that markers mentioned above, SDC-1, IL-6, and IL-18 are valuable indicators in evaluating the activity of COVID-19. All in all, it seems that the serum SDC-1 levels alone or combined with other markers might be a good candidate for disease activity monitoring.
Collapse
Affiliation(s)
- Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Hamid Zahednasab
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Farahmand
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farhad Zamani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabibzadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Nikkhah
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Melika Razavi Hashemi
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Azadeh Laali
- Department of Infectious Disease, School of Medicine, Firoozgar General Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
45
|
Tsuchiya H, Shiota G. Immune evasion by cancer stem cells. Regen Ther 2021; 17:20-33. [PMID: 33778133 PMCID: PMC7966825 DOI: 10.1016/j.reth.2021.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/10/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022] Open
Abstract
Tumor immunity represents a new avenue for cancer therapy. Immune checkpoint inhibitors have successfully improved outcomes in several tumor types. In addition, currently, immune cell-based therapy is also attracting significant attention. However, the clinical efficacy of these treatments requires further improvement. The mechanisms through which cancer cells escape the immune response must be identified and clarified. Cancer stem cells (CSCs) play a central role in multiple aspects of malignant tumors. CSCs can initiate tumors in partially immunocompromised mice, whereas non-CSCs fail to form tumors, suggesting that tumor initiation is a definitive function of CSCs. However, the fact that non-CSCs also initiate tumors in more highly immunocompromised mice suggests that the immune evasion property may be a more fundamental feature of CSCs rather than a tumor-initiating property. In this review, we summarize studies that have elucidated how CSCs evade tumor immunity and create an immunosuppressive milieu with a focus on CSC-specific characteristics and functions. These profound mechanisms provide important clues for the development of novel tumor immunotherapies. Cancer stem cells (CSCs) play a central role in multiple aspects of malignant tumors. Immune evasion is a fundamental feature of CSCs. Immune evasion mechanisms must be precisely clarified to improve tumor immunotherapy. CSCs are promising targets for tumor immunotherapy.
Collapse
Key Words
- ADCC, antibody-dependent cell mediated cytotoxicity
- ALDH, alcohol dehydrogenase
- AML, acute myeloid leukemia
- ARID3B, AT-rich interaction domain-containing protein 3B
- CCR7, C–C motif chemokine receptor 7
- CIK, cytokine-induced killer cell
- CMV, cytomegalovirus
- CSC, cancer stem cell
- CTL, cytotoxic T lymphocytes
- CTLA-4, cytotoxic T-cell-associated antigen-4
- Cancer stem cells
- DC, dendritic cell
- DNMT, DNA methyltransferase
- EMT, epithelial–mesenchymal transition
- ETO, fat mass and obesity associated protein
- EV, extracellular vesicle
- HNSCC, head and neck squamous cell carcinoma
- Immune checkpoints
- Immune evasion
- KDM4, lysine-specific demethylase 4C
- KIR, killer immunoglobulin-like receptor
- LAG3, lymphocyte activation gene 3
- LILR, leukocyte immunoglobulin-like receptor
- LMP, low molecular weight protein
- LOX, lysyl oxidase
- MDSC, myeloid-derived suppressor cell
- MHC, major histocompatibility complex
- MIC, MHC class I polypeptide-related sequence
- NGF, nerve growth factor
- NK cells
- NK, natural killer
- NOD, nonobese diabetic
- NSG, NOD/SCID IL-2 receptor gamma chain null
- OCT4, octamer-binding transcription factor 4
- PD-1, programmed death receptor-1
- PD-L1/2, ligands 1/2
- PI9, protease inhibitor 9
- PSME3, proteasome activator subunit 3
- SCID, severe combined immunodeficient
- SOX2, sex determining region Y-box 2
- T cells
- TAM, tumor-associated macrophage
- TAP, transporter associated with antigen processing
- TCR, T cell receptor
- Treg, regulatory T cell
- ULBP, UL16 binding protein
- uPAR, urokinase-type plasminogen activator receptor
Collapse
|