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Wu M, Tao H, Xu T, Zheng X, Wen C, Wang G, Peng Y, Dai Y. Spatial proteomics: unveiling the multidimensional landscape of protein localization in human diseases. Proteome Sci 2024; 22:7. [PMID: 39304896 DOI: 10.1186/s12953-024-00231-2] [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: 04/29/2024] [Accepted: 09/01/2024] [Indexed: 09/22/2024] Open
Abstract
Spatial proteomics is a multidimensional technique that studies the spatial distribution and function of proteins within cells or tissues across both spatial and temporal dimensions. This field multidimensionally reveals the complex structure of the human proteome, including the characteristics of protein spatial distribution, dynamic protein translocation, and protein interaction networks. Recently, as a crucial method for studying protein spatial localization, spatial proteomics has been applied in the clinical investigation of various diseases. This review summarizes the fundamental concepts and characteristics of tissue-level spatial proteomics, its research progress in common human diseases such as cancer, neurological disorders, cardiovascular diseases, autoimmune diseases, and anticipates its future development trends. The aim is to highlight the significant impact of spatial proteomics on understanding disease pathogenesis, advancing diagnostic methods, and developing potential therapeutic targets in clinical research.
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Affiliation(s)
- Mengyao Wu
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Huihui Tao
- School of Medicine, Anhui University of Science & Technology, Huainan, China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Huainan, China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Huainan, China.
| | - Tiantian Xu
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Xuejia Zheng
- The First Hospital of Anhui University of Science and Technology, Huainan, China
| | - Chunmei Wen
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Guoying Wang
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Yali Peng
- School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Yong Dai
- School of Medicine, Anhui University of Science & Technology, Huainan, China
- The First Hospital of Anhui University of Science and Technology, Huainan, China
- Joint Research Center for Occupational Medicine and Health of IHM, Anhui University of Science and Technology, Huainan, China
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Yang L, Gilbertsen A, Jacobson B, Kratzke R, Henke CA. Serum Splicing Factor Proline- and Glutamine-Rich Is a Diagnostic Marker for Non-Small-Cell Lung Cancer and Other Solid Cancers. Int J Mol Sci 2024; 25:8766. [PMID: 39201453 PMCID: PMC11354699 DOI: 10.3390/ijms25168766] [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: 07/02/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Cancer markers are measurable molecules in blood or tissues that are produced by tumor cells or immune cells in response to cancer progression. They play an important role in clinical diagnosis, prognosis, and therapy monitoring. Splicing factor proline- and glutamine-rich (SFPQ) plays an important role in cancer growth and metastasis. SFPQ is not only more highly expressed in non-small-cell lung cancer (NSCLC) cells than it is in controls, but also highly expressed in cancer cells in patients with other solid cancers. Thus, a new enzyme-linked immunosorbent assay (ELISA) for detecting SFPQ was developed, in which the SFPQ protein is trapped by the first specific mAb coated on a microplate, and then recognized by a second specific mAb. This assay allows for the specific detection of SFPQ in the serum of patients with solid cancer. Regarding NSCLC, the serum SFPQ levels distinguished the non-cancer controls from the patients with NSCLC, with an area under the curve of 0.876, a sensitivity of 87%, and a specificity of 94%. The serum SFPQ levels were significantly elevated in the patients with NSCLC or other solid cancers. In conclusion, serum SFPQ could be a promising novel diagnostic biomarker for NSCLC and other malignancies.
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Affiliation(s)
- Libang Yang
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (A.G.)
| | - Adam Gilbertsen
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (A.G.)
| | - Blake Jacobson
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (B.J.); (R.K.)
| | - Robert Kratzke
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (B.J.); (R.K.)
| | - Craig A. Henke
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; (A.G.)
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [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: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Lodewijk I, Dueñas M, Paramio JM, Rubio C. CD44v6, STn & O-GD2: promising tumor associated antigens paving the way for new targeted cancer therapies. Front Immunol 2023; 14:1272681. [PMID: 37854601 PMCID: PMC10579806 DOI: 10.3389/fimmu.2023.1272681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/14/2023] [Indexed: 10/20/2023] Open
Abstract
Targeted therapies are the state of the art in oncology today, and every year new Tumor-associated antigens (TAAs) are developed for preclinical research and clinical trials, but few of them really change the therapeutic scenario. Difficulties, either to find antigens that are solely expressed in tumors or the generation of good binders to these antigens, represent a major bottleneck. Specialized cellular mechanisms, such as differential splicing and glycosylation processes, are a good source of neo-antigen expression. Changes in these processes generate surface proteins that, instead of showing decreased or increased antigen expression driven by enhanced mRNA processing, are aberrant in nature and therefore more specific targets to elicit a precise anti-tumor therapy. Here, we present promising TAAs demonstrated to be potential targets for cancer monitoring, targeted therapy and the generation of new immunotherapy tools, such as recombinant antibodies and chimeric antigen receptor (CAR) T cell (CAR-T) or Chimeric Antigen Receptor-Engineered Natural Killer (CAR-NK) for specific tumor killing, in a wide variety of tumor types. Specifically, this review is a detailed update on TAAs CD44v6, STn and O-GD2, describing their origin as well as their current and potential use as disease biomarker and therapeutic target in a diversity of tumor types.
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Affiliation(s)
- Iris Lodewijk
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Marta Dueñas
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Jesus M. Paramio
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Carolina Rubio
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
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Yang L, Gilbertsen A, Jacobson B, Pham J, Fujioka N, Henke CA, Kratzke RA. SFPQ and Its Isoform as Potential Biomarker for Non-Small-Cell Lung Cancer. Int J Mol Sci 2023; 24:12500. [PMID: 37569873 PMCID: PMC10419845 DOI: 10.3390/ijms241512500] [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: 07/12/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Cancer markers are measurable molecules in the blood or tissue that are produced by tumor cells or immune cells in response to cancer progression. They play an important role in clinical diagnosis, prognosis, and anti-drug monitoring. Although DNA, RNA, and even physical images have been used, proteins continue to be the most common marker. There are currently no specific markers for lung cancer. Metastatic lung cancer, particularly non-small-cell lung cancer (NSCLC), is one of the most common causes of death. SFPQ, YY1, RTN4, RICTOR, LARP6, and HELLS are expressed at higher levels in cells from NSCLC than in control or cells from inflammatory diseases. SFPQ shows the most difference between the three cell types. Furthermore, the cytoplasmic isoform of SFPQ is only found in advanced cancers. We have developed ELISAs to detect SFPQ and the long and short isoforms. Evidence has shown that the short isoform exists primarily in cancers. Furthermore, immunocytometry studies and IHC analysis have revealed that SFPQ levels are consistent with ELISA results. In addition, enhanced DNA methylation in the SFPQ gene may facilitate the SFPQ expression differences between control and cancer cells. Considering this, elevated SFPQ level and the isoform location could serve as a cancer diagnostic and prognostic marker.
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Affiliation(s)
- Libang Yang
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (L.Y.); (A.G.); (C.A.H.)
| | - Adam Gilbertsen
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (L.Y.); (A.G.); (C.A.H.)
| | - Blake Jacobson
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (B.J.); (N.F.)
| | - Jenny Pham
- Clinical and Translational Science Institute, School of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA;
| | - Naomi Fujioka
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (B.J.); (N.F.)
| | - Craig A. Henke
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (L.Y.); (A.G.); (C.A.H.)
| | - Robert A. Kratzke
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; (B.J.); (N.F.)
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Li Y, Nie J, Deng C, Li H. P-15 promotes chondrocyte proliferation in osteoarthritis by regulating SFPQ to target the Akt-RUNX2 axis. J Orthop Surg Res 2023; 18:199. [PMID: 36915153 PMCID: PMC10012506 DOI: 10.1186/s13018-023-03658-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/28/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND The disruption of chondrocyte proliferation and differentiation is a critical event during the process of joint injury in osteoarthritis (OA). P-15 peptides could bind to integrin receptors on various precursor cells, promote cell adhesion, release growth factors, and promote the differentiation of osteoblast precursor cells. However, the role of P-15 in OA, particularly in chondrocyte proliferation, is not fully understood. METHODS The activity of SFPQ and RUNX2 in the bone tissue of patients with osteoarthritis was analyzed using quantitative real-time polymerase chain reaction (qRT-PCR). Interleukin-1β (IL-1β) inducer was performed to establish an in vitro model of OA. Cell proliferation was measured by CCK-8 assay. The expressions of COL2a1, ACAN, COMP, SOX9, and BMP2 related to cartilage differentiation were detected using qRT-PCR. In addition, the expression levels of SFPQ, AKT, p-AKT, and RUNX2 were detected using Western blotting. RESULTS The results showed that the expression of SFPQ was significantly decreased and the expression of RUNX2 was significantly increased in osteoarthritis cartilage tissue. P-15 peptide reversed IL-1β-induced cell proliferation obstruction and alleviated chondrocyte damage. Furthermore, P-15 polypeptide increased the expression levels of cartilage differentiation genes COL2a1, ACAN, and BMP2, while decreasing the expression of COMP and SOX9 in an inverse dose-dependent manner. Then specific interfering RNA proved that P-15 maintains chondrocyte stability and is associated with the SFPQ gene. Finally, we confirmed that P-15 inhibited the Akt-RUNX2 pathway, which is regulated in the expression of SFPQ. CONCLUSIONS P-15 can mitigate chondrocyte damage and osteoarthritis progression by inhibiting cell death and modulating SFPQ-Akt-RUNX2 pathway, offering an opportunity to develop new strategies for the treatment of osteoarthritis.
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Affiliation(s)
- Yuanli Li
- Affiliated Hospital of North Sichuan Medical College, 1 Maoyuan South Road, Shunqing District, Nanchong, 637000, Sichuan, China.
| | - Junlan Nie
- Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Changgong Deng
- Anatomy Teaching and Research Section, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Hong Li
- Affiliated Hospital of North Sichuan Medical College, 1 Maoyuan South Road, Shunqing District, Nanchong, 637000, Sichuan, China
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Rothzerg E, Feng W, Song D, Li H, Wei Q, Fox A, Wood D, Xu J, Liu Y. Single-Cell Transcriptome Analysis Reveals Paraspeckles Expression in Osteosarcoma Tissues. Cancer Inform 2022; 21:11769351221140101. [PMID: 36507075 PMCID: PMC9730017 DOI: 10.1177/11769351221140101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
Nuclear paraspeckles are subnuclear bodies contracted by nuclear-enriched abundant transcript 1 (NEAT1) long non-coding RNA, localised in the interchromatin space of mammalian cell nuclei. Paraspeckles have been critically involved in tumour progression, metastasis and chemoresistance. To this date, there are limited findings to suggest that paraspeckles, NEAT1 and heterogeneous nuclear ribonucleoproteins (hnRNPs) directly or indirectly play roles in osteosarcoma progression. Herein, we analysed NEAT1, paraspeckle proteins (SFPQ, PSPC1 and NONO) and hnRNP members (HNRNPK, HNRNPM, HNRNPR and HNRNPD) gene expression in 6 osteosarcoma tumour tissues using the single-cell RNA-sequencing method. The normalised data highlighted that the paraspeckles transcripts were highly abundant in osteoblastic OS cells, except NEAT1, which was highly expressed in myeloid cell 1 and 2 subpopulations.
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Affiliation(s)
- Emel Rothzerg
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Perron Institute for Neurological and Translational Science, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Wenyu Feng
- Department of Orthopaedics, Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Dezhi Song
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Orthopaedics, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hengyuan Li
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Orthopedics, Centre for Orthopedic Research, Second Affiliated Hospital, School of Medicine, Orthopedics Research Institute, Zhejiang University, Hangzhou, China
| | - Qingjun Wei
- Department of Orthopaedics, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Archa Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - David Wood
- Medical School, The University of Western Australia, Perth, WA, Australia
| | - Jiake Xu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Jiake Xu, School of Biomedical Sciences, The University of Western Australia, 35 Stirling Hwy, Perth, WA 6009, Australia.
| | - Yun Liu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Orthopaedics, First Affiliated Hospital of Guangxi Medical University, Nanning, China,Yun Liu, School of Biomedical Sciences, The University of Western Australia, 35 Stirling Hwy, Perth, WA 6009, Australia.
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