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Tang S, Wang Y, Luo R, Fang R, Liu Y, Xiang H, Ran P, Tong Y, Sun M, Tan S, Huang W, Huang J, Lv J, Xu N, Yao Z, Zhang Q, Xu Z, Yue X, Yu Z, Akesu S, Ding Y, Xu C, Lu W, Zhou Y, Hou Y, Ding C. Proteomic characterization identifies clinically relevant subgroups of soft tissue sarcoma. Nat Commun 2024; 15:1381. [PMID: 38360860 PMCID: PMC10869728 DOI: 10.1038/s41467-024-45306-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024] Open
Abstract
Soft tissue sarcoma is a broad family of mesenchymal malignancies exhibiting remarkable histological diversity. We portray the proteomic landscape of 272 soft tissue sarcomas representing 12 major subtypes. Hierarchical classification finds the similarity of proteomic features between angiosarcoma and epithelial sarcoma, and elevated expression of SHC1 in AS and ES is correlated with poor prognosis. Moreover, proteomic clustering classifies patients of soft tissue sarcoma into 3 proteomic clusters with diverse driven pathways and clinical outcomes. In the proteomic cluster featured with the high cell proliferation rate, APEX1 and NPM1 are found to promote cell proliferation and drive the progression of cancer cells. The classification based on immune signatures defines three immune subtypes with distinctive tumor microenvironments. Further analysis illustrates the potential association between immune evasion markers (PD-L1 and CD80) and tumor metastasis in soft tissue sarcoma. Overall, this analysis uncovers sarcoma-type-specific changes in proteins, providing insights about relationships of soft tissue sarcoma.
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Affiliation(s)
- Shaoshuai Tang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yufeng Liu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hang Xiang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Peng Ran
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Yexin Tong
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Mingjun Sun
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Subei Tan
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiacheng Lv
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Ning Xu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Zhenmei Yao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Qiao Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Ziyan Xu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Xuetong Yue
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuqin Ding
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Medical Imaging, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Weiqi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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Saadeldin MK, Shawer H, Mostafa A, Kassem NM, Amleh A, Siam R. New genetic variants of LATS1 detected in urinary bladder and colon cancer. Front Genet 2015; 5:425. [PMID: 25628642 PMCID: PMC4292772 DOI: 10.3389/fgene.2014.00425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/19/2014] [Indexed: 11/13/2022] Open
Abstract
LATS1, the large tumor suppressor 1 gene, encodes for a serine/threonine kinase protein and is implicated in cell cycle progression. LATS1 is down-regulated in various human cancers, such as breast cancer, and astrocytoma. Point mutations in LATS1 were reported in human sarcomas. Additionally, loss of heterozygosity of LATS1 chromosomal region predisposes to breast, ovarian, and cervical tumors. In the current study, we investigated LATS1 genetic variations including single nucleotide polymorphisms (SNPs), in 28 Egyptian patients with either urinary bladder or colon cancers. The LATS1 gene was amplified and sequenced and the expression of LATS1 at the RNA level was assessed in 12 urinary bladder cancer samples. We report, the identification of a total of 29 variants including previously identified SNPs within LATS1 coding and non-coding sequences. A total of 18 variants were novel. Majority of the novel variants, 13, were mapped to intronic sequences and un-translated regions of the gene. Four of the five novel variants located in the coding region of the gene, represented missense mutations within the serine/threonine kinase catalytic domain. Interestingly, LATS1 RNA steady state levels was lost in urinary bladder cancerous tissue harboring four specific SNPs (16045 + 41736 + 34614 + 56177) positioned in the 5'UTR, intron 6, and two silent mutations within exon 4 and exon 8, respectively. This study identifies novel single-base-sequence alterations in the LATS1 gene. These newly identified variants could potentially be used as novel diagnostic or prognostic tools in cancer.
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Affiliation(s)
- Mona K Saadeldin
- Biotechnology Department, American University in Cairo New Cairo, Egypt
| | - Heba Shawer
- Biotechnology Department, American University in Cairo New Cairo, Egypt
| | - Ahmed Mostafa
- National Cancer Institute, Cairo University New Cairo, Egypt
| | - Neemat M Kassem
- Clinical Pathology Department, Cairo University New Cairo, Egypt
| | - Asma Amleh
- Biotechnology Department, American University in Cairo New Cairo, Egypt ; Biology Department, American University in Cairo New Cairo, Egypt
| | - Rania Siam
- Biotechnology Department, American University in Cairo New Cairo, Egypt ; Biology Department, American University in Cairo New Cairo, Egypt ; YJ-Science and Technology Research Center, American University in Cairo New Cairo, Egypt
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Ono H, Yoshikawa H, Ueda T, Yamamura H, Kudawara I, Manou M, Ishiguro S, Funai H, Koyanagi Y, Araki N, Hashimoto N, Sonobe H, Tatsuta M, Takahashi K. Expression of smooth muscle calponin in synovial sarcoma. Sarcoma 2011; 3:107-13. [PMID: 18521272 PMCID: PMC2395415 DOI: 10.1080/13577149977730] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Purpose. Histogenesis of synovial sarcoma remains controversial and reliable molecular markers for diagnosis are necessary. Expression of basic calponin, a smooth muscle differentiation-specific actin-binding protein, was studied in synovial sarcoma.Subjects and Methods. The basic calponin gene and the gene product were analyzed by reverse transcription PCR analysis (RT-PCR) and immunohistochemistry in 14 synovial sarcomas and a human synovial sarcoma cell line (HS-SY-II).Results and Discussion. Immunoreactivity for basic calponin was detected in the cytoplasm of 6 synovial sarcomas (43% positive). In the basic calponin-positive tumors and the HS-SY-II cells, expression for smooth muscle-specific genes, including basic calponin and SM22alpha , was detected by RT-PCR, suggesting a lineage relationship between synovial sarcoma cells and smooth muscle-like mesenchymal cells.Conclusions. A subset of synovial sarcomas expressing the basic calponin gene and the gene product were identified. The basic calponin may have potential utility as a novel molecular marker identifying certain synovial sarcomas.
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Affiliation(s)
- H Ono
- Department of Orthopaedic Surgery Osaka Medical Center for Cancer and Cardiovascular Diseases 1-3-3, Nakamichi Higashinari-ku Osaka 537-8511 Japan
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Hisaoka M, Wei-Qi S, Jian W, Morio T, Hashimoto H. Specific but variable expression of h-caldesmon in leiomyosarcomas: an immunohistochemical reassessment of a novel myogenic marker. Appl Immunohistochem Mol Morphol 2001; 9:302-8. [PMID: 11759055 DOI: 10.1097/00129039-200112000-00003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
h-Caldesmon is considered a novel specific marker for tumors with smooth muscle differentiation. To reassess its diagnostic use, the authors evaluated the immunohistochemical expression of h-caldesmon and other myogenic markers (calponin, alpha-smooth muscle actin, HHF35, and desmin) in 30 leiomyosarcomas (external soft tissues [15], retroperitoneum [8], uterus [5], other sites [2]), 26 myofibroblastic lesions, and 26 fibrohistiocytic tumors of varying biologic potential and histology. In contrast with previous data, h-caldesmon was expressed only in 11 (36%) of the 30 leiomyosarcomas analyzed, whereas they consistently expressed actins and frequently expressed calponin (86%) and desmin (76%). Leiomyosarcomas with the expression of h-caldesmon were well or moderately differentiated and primarily confined to the retroperitoneum or uterus. All but one leiomyosarcomas in the external soft tissues examined were negative for h-caldesmon, and the h-caldesmon-negative tumors showed moderately to poorly differentiated morphology. All myofibroblastic lesions examined were negative for h-caldesmon despite their constant expressions of at least one of the other markers. h-Caldesmon was not expressed in fibrohistiocytic tumors either, although focal positivity for the other markers was seen in subsets of the tumors. Thus, h-caldesmon can be regarded as a specific myogenic marker. However, one should be aware that the expression of h-caldesmon in leiomyosarcomas can be more variable according to their locations and/or extent of smooth muscle differentiation than considered previously.
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Affiliation(s)
- M Hisaoka
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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Tazawa K, Tsukada K, Makuuchi H, Tsutsumi Y. An immunohistochemical and clinicopathological study of gastrointestinal stromal tumors. Pathol Int 1999; 49:786-98. [PMID: 10504550 DOI: 10.1046/j.1440-1827.1999.00947.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Immunohistochemical and clinicopathological features of 58 gastrointestinal stromal tumors (GIST) were studied. One occurred in the esophagus, 41 in the stomach, nine in the small intestine, and seven in the large intestine. By using indirect immunoperoxidase staining for Cajal cell markers (c-kit protein and CD34), smooth muscle markers (alpha-smooth muscle actin, desmin, heavy caldesmon and calponin) and Schwann cell markers (S-100 protein and Leu 7), GIST were classified into five groups, such as Cajal cell type (n = 9), myogenic type (n = 5), Schwann cell type (n = 2), mixed cell type (n = 40) and undifferentiated type (n = 2). c-kit Protein (42/58; 72%) and CD34 (45/58; 78%) were commonly and diffusely expressed in GIST. Novel smooth muscle markers, caldesmon (29/58; 50%) and calponin (18/58; 31%), were useful in detecting myogenic characters of GIST. S-100 protein was expressed in 16 (28%) tumors, two of which were also reactive with Leu 7 (CD57). Three small bowel tumors with skeinoid fibers expressed the Cajal cell markers, and were categorizable in GIST. Clinicopathological analyses using aggressive (n = 21) and non-aggressive (n = 21) GIST indicated that the malignant potential was correlated with the intestinal location, large tumor size, high cellularity, necrosis, solid (non-interlacing bundled) pattern of growth, negativity of c-kit protein and/or CD34, high mitotic count, and high MIB-1 labeling.
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Affiliation(s)
- K Tazawa
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
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