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Southard KM, Ardy RC, Tang A, O’Sullivan DD, Metzner E, Guruvayurappan K, Norman TM. Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606073. [PMID: 39131349 PMCID: PMC11312553 DOI: 10.1101/2024.07.31.606073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Cell atlas projects have nominated recurrent transcriptional states as drivers of biological processes and disease, but their origins, regulation, and properties remain unclear. To enable complementary functional studies, we developed a scalable approach for recapitulating cell states in vitro using CRISPR activation (CRISPRa) Perturb-seq. Aided by a novel multiplexing method, we activated 1,836 transcription factors in two cell types. Measuring 21,958 perturbations showed that CRISPRa activated targets within physiological ranges, that epigenetic features predicted activatable genes, and that the protospacer seed region drove an off-target effect. Perturbations recapitulated in vivo fibroblast states, including universal and inflammatory states, and identified KLF4 and KLF5 as key regulators of the universal state. Inducing the universal state suppressed disease-associated states, highlighting its therapeutic potential. Our findings cement CRISPRa as a tool for perturbing differentiated cells and indicate that in vivo states can be elicited via perturbation, enabling studies of clinically relevant states ex vivo.
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Affiliation(s)
- Kaden M. Southard
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rico C. Ardy
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anran Tang
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deirdre D. O’Sullivan
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Eli Metzner
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Karthik Guruvayurappan
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Thomas M. Norman
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Li Z, Cai X. Baicalein targets STMN1 to inhibit the progression of nasopharyngeal carcinoma via regulating the Wnt/β-catenin pathway. ENVIRONMENTAL TOXICOLOGY 2024; 39:3003-3013. [PMID: 38317500 DOI: 10.1002/tox.24173] [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: 11/25/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUNDS Nasopharyngeal carcinoma is a common malignancy in the head and neck. Baicalein has been reported to exert the anticancer effects on various cancers. In this study, our aim was to explore the function of baicalein in the development of nasopharyngeal carcinoma and further investigate the potential underlying mechanisms. METHODS Cell Counting Kit (CCK)-8 assay, EdU assay, sphere formation assay, flow cytometry, and transwell invasion assay were conducted to determine cell proliferation, stemness, apoptosis, and invasion, respectively. Western blot was performed to examine the protein levels of PCNA, MMP9, STMN1, β-catenin, and Wnt3A. The mRNA level of STMN1 was assessed using real-time quantitative polymerase chain reaction (RT-qPCR). Xenograft tumor model was carried out to evaluate the effects of baicalein on tumor growth in vivo. Immunohistochemistry (IHC) assay was used to detect the levels of PCNA, MMP9, and STMN1 in tumor tissues from mice. RESULTS Baicalein significantly induced cell apoptosis and impeded cell proliferation, invasion, and stemness of nasopharyngeal carcinoma cells. STMN1 was highly expressed in nasopharyngeal carcinoma, and baicalein could directly downregulate STMN1 expression. STMN1 knockdown hampered the progression of nasopharyngeal carcinoma cells. Moreover, the effects of baicalein on cell proliferation, stemness, invasion, and apoptosis in nasopharyngeal carcinoma cells were harbored by STMN1 overexpression. Baicalein regulated STMN1 to inhibit the activation of the Wnt/β-catenin pathway. SKL2001, an agonist of the Wnt/β-catenin pathway, could reverse the effects of STMN1 knockdown on the progression of nasopharyngeal carcinoma. In addition, baicalein markedly impeded tumor growth in vivo. CONCLUSION Baicalein regulated the STMN1/Wnt/β-catenin pathway to restrain the development of nasopharyngeal carcinoma.
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Affiliation(s)
- Zheng Li
- Department of Otolaryngology, Nanyang First People's Hospital, Nanyang, China
| | - Xiaohang Cai
- The Second Department of Cardiology, Nanyang First People's Hospital, Nanyang, China
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Sugimori A, Omori I, Iwasawa O, Saito H, Nakajima H, Matsuno A, Sato S, Sumida H. Association of serum Ly6/PLAUR domain-containing protein 1 levels with skin sclerosis in systemic sclerosis. Sci Rep 2024; 14:5572. [PMID: 38448661 PMCID: PMC10918060 DOI: 10.1038/s41598-024-56221-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/04/2024] [Indexed: 03/08/2024] Open
Abstract
Systemic sclerosis (SSc) is a connective tissue disease characterized by aberrant immune activation, vascular injury, and fibrosis of the skin and internal organs. Ly6/PLAUR domain-containing protein 1 (LYPD1) was reported to be secreted and to have various physiological functions such as anti-angiogenic effects. Here we investigated serum LYPD1 levels in SSc patients and the association of serum LYPD1 levels with clinical features of SSc. Serum samples were obtained from 75 SSc patients and 22 healthy individuals as controls. We measured serum LYPD1 levels using enzyme-linked immunosorbent assay kits. Then, the relationship between serum LYPD1 levels and clinical features of SSc was analyzed. Serum LYPD1 levels in diffuse cutaneous SSc (dcSSc) patients were significantly higher than those in the limited cutaneous SSc (lcSSc) patients (median [25-75th percentiles], 1693.43 [1086.61-1917.57] vs. 904.55 [714.356-1285.56] pg/mL), while there were no significant differences in the serum LYPD1 levels between lcSSc and healthy controls (904.55 [714.356-1285.56] vs. 750.71 pg/mL [544.00-912.14]). Further analysis revealed that serum LYPD1 levels in patients correlated with skin thickness scores and serum interleukin (IL)-6 levels, which were known to reflect the extent of skin thickening in SSc. Moreover, serum LYPD1 levels showed a decrease with improvement in skin thickness after treatment, along with a decrease in serum IL-6 levels. These results indicate that LYPD1 might be a potential marker for monitoring skin sclerosis and evaluating the efficacy of skin fibrosis treatment in SSc patients.
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Affiliation(s)
- Ayaka Sugimori
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Issei Omori
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Okuto Iwasawa
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hinako Saito
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hibari Nakajima
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Ai Matsuno
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shinichi Sato
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hayakazu Sumida
- Department of Dermatology, Graduate School of Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
- Scleroderma Center, The University of Tokyo Hospital, Tokyo, Japan.
- SLE Center, The University of Tokyo Hospital, Tokyo, Japan.
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Li A, Gu L, He C, Li Y, Peng M, Liao J, Xiao R, Xu L, Guo S. GATA6 promotes fibrotic repair of tracheal injury through NLRP3 inflammasome-mediated epithelial pyroptosis. Int Immunopharmacol 2023; 123:110657. [PMID: 37531826 DOI: 10.1016/j.intimp.2023.110657] [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: 06/06/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
Tracheal injury is a challenging emergency condition that is characterized by the abnormal repair of the trachea. GATA6, a well-established transcription factor, plays a crucial role in tissue injury and epithelial regenerative repair. This study aims to evaluate the role of GATA6 in NF-κB-mediated NLRP3 inflammasome activation and pyroptosis after tracheal injury. Tracheal tissues and serum samples were collected from clinical patients and a rat model of tracheal injury. Upon GATA6 knockdown or overexpression, BEAS-2B and rat tracheal epithelial (RTE) cells were treated with lipopolysaccharides and nigericin before being co-cultured with primary tracheal fibroblasts. The changes of NLRP3 inflammasome activation and pyroptosis and their underlying mechanisms were detected. Additionally, the role of GATA6 downregulation in tracheal injury was verified in rats. GATA6 expression and NLRP3 inflammasome activation were upregulated following tracheal injury in the epithelium of granulation tissues. GATA6 silencing inhibited NLRP3 priming, NLRP3 inflammasome activation, and pyroptosis in BEAS-2B and RTE cells. Mechanistically, GATA6 was determined to have bound to the promoter region of NLRP3 and synergistically upregulated NLRP3 promoter activity with NF-κB. Furthermore, GATA6 overexpression promoted epithelial-mesenchymal transition via modulating the NF-κB/NLRP3 pathway. Epithelial NLRP3 inflammasome activation triggered ECM production in fibroblasts, which was suppressed by GATA6 knockdown and induced by GATA6 overexpression. Finally, the downregulation of GATA6 alleviated NLRP3 inflammasome-mediated pyroptosis induced by tracheal injury in rats, thereby reducing tracheal stenosis, inflammation, and fibrosis. GATA6 promotes fibrotic repair in tracheal injury through NLRP3 inflammasome-mediated epithelial pyroptosis, making it a potential biological therapeutic target for tracheal injury.
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Affiliation(s)
- Anmao Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Gu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunyan He
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yishi Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingyu Peng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiaxin Liao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Rui Xiao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuliang Guo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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