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Gardner EE, Earlie EM, Li K, Thomas J, Hubisz MJ, Stein BD, Zhang C, Cantley LC, Laughney AM, Varmus H. Lineage-specific intolerance to oncogenic drivers restricts histological transformation. Science 2024; 383:eadj1415. [PMID: 38330136 PMCID: PMC11155264 DOI: 10.1126/science.adj1415] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/08/2023] [Indexed: 02/10/2024]
Abstract
Lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC) are thought to originate from different epithelial cell types in the lung. Intriguingly, LUAD can histologically transform into SCLC after treatment with targeted therapies. In this study, we designed models to follow the conversion of LUAD to SCLC and found that the barrier to histological transformation converges on tolerance to Myc, which we implicate as a lineage-specific driver of the pulmonary neuroendocrine cell. Histological transformations are frequently accompanied by activation of the Akt pathway. Manipulating this pathway permitted tolerance to Myc as an oncogenic driver, producing rare, stem-like cells that transcriptionally resemble the pulmonary basal lineage. These findings suggest that histological transformation may require the plasticity inherent to the basal stem cell, enabling tolerance to previously incompatible oncogenic driver programs.
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Affiliation(s)
| | - Ethan M. Earlie
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Kate Li
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Jerin Thomas
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Melissa J. Hubisz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY
| | - Benjamin D. Stein
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine
| | - Chen Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine
| | - Ashley M. Laughney
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Harold Varmus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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Chen C, Cai H, Shen J, Zhang X, Peng W, Li C, Lv H, Wen T. Exploration of a hypoxia-immune-related microenvironment gene signature and prediction model for hepatitis C-induced early-stage fibrosis. J Transl Med 2024; 22:116. [PMID: 38287425 PMCID: PMC10826039 DOI: 10.1186/s12967-024-04912-6] [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: 08/26/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Liver fibrosis contributes to significant morbidity and mortality in Western nations, primarily attributed to chronic hepatitis C virus (HCV) infection. Hypoxia and immune status have been reported to be significantly correlated with the progression of liver fibrosis. The current research aimed to investigate the gene signature related to the hypoxia-immune-related microenvironment and identify potential targets for liver fibrosis. METHOD Sequencing data obtained from GEO were employed to assess the hypoxia and immune status of the discovery set utilizing UMAP and ESTIMATE methods. The prognostic genes were screened utilizing the LASSO model. The infiltration level of 22 types of immune cells was quantified utilizing CIBERSORT, and a prognosis-predictive model was established based on the selected genes. The model was also verified using qRT-PCR with surgical resection samples and liver failure samples RNA-sequencing data. RESULTS Elevated hypoxia and immune status were linked to an unfavorable prognosis in HCV-induced early-stage liver fibrosis. Increased plasma and resting NK cell infiltration were identified as a risk factor for liver fibrosis progression. Additionally, CYP1A2, CBS, GSTZ1, FOXA1, WDR72 and UHMK1 were determined as hypoxia-immune-related protective genes. The combined model effectively predicted patient prognosis. Furthermore, the preliminary validation of clinical samples supported most of the conclusions drawn from this study. CONCLUSION The prognosis-predictive model developed using six hypoxia-immune-related genes effectively predicts the prognosis and progression of liver fibrosis. The current study opens new avenues for the future prediction and treatment of liver fibrosis.
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Affiliation(s)
- Chuwen Chen
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China
| | - Haozheng Cai
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China
| | - Junyi Shen
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China
| | - Xiaoyun Zhang
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China
| | - Wei Peng
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China
| | - Chuan Li
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China
| | - Haopeng Lv
- Department of General Surgery, ChengDu Shi Xinjin Qu Renmin Yiyuan: People's Hospital of Xinjin District, Chengdu, China
| | - Tianfu Wen
- Division of Liver Surgery, Department of General Surgery, West China Hospital, Si Chuan University, Chengdu, 610041, China.
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Kim YJ, Zhang H, Lee Y, Seymen F, Koruyucu M, Kasimoglu Y, Simmer JP, Hu JCC, Kim JW. Novel WDR72 Mutations Causing Hypomaturation Amelogenesis Imperfecta. J Pers Med 2023; 13:326. [PMID: 36836560 PMCID: PMC9965932 DOI: 10.3390/jpm13020326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Amelogenesis imperfecta (AI) is a heterogeneous collection of hereditary enamel defects. The affected enamel can be classified as hypoplastic, hypomaturation, or hypocalcified in form. A better understanding of normal amelogenesis and improvements in our ability to diagnose AI through genetic testing can be realized through more complete knowledge of the genes and disease-causing variants that cause AI. In this study, mutational analysis was performed with whole exome sequencing (WES) to identify genetic etiology underlying the hypomaturation AI condition in affected families. Mutational analyses identified biallelic WDR72 mutations in four hypomaturation AI families. Novel mutations include a homozygous deletion and insertion mutation (NM_182758.4: c.2680_2699delinsACTATAGTT, p.(Ser894Thrfs*15)), compound heterozygous mutations (paternal c.2332dupA, p.(Met778Asnfs*4)) and (maternal c.1287_1289del, p.(Ile430del)) and a homozygous 3694 bp deletion that includes exon 14 (NG_017034.2:g.96472_100165del). A homozygous recurrent mutation variant (c.1467_1468delAT, p.(Val491Aspfs*8)) was also identified. Current ideas on WDR72 structure and function are discussed. These cases expand the mutational spectrum of WDR72 mutations causing hypomaturation AI and improve the possibility of genetic testing to accurately diagnose AI caused by WDR72 defects.
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Affiliation(s)
- Youn Jung Kim
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - Hong Zhang
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yejin Lee
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
| | - Figen Seymen
- Department of Paediatric Dentistry, Faculty of Dentistry, Altinbas University, Istanbul 34147, Turkey
| | - Mine Koruyucu
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul 34116, Turkey
| | - Yelda Kasimoglu
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Istanbul 34116, Turkey
| | - James P. Simmer
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jan C.-C. Hu
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jung-Wook Kim
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Genetics & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
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