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Yang W, Zhao X, Zheng A, Liu Z, Ma J, Zhang X, Li W, Wang D, Zhu J, Tao H, Zhang Y, Ma T, Liu Q. Identification of MET fusions in solid tumors: A multicenter, large scale study in China. Int J Cancer 2023; 152:1259-1268. [PMID: 36408924 DOI: 10.1002/ijc.34361] [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: 07/24/2022] [Revised: 10/15/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022]
Abstract
MET amplification and exon 14 skipping are well known as oncogenic drivers in multiple cancer types. However, MET fusions in most cancer types are poorly defined. To explore the profile and analyze the characteristics of MET fusions, a large-cohort study was conducted to screen MET fusions in clinical samples (n = 10 882) using DNA-based NGS. A total of 37 potentially functional MET fusions containing the intact tyrosine kinase domain (TKD) of MET were identified in 36 samples. Further, 15 novel MET fusions were identified in five cancer types, and the incidence of novel MET fusions accounted for 40.5% (15/37). Brain cancer had the highest incidence of MET fusion, with PTPRZ1-MET as the most common fusion (37.0%). All MET breakpoints in brain cancer (n = 27) were also located in intron 1, while those in lung cancer (n = 4) occurred in intron 1, intron 11, intron 14 and exon 14, respectively. The positive consistency of the common fusion group was 100% (11/11), while that of the rare fusion group was 53.8% (7/13). In conclusion, we provided a comprehensive genomic landscape of MET rearrangement and updated the MET fusions database for clinical test. In addition, we revealed that DNA-based NGS might serve as the clinical test for common MET fusions; however, rare MET fusions must be validated by both DNA-based NGS and RNA-based NGS. Prospective trials are necessary to confirm the treatment efficacy of MET inhibitors.
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Affiliation(s)
- Wenhui Yang
- Department of Digestive Oncology, Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ximeng Zhao
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Aiwen Zheng
- Department of Gynecologic Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jie Ma
- Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xiang Zhang
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Wei Li
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Dan Wang
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Jianhua Zhu
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | | | - Tonghui Ma
- Jichenjunchuang Clinical Laboratory, Hangzhou, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital Central South University, Changsha, China
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Kalikiri MKR, Manjunath HS, Vempalli FR, Mathew LS, Liu L, Wang L, Wang G, Wang K, Soloviov O, Lorenz S, Tomei S. Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood. Sci Rep 2023; 13:3598. [PMID: 36869090 PMCID: PMC9984369 DOI: 10.1038/s41598-023-30629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptome profiling of human whole blood is used to discover biomarkers of diseases and to assess phenotypic traits. Recently, finger-stick blood collection systems have allowed a less invasive and quicker collection of peripheral blood. Such non-invasive sampling of small volumes of blood offers practical advantages. The quality of gene expression data is strictly dependent on the steps used for the sample collection, extraction, preparation and sequencing. Here we have: (i) compared the manual and automated RNA extraction of small volumes of blood using the Tempus Spin RNA isolation kit and the MagMAX for Stabilized Blood RNA Isolation kit , respectively; and (ii) assessed the effect of TURBO DNA Free treatment on the transcriptomic data of RNA isolated from small volumes of blood. We have used the QuantSeq 3' FWD mRNA-Seq Library Prep kit to prepare RNA-seq libraries, which were sequenced on the Illumina NextSeq 500 system. The samples isolated manually displayed a higher variability in the transcriptomic data as compared to the other samples. The TURBO DNA Free treatment affected the RNA samples negatively, decreasing the RNA yield and reducing the quality and reproducibility of the transcriptomic data. We conclude that automated extraction systems should be preferred over manual extraction systems for data consistency, and that the TURBO DNA Free treatment should be avoided when working on RNA samples isolated manually from small volumes of blood.
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Affiliation(s)
| | | | | | - Lisa Sara Mathew
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Li Liu
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Li Wang
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Guishuang Wang
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Kun Wang
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Oleksandr Soloviov
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Stephan Lorenz
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
- Omics Core, Integrated Genomic Services, Sidra Medicine, Doha, Qatar
- Bioinformatics Core, Integrated Genomics Services, Sidra Medicine, Doha, Qatar
| | - Sara Tomei
- Omics Core, Integrated Genomic Services, Sidra Medicine, Doha, Qatar.
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LaFever BJ, Kawasawa YI, Ito A, Imamura F. Pathological consequences of chronic olfactory inflammation on neurite morphology of olfactory bulb projection neurons. Brain Behav Immun Health 2022; 21:100451. [PMID: 35360408 PMCID: PMC8960895 DOI: 10.1016/j.bbih.2022.100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/22/2022] Open
Abstract
Chronic olfactory inflammation (COI) in conditions such as chronic rhinosinusitis significantly impairs the functional and anatomical components of the olfactory system. COI induced by intranasal administration of lipopolysaccharide (LPS) results in atrophy, gliosis, and pro-inflammatory cytokine production in the olfactory bulb (OB). Although chronic rhinosinusitis patients have smaller OBs, the consequences of olfactory inflammation on OB neurons are largely unknown. In this study, we investigated the neurological consequences of COI on OB projection neurons, mitral cells (MCs) and tufted cells (TCs). To induce COI, we performed unilateral intranasal administration of LPS to mice for 4 and 10 weeks. Effects of COI on the OB were examined using RNA-sequencing approaches and immunohistochemical analyses. We found that repeated LPS administration upregulated immune-related biological pathways in the OB after 4 weeks. We also determined that the length of TC lateral dendrites in the OB significantly decreased after 10 weeks of COI. The axon initial segment of TCs decreased in number and in length after 10 weeks of COI. The lateral dendrites and axon initial segments of MCs, however, were largely unaffected. In addition, dendritic arborization and AIS reconstruction both took place following a 10-week recovery period. Our findings suggest that olfactory inflammation specifically affects TCs and their integrated circuitry, whereas MCs are potentially protected from this condition. This data demonstrates unique characteristics of the OBs ability to undergo neuroplastic changes in response to stress. Early-stage chronic olfactory inflammation activates the interferon-γ-driven inflammatory pathways in the olfactory bulb. Tufted cells undergo neurite dysregulation in response to chronic olfactory inflammation. Mitral cells and interneurons in the external plexiform layer are largely unaffected by chronic olfactory inflammation. Tufted cells experience complete recovery from neurite dysregulation following a period of ceased inflammation
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Affiliation(s)
- Brandon J. LaFever
- Department of Pharmacology, Penn State College of Medicine, 500 University Dr., Hershey, PA, 17033, USA
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Penn State College of Medicine, 500 University Dr., Hershey, PA, 17033, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Dr., Hershey, PA, 17033, USA
- Institute for Personalized Medicine, Penn State College of Medicine, 500 University Dr., Hershey, PA, 17033, USA
| | - Ayako Ito
- Department of Pharmacology, Penn State College of Medicine, 500 University Dr., Hershey, PA, 17033, USA
| | - Fumiaki Imamura
- Department of Pharmacology, Penn State College of Medicine, 500 University Dr., Hershey, PA, 17033, USA
- Corresponding author. Department of Pharmacology, Penn State College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
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