1
|
Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
Collapse
Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Aili Y, Maimaitiming N, Qin H, Ji W, Fan G, Wang Z, Wang Y. Tumor microenvironment and exosomes in brain metastasis: Molecular mechanisms and clinical application. Front Oncol 2022; 12:983878. [PMID: 36338717 PMCID: PMC9631487 DOI: 10.3389/fonc.2022.983878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/28/2022] [Indexed: 12/03/2022] Open
Abstract
Metastasis is one of the important biological features of malignant tumors and one of the main factors responsible for poor prognosis. Although the widespread application of newer clinical technologies and their continuous development have significantly improved survival in patients with brain metastases, there is no uniform standard of care. More effective therapeutic measures are therefore needed to improve prognosis. Understanding the mechanisms of tumor cell colonization, growth, and invasion in the central nervous system is of particular importance for the prevention and treatment of brain metastases. This process can be plausibly explained by the “seed and soil” hypothesis, which essentially states that tumor cells can interact with various components of the central nervous system microenvironment to produce adaptive changes; it is this interaction that determines the development of brain metastases. As a novel form of intercellular communication, exosomes play a key role in the brain metastasis microenvironment and carry various bioactive molecules that regulate receptor cell activity. In this paper, we review the roles and prospects of brain metastatic tumor cells, the brain metastatic tumor microenvironment, and exosomes in the development and clinical management of brain metastases.
Collapse
Affiliation(s)
- Yirizhati Aili
- Department of Neurosurgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Nuersimanguli Maimaitiming
- Department of Four Comprehensive Internal Medicine, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Hu Qin
- Department of Neurosurgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Wenyu Ji
- Department of Neurosurgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Guofeng Fan
- Department of Neurosurgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zengliang Wang
- Department of Neurosurgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- School of Health Management, Xinjiang Medical University, Urumqi, China
- Department of Neurosurgery, Xinjiang Bazhou People’s Hospital, Xinjiang, China
- *Correspondence: Zengliang Wang, ; Yongxin Wang,
| | - Yongxin Wang
- Department of Neurosurgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Zengliang Wang, ; Yongxin Wang,
| |
Collapse
|
3
|
Li J, Song Y, Zhang C, Wang R, Hua L, Guo Y, Gan D, Zhu L, Li S, Ma P, Yang C, Li H, Yang J, Shi J, Liu X, Su H. TMEM43 promotes pancreatic cancer progression by stabilizing PRPF3 and regulating RAP2B/ERK axis. Cell Mol Biol Lett 2022; 27:24. [PMID: 35260078 PMCID: PMC8903684 DOI: 10.1186/s11658-022-00321-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Transmembrane protein 43 (TMEM43), a member of the transmembrane protein subfamily, plays a critical role in the initiation and development of cancers. However, little is known concerning the biological function and molecular mechanisms of TMEM43 in pancreatic cancer. METHODS In this study, TMEM43 expression levels were analyzed in pancreatic cancer samples compared with control samples. The relationship of TMEM43 expression and disease-free survival (DFS) and overall survival (OS) were assessed in pancreatic cancer patients. In vitro and in vivo assays were performed to explore the function and role of TMEM43 in pancreatic cancer. Coimmunoprecipitation (co-IP) followed by protein mass spectrometry was applied to analyze the molecular mechanisms of TMEM43 in pancreatic cancer. RESULTS We demonstrated that TMEM43 expression level is elevated in pancreatic cancer samples compared with control group, and is correlated with poor DFS and OS in pancreatic cancer patients. Knockdown of TMEM43 inhibited pancreatic cancer progression in vitro, decreased the percentage of S phase, and inhibited the tumorigenicity of pancreatic cancer in vivo. Moreover, we demonstrated that TMEM43 promoted pancreatic cancer progression by stabilizing PRPF3 and regulating the RAP2B/ERK axis. CONCLUSIONS The present study suggests that TMEM43 contributes to pancreatic cancer progression through the PRPF3/RAP2B/ERK axis, and might be a novel therapeutic target for pancreatic cancer.
Collapse
Affiliation(s)
- Junqiang Li
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Yang Song
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Chao Zhang
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Ronglin Wang
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Lei Hua
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Yongdong Guo
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Dongxue Gan
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Liaoliao Zhu
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Shanshan Li
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Peixiang Ma
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Cheng Yang
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Hong Li
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Jing Yang
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Jingjie Shi
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| | - Xiaonan Liu
- grid.233520.50000 0004 1761 4404Ambulatory Surgery Center, Xijing Hospital, Air Force Medical University, Xi’an, 710032 Shaanxi China
| | - Haichuan Su
- grid.233520.50000 0004 1761 4404Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an, 710038 Shaanxi China
| |
Collapse
|
4
|
Zhao WJ, Fan YP, Ou GY, Qiao XY. LASS2 impairs proliferation of glioma stem cells and migration and invasion of glioma cells mainly via inhibition of EMT and apoptosis promotion. J Cancer 2022; 13:2281-2292. [PMID: 35517425 PMCID: PMC9066216 DOI: 10.7150/jca.71256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
LAG1 longevity assurance homolog 2 (LASS2), a highly conserved transmembrane protein, has been reported in several cancer types. However, the roles of LASS2 in glioma biology remain elusive. In the present study, we investigated the expression of LAAS2 in human glioma tissues and the effects of LASS2 on glioma stem cell (GSC) proliferation. Roles of LASS2 in glioma cell migration and invasion were also researched both in vitro and in vivo. Our results demonstrated that the level of LASS2 is gradually reduced with the increase of glioma grade. The level of LASS2 is significantly lower in GSCs than in non GSCs, whereas LASS2 overexpression reduced the sphere formation and promoted the differentiation of CD133+ glioblastoma cells, as was indicated by reduced levels of CD133 and Nestin. In addition, LASS2 overexpression significantly reduced colony formation, migration, and invasion of glioma cells by promoting tumor cell apoptosis and inhibiting epithelial-mesenchymal transition (EMT). Overexpression of LASS2 inhibited U-87 MG cell-derived glioma xenograft growth in nude mice in a manner similar to in vitro. Our findings indicate that LASS2 can function as a suppressor of glioma growth, suggesting that modulation of LASS2 expression may contribute to a novel strategy for the management of glioma via inhibition of GSCs.
Collapse
Affiliation(s)
- Wei-Jiang Zhao
- Cell Biology Department, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Center for Neuroscience, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Yi-Pu Fan
- Center for Neuroscience, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Guan-Yong Ou
- Center for Neuroscience, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Xin-Yu Qiao
- Cell Biology Department, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| |
Collapse
|
5
|
C3G Protein, a New Player in Glioblastoma. Int J Mol Sci 2021; 22:ijms221810018. [PMID: 34576182 PMCID: PMC8466177 DOI: 10.3390/ijms221810018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/09/2021] [Accepted: 09/13/2021] [Indexed: 12/04/2022] Open
Abstract
C3G (RAPGEF1) is a guanine nucleotide exchange factor (GEF) for GTPases from the Ras superfamily, mainly Rap1, although it also acts through GEF-independent mechanisms. C3G regulates several cellular functions. It is expressed at relatively high levels in specific brain areas, playing important roles during embryonic development. Recent studies have uncovered different roles for C3G in cancer that are likely to depend on cell context, tumour type, and stage. However, its role in brain tumours remained unknown until very recently. We found that C3G expression is downregulated in GBM, which promotes the acquisition of a more mesenchymal phenotype, enhancing migration and invasion, but not proliferation. ERKs hyperactivation, likely induced by FGFR1, is responsible for this pro-invasive effect detected in C3G silenced cells. Other RTKs (Receptor Tyrosine Kinases) are also dysregulated and could also contribute to C3G effects. However, it remains undetermined whether Rap1 is a mediator of C3G actions in GBM. Various Rap1 isoforms can promote proliferation and invasion in GBM cells, while C3G inhibits migration/invasion. Therefore, other RapGEFs could play a major role regulating Rap1 activity in these tumours. Based on the information available, C3G could represent a new biomarker for GBM diagnosis, prognosis, and personalised treatment of patients in combination with other GBM molecular markers. The quantification of C3G levels in circulating tumour cells (CTCs) in the cerebrospinal liquid and/or circulating fluids might be a useful tool to improve GBM patient treatment and survival.
Collapse
|