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McGovern MM, Hosamani IV, Niu Y, Nguyen KY, Zong C, Groves AK. Expression of Atoh1, Gfi1, and Pou4f3 in the mature cochlea reprograms nonsensory cells into hair cells. Proc Natl Acad Sci U S A 2024; 121:e2304680121. [PMID: 38266052 PMCID: PMC10835112 DOI: 10.1073/pnas.2304680121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 12/08/2023] [Indexed: 01/26/2024] Open
Abstract
Mechanosensory hair cells of the mature mammalian organ of Corti do not regenerate; consequently, loss of hair cells leads to permanent hearing loss. Although nonmammalian vertebrates can regenerate hair cells from neighboring supporting cells, many humans with severe hearing loss lack both hair cells and supporting cells, with the organ of Corti being replaced by a flat epithelium of nonsensory cells. To determine whether the mature cochlea can produce hair cells in vivo, we reprogrammed nonsensory cells adjacent to the organ of Corti with three hair cell transcription factors: Gfi1, Atoh1, and Pou4f3. We generated numerous hair cell-like cells in nonsensory regions of the cochlea and new hair cells continued to be added over a period of 9 wk. Significantly, cells adjacent to reprogrammed hair cells expressed markers of supporting cells, suggesting that transcription factor reprogramming of nonsensory cochlear cells in adult animals can generate mosaics of sensory cells like those seen in the organ of Corti. Generating such sensory mosaics by reprogramming may represent a potential strategy for hearing restoration in humans.
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Affiliation(s)
- Melissa M McGovern
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - Ishwar V Hosamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Yichi Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Ken Y Nguyen
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Andrew K Groves
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
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2
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Niu M, Zong C. From high-throughput transcriptome characterization of individual synaptosomes to constructing the whole-brain connectome. Neuropsychopharmacology 2024; 49:325-326. [PMID: 37550440 PMCID: PMC10700480 DOI: 10.1038/s41386-023-01697-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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3
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Niu M, Zhang Y, Luo J, Sinson JC, Thompson AM, Zong C. Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells. bioRxiv 2023:2023.10.09.561356. [PMID: 37873375 PMCID: PMC10592685 DOI: 10.1101/2023.10.09.561356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Accurate detection of somatic mutations in single tumor cells is greatly desired as it allows us to quantify the single-cell mutation burden and construct the mutation-based phylogenetic tree. Here we developed scNanoSeq chemistry and profiled 842 single cells from 21 human breast cancer samples. The majority of the mutation-based phylogenetic trees comprise a characteristic stem evolution followed by the clonal sweep. We observed the subtype-dependent lengths in the stem evolution. To explain this phenomenon, we propose that the differences are related to different reprogramming required for different subtypes of breast cancer. Furthermore, we reason that the time that the tumor-initiating cell took to acquire the critical clonal-sweep-initiating mutation by random chance set the time limit for the reprogramming process. We refer to this model as a reprogramming and critical mutation co-timing (RCMC) subtype model. Next, in the sweeping clone, we observed that tumor cells undergo a branched evolution with rapidly decreasing selection. In the most recent clades, effectively neutral evolution has been reached, resulting in a substantially large number of mutational heterogeneities. Integrative analysis with 522-713X ultra-deep bulk whole genome sequencing (WGS) further validated this evolution mode. Mutation-based phylogenetic trees also allow us to identify the early branched cells in a few samples, whose phylogenetic trees support the gradual evolution of copy number variations (CNVs). Overall, the development of scNanoSeq allows us to unveil novel insights into breast cancer evolution.
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4
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Niu M, Zong C. Reply to: Methodological concerns and lack of evidence for single-synapse RNA-seq. Nat Biotechnol 2023; 41:1225-1228. [PMID: 37500916 DOI: 10.1038/s41587-023-01878-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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Niu M, Cao W, Wang Y, Zhu Q, Luo J, Wang B, Zheng H, Weitz DA, Zong C. Droplet-based transcriptome profiling of individual synapses. Nat Biotechnol 2023; 41:1332-1344. [PMID: 36646931 DOI: 10.1038/s41587-022-01635-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/06/2022] [Indexed: 01/17/2023]
Abstract
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological and electrophysiological heterogeneity. So far we still lack a high-throughput method to profile the molecular heterogeneity among individual synapses. In the present study, we develop a droplet-based single-cell (sc) total-RNA-sequencing platform, called Multiple-Annealing-and-Tailing-based Quantitative scRNA-seq in Droplets, for transcriptome profiling of individual neurites, primarily composed of synaptosomes. In the synaptosome transcriptome, or 'synaptome', profiling of both mouse and human brain samples, we detect subclusters among synaptosomes that are associated with neuronal subtypes and characterize the landscape of transcript splicing that occurs within synapses. We extend synaptome profiling to synaptopathy in an Alzheimer's disease (AD) mouse model and discover AD-associated synaptic gene expression changes that cannot be detected by single-nucleus transcriptome profiling. Overall, our results show that this platform provides a high-throughput, single-synaptosome transcriptome profiling tool that will facilitate future discoveries in neuroscience.
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Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Wenjian Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Wyss Institute of Bioinspired Engineering, Harvard University, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Qiangyuan Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, China
| | - Jiayi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Baiping Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Hui Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - David A Weitz
- Wyss Institute of Bioinspired Engineering, Harvard University, Cambridge, MA, USA.
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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6
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Yu WK, Wang YC, Li YP, Gao Y, Zong C, Xu YM, Li YS. [The correlation between plasma heat shock proteins 90α levels and white matter hyperintensity in patients with cerebral small vessel disease]. Zhonghua Yi Xue Za Zhi 2022; 102:2602-2606. [PMID: 36058685 DOI: 10.3760/cma.j.cn112137-20211215-02795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To investigate the relationship between plasma heat shock proteins 90α(Hsp90α) levels and the white matter hyperintensity(WMH) in patients with cerebral small vessel disease(SVD). Methods: Patients admitted to the Department of Neurology, the First Affiliated Hospital of Zhengzhou University from March to August 2021 and diagnosed with WMH by magnetic resonance examination (MRI) were selected as the case group, matched with physical examination patients who visited the Department of Medical Examination during the same period and showed no WMH on MRI and no history of neurological diseases as the control group, and the level of plasma Hsp90α was quantitatively detected by enzyme-linked immunosorbent assay. Mann-Whitney U test was used to compare whether there was a difference in plasma Hsp90α levels between the control group and the case group.Multivariate logistic regression analysis was used to explore the related factors of WMH in patients with SVD. Results: Of the 183 subjects, the control group (n=73) consisted of 28 males and 45 females, aged (54±10) years, while the case group (n=110) consisted of 71 males and 39 females, aged (64±10) years old. Plasma Hsp90α level was higher in the case group than that of the control group [53.33(35.33, 70.09) ng/ml vs 35.02(18.51, 54.95) ng/ml, P<0.001]. After adjusting for confounding factors by multivariate analysis, the results showed that plasma Hsp90α levels greater than 58.34 ng/ml was associated with WMH (P=0.002, OR=5.931, 95%CI:1.955-17.995). Conclusion: Higher level of plasma Hsp90α is associated with WMH in patients with SVD.
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Affiliation(s)
- W K Yu
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Y C Wang
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Y P Li
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Y Gao
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - C Zong
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Y M Xu
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Y S Li
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
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7
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Niu Y, Zhu Q, Zong C. Single-cell Damagenome Profiling by Linear Copying and Splitting based Whole Genome Amplification (LCS-WGA). Bio Protoc 2022; 12:e4357. [PMID: 35434195 PMCID: PMC8983167 DOI: 10.21769/bioprotoc.4357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 10/19/2021] [Accepted: 02/01/2022] [Indexed: 02/08/2024] Open
Abstract
Spontaneous DNA damage frequently occurs on the human genome, and it could alter gene expression by inducing mutagenesis or epigenetic changes. Therefore, it is highly desired to profile DNA damage distribution on the human genome and identify the genes that are prone to DNA damage. Here, we present a novel single-cell whole-genome amplification method which employs linear-copying followed by a split-amplification scheme, to efficiently remove amplification errors and achieve accurate detection of DNA damage in individual cells. In comparison to previous methods that measure DNA damage, our method uses a next-generation sequencing platform to detect misincorporated bases derived from spontaneous DNA damage with single-cell resolution.
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Affiliation(s)
- Yichi Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
- Genetics & Genomics Program, Baylor College of Medicine, TX, USA
| | - Qiangyuan Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
- Genetics & Genomics Program, Baylor College of Medicine, TX, USA
- Cancer and Cell Biology Program, Baylor College of Medicine, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, TX, USA
- McNair Medical Institute, Baylor College of Medicine, TX, USA
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8
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Zhu Q, Niu Y, Gundry M, Zong C. Single-cell damagenome profiling unveils vulnerable genes and functional pathways in human genome toward DNA damage. Sci Adv 2021; 7:eabf3329. [PMID: 34215579 PMCID: PMC11060043 DOI: 10.1126/sciadv.abf3329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
We report a novel single-cell whole-genome amplification method (LCS-WGA) that can efficiently capture spontaneous DNA damage existing in single cells. We refer to these damage-associated single-nucleotide variants as "damSNVs," and the whole-genome distribution of damSNVs as the damagenome. We observed that in single human neurons, the damagenome distribution was significantly correlated with three-dimensional genome structures. This nonuniform distribution indicates different degrees of DNA damage effects on different genes. Next, we identified the functionals that were significantly enriched in the high-damage genes. Similar functionals were also enriched in the differentially expressed genes (DEGs) detected by single-cell transcriptome of both Alzheimer's disease (AD) and autism spectrum disorder (ASD). This result can be explained by the significant enrichment of high-damage genes in the DEGs of neurons for both AD and ASD. The discovery of high-damage genes sheds new lights on the important roles of DNA damage in human diseases and disorders.
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Affiliation(s)
- Qiangyuan Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yichi Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael Gundry
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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9
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Liu S, Cao W, Niu Y, Luo J, Zhao Y, Hu Z, Zong C. Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence. eLife 2021; 10:e64204. [PMID: 33983114 PMCID: PMC8203294 DOI: 10.7554/elife.64204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/12/2021] [Indexed: 12/13/2022] Open
Abstract
ARID1A is one of the most frequently mutated epigenetic regulators in a wide spectrum of cancers. Recent studies have shown that ARID1A deficiency induces global changes in the epigenetic landscape of enhancers and promoters. These broad and complex effects make it challenging to identify the driving mechanisms of ARID1A deficiency in promoting cancer progression. Here, we identified the anti-senescence effect of Arid1a deficiency in the progression of pancreatic intraepithelial neoplasia (PanIN) by profiling the transcriptome of individual PanINs in a mouse model. In a human cell line model, we found that ARID1A deficiency upregulates the expression of aldehyde dehydrogenase 1 family member A1 (ALDH1A1), which plays an essential role in attenuating the senescence induced by oncogenic KRAS through scavenging reactive oxygen species. As a subunit of the SWI/SNF chromatin remodeling complex, our ATAC sequencing data showed that ARID1A deficiency increases the accessibility of the enhancer region of ALDH1A1. This study provides the first evidence that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence through the upregulation of ALDH1A1 expression.
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Affiliation(s)
- Shou Liu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Wenjian Cao
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Genetics and Genomics Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Yichi Niu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Genetics and Genomics Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Jiayi Luo
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Cancer and Cell, Biology Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Yanhua Zhao
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Zhiying Hu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Genetics and Genomics Graduate Program, Baylor College of MedicineHoustonUnited States
- Cancer and Cell, Biology Graduate Program, Baylor College of MedicineHoustonUnited States
- Dan L Duncan Comprehensive Cancer Center, Baylor College of MedicineHoustonUnited States
- McNair Medical Institute, Baylor College of MedicineHoustonUnited States
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10
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Bota-Rabassedas N, Banerjee P, Niu Y, Cao W, Luo J, Xi Y, Tan X, Sheng K, Ahn YH, Lee S, Parra ER, Rodriguez-Canales J, Albritton J, Weiger M, Liu X, Guo HF, Yu J, Rodriguez BL, Firestone JJA, Mino B, Creighton CJ, Solis LM, Villalobos P, Raso MG, Sazer DW, Gibbons DL, Russell WK, Longmore GD, Wistuba II, Wang J, Chapman HA, Miller JS, Zong C, Kurie JM. Contextual cues from cancer cells govern cancer-associated fibroblast heterogeneity. Cell Rep 2021; 35:109009. [PMID: 33882319 PMCID: PMC8142261 DOI: 10.1016/j.celrep.2021.109009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 01/21/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer cells function as primary architects of the tumor microenvironment. However, the molecular features of cancer cells that govern stromal cell phenotypes remain unclear. Here, we show that cancer-associated fibroblast (CAF) heterogeneity is driven by lung adenocarcinoma (LUAD) cells at either end of the epithelial-to-mesenchymal transition (EMT) spectrum. LUAD cells that have high expression of the EMT-activating transcription factor ZEB1 reprogram CAFs through a ZEB1-dependent secretory program and direct CAFs to the tips of invasive projections through a ZEB1-driven CAF repulsion process. The EMT, in turn, sensitizes LUAD cells to pro-metastatic signals from CAFs. Thus, CAFs respond to contextual cues from LUAD cells to promote metastasis. Bota-Rabassedas et al. show that EMT in lung adenocarcinoma cells activates a secretory process that governs CAF heterogeneity and, in turn, sensitizes lung adenocarcinoma cells to pro-metastatic signals from CAFs. Thus, EMT positions lung adenocarcinoma cells at the apex of a signaling hierarchy in the tumor microenvironment.
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Affiliation(s)
- Neus Bota-Rabassedas
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyam Banerjee
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yichi Niu
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wenjian Cao
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiayi Luo
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yuanxin Xi
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaochao Tan
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kuanwei Sheng
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Young-Ho Ahn
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Sieun Lee
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Edwin Roger Parra
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaime Rodriguez-Canales
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacob Albritton
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Michael Weiger
- Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Liu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hou-Fu Guo
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiang Yu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - B Leticia Rodriguez
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Barbara Mino
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad J Creighton
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Luisa M Solis
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pamela Villalobos
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Gabriela Raso
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel W Sazer
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Don L Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gregory D Longmore
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Cell Biology & Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ignacio I Wistuba
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harold A Chapman
- Department of Medicine, University of California, San Francisco Cardiovascular Research Institute, San Francisco, CA, USA
| | - Jordan S Miller
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Chenghang Zong
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Jonathan M Kurie
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Wu J, Zong C, Shao T, Liang Y, McCann JC, Dong Z, Li J, Zhang J, Liu Q. Clarifying the relationships among bacteria, lipid-related enzymes, main polyunsaturated fatty acids and fat-soluble vitamins in alfalfa (Medicago sativa L.) silage using various sugar supplementations. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2020.114799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Chen Y, Zong C, Jia J, Liu Y, Zhang Z, Cai B, Tian L. A study on the protective effect of molecular hydrogen on osteoradionecrosis of the jaw in rats. Int J Oral Maxillofac Surg 2020; 49:1648-1654. [PMID: 32451233 DOI: 10.1016/j.ijom.2020.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/04/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022]
Abstract
The aim of this study was to investigate the protective effect of hydrogen in a rat model of osteoradionecrosis of the jaw (ORNJ). The rats and bone marrow-derived mesenchymal stem cells (BMSCs) were pre-treated with hydrogen before receiving irradiation (7Gy per fraction, five fractions in total once a day for rats, 4Gy for BMSCs). Reactive oxygen species (ROS) and cell differentiation were measured in the BMSCs. Also, the radioprotective effect of hydrogen for ORNJ in Sprague-Dawley rats was examined by gross clinical manifestations, micro-computed tomography, and histology. Hydrogen significantly reduced the production of ROS in BMSCs after irradiation. The cell viability was significantly decreased after irradiation (P= 0.001), but pre-treatment with hydrogen before irradiation increased the cell viability (P= 0.025). Hydrogen considerably increased the cellular differentiation potential of the irradiated cells. Comparing with the rats underwent irradiaton only, those rats treated by hydrogen-rich saline significantly appeared improved occlusion, salivation, alopecia, oral ulcer, and less bone necrosis. Myofibroblasts accumulated overwhelmingly in the fibrosis medulla and around the sequestrum after irradiation, and this was decreased in the group pre-treated with hydrogen. Hydrogen may represent a strategy for the prevention and treatment of ORNJ. Its high efficacy and low toxicity suggest possible therapeutic application.
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Affiliation(s)
- Y Chen
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, and Department of Oral and Maxillofacial Surgery, School of Stomatology, the Fourth Military Medical University, Xi'an, China; State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - C Zong
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, and Department of Oral and Maxillofacial Surgery, School of Stomatology, the Fourth Military Medical University, Xi'an, China; State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - J Jia
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - Y Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, and Department of Oral and Maxillofacial Surgery, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - Z Zhang
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - B Cai
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, and Department of Oral and Maxillofacial Surgery, School of Stomatology, the Fourth Military Medical University, Xi'an, China; State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, School of Stomatology, the Fourth Military Medical University, Xi'an, China
| | - L Tian
- State Key Laboratory of Military Stomatology and National Clinical Research Centre for Oral Diseases, and Department of Oral and Maxillofacial Surgery, School of Stomatology, the Fourth Military Medical University, Xi'an, China.
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13
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Yamauchi M, Gibbons DL, Zong C, Fradette JJ, Bota-Rabassedas N, Kurie JM. Fibroblast heterogeneity and its impact on extracellular matrix and immune landscape remodeling in cancer. Matrix Biol 2020; 91-92:8-18. [PMID: 32442601 DOI: 10.1016/j.matbio.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022]
Abstract
Tumor progression is marked by dense collagenous matrix accumulations that dynamically reorganize to accommodate a growing and invasive tumor mass. Cancer-associated fibroblasts (CAFs) play an essential role in matrix remodeling and influence other processes in the tumor microenvironment, including angiogenesis, immunosuppression, and invasion. These findings have spawned efforts to elucidate CAF functionality at the single-cell level. Here, we will discuss how those efforts have impacted our understanding of the ways in which CAFs govern matrix remodeling and the influence of matrix remodeling on the development of an immunosuppressive tumor microenvironment.
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Affiliation(s)
- Mitsuo Yamauchi
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NS, United States
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas - MD Anderson Cancer Center, Houston, TX, United States
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jared J Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas - MD Anderson Cancer Center, Houston, TX, United States
| | - Neus Bota-Rabassedas
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas - MD Anderson Cancer Center, Houston, TX, United States
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas - MD Anderson Cancer Center, Houston, TX, United States.
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14
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Wang Y, Cao T, Ko J, Shen Y, Zong W, Sheng K, Cao W, Sun S, Cai L, Zhou Y, Zhang X, Zong C, Weissleder R, Weitz D. Dissolvable Polyacrylamide Beads for High-Throughput Droplet DNA Barcoding. Adv Sci (Weinh) 2020; 7:1903463. [PMID: 32328429 PMCID: PMC7175265 DOI: 10.1002/advs.201903463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Indexed: 05/24/2023]
Abstract
Droplet-based single cell sequencing technologies, such as inDrop, Drop-seq, and 10X Genomics, are catalyzing a revolution in the understanding of biology. Barcoding beads are key components for these technologies. What is limiting today are barcoding beads that are easy to fabricate, can efficiently deliver primers into drops, and thus achieve high detection efficiency. Here, this work reports an approach to fabricate dissolvable polyacrylamide beads, by crosslinking acrylamide with disulfide bridges that can be cleaved with dithiothreitol. The beads can be rapidly dissolved in drops and release DNA barcode primers. The dissolvable beads are easy to synthesize, and the primer cost for the beads is significantly lower than that for the previous barcoding beads. Furthermore, the dissolvable beads can be loaded into drops with >95% loading efficiency of a single bead per drop and the dissolution of beads does not influence reverse transcription or the polymerase chain reaction (PCR) in drops. Based on this approach, the dissolvable beads are used for single cell RNA and protein analysis.
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Affiliation(s)
- Yongcheng Wang
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeMA02138USA
| | - Ting Cao
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
- Beijing National Laboratory for Molecular Sciences (BNLMS)MOE Key Laboratory of Bioorganic Chemistry and Molecular EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Jina Ko
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Yinan Shen
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Will Zong
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Kuanwei Sheng
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Wenjian Cao
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Sijie Sun
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Liheng Cai
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Ying‐Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS)MOE Key Laboratory of Bioorganic Chemistry and Molecular EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xin‐Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)MOE Key Laboratory of Bioorganic Chemistry and Molecular EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Chenghang Zong
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Ralph Weissleder
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Department of Systems BiologyHarvard Medical SchoolBostonMA02115USA
| | - David Weitz
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
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15
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Jen HI, Hill MC, Tao L, Sheng K, Cao W, Zhang H, Yu HV, Llamas J, Zong C, Martin JF, Segil N, Groves AK. Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1. eLife 2019; 8:e44328. [PMID: 31033441 PMCID: PMC6504235 DOI: 10.7554/elife.44328] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/28/2019] [Indexed: 12/30/2022] Open
Abstract
The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.
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Affiliation(s)
- Hsin-I Jen
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Matthew C Hill
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Litao Tao
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Kuanwei Sheng
- Program in Integrative Molecular and Biomedical SciencesBaylor College of MedicineHoustonUnited States
| | - Wenjian Cao
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Hongyuan Zhang
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Haoze V Yu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Chenghang Zong
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - James F Martin
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of Molecular Physiology and BiophysicsBaylor College of MedicineHoustonUnited States
- The Texas Heart InstituteHoustonUnited States
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Andrew K Groves
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
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16
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Scavuzzo MA, Hill MC, Chmielowiec J, Yang D, Teaw J, Sheng K, Kong Y, Bettini M, Zong C, Martin JF, Borowiak M. Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis. Nat Commun 2018; 9:3356. [PMID: 30135482 PMCID: PMC6105717 DOI: 10.1038/s41467-018-05740-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
Decoding the molecular composition of individual Ngn3 + endocrine progenitors (EPs) during pancreatic morphogenesis could provide insight into the mechanisms regulating hormonal cell fate. Here, we identify population markers and extensive cellular diversity including four EP subtypes reflecting EP maturation using high-resolution single-cell RNA-sequencing of the e14.5 and e16.5 mouse pancreas. While e14.5 and e16.5 EPs are constantly born and share select genes, these EPs are overall transcriptionally distinct concomitant with changes in the underlying epithelium. As a consequence, e16.5 EPs are not the same as e14.5 EPs: e16.5 EPs have a higher propensity to form beta cells. Analysis of e14.5 and e16.5 EP chromatin states reveals temporal shifts, with enrichment of beta cell motifs in accessible regions at later stages. Finally, we provide transcriptional maps outlining the route progenitors take as they make cell fate decisions, which can be applied to advance the in vitro generation of beta cells. Endocrine progenitors form early in pancreatic development but the diversity of this cell population is unclear. Here, the authors use single cell RNA sequencing of the mouse pancreas at e14.5 and e16.5 to show that endocrine progenitors are temporally distinct and those formed later are more likely to become beta cells
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Affiliation(s)
- Marissa A Scavuzzo
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Yang
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jessica Teaw
- Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kuanwei Sheng
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuelin Kong
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James F Martin
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,The Texas Heart Institute, Houston, TX, 77030, USA. .,Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Malgorzata Borowiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA. .,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Yang L, Zha Y, Feng J, Dong H, Zong C, Lei X, Liang N, Wang X, Gao G, Bai X. Treatment of a Pediatric Case of Severe Hemorrhagic Cystitis: Case Report and Review of Literature. Transplant Proc 2017; 49:2365-2367. [PMID: 29198679 DOI: 10.1016/j.transproceed.2017.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Hemorrhagic cystitis is one of the complications of allogeneic hematopoietic stem cell transplantation. Treatment of hemorrhagic cystitis is difficult, especially in pediatric patients. A pediatric case of severe hemorrhagic cystitis after hematopoietic stem cell transplantation was treated in our hospital with arterial embolization combined with corticosteroid therapy because the conventional therapy was invalid for him. After the treatment, hemorrhagic cystitis was cured. During follow-up, the patient was in stable condition, with normal urine, blood cells returned to normal, bone marrow was in complete remission state, and disease-free survival for more than 8 months. Selective bladder arterial embolism followed by corticosteroid therapy successfully treated the patient.
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Affiliation(s)
- L Yang
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - Y Zha
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - J Feng
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - H Dong
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - C Zong
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - X Lei
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - N Liang
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - X Wang
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - G Gao
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China
| | - X Bai
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, China.
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18
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Tian L, Goldstein A, Wang H, Ching Lo H, Sun Kim I, Welte T, Sheng K, Dobrolecki LE, Zhang X, Putluri N, Phung TL, Mani SA, Stossi F, Sreekumar A, Mancini MA, Decker WK, Zong C, Lewis MT, Zhang XHF. Mutual regulation of tumour vessel normalization and immunostimulatory reprogramming. Nature 2017; 544:250-254. [PMID: 28371798 PMCID: PMC5788037 DOI: 10.1038/nature21724] [Citation(s) in RCA: 474] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
Abstract
Blockade of angiogenesis can retard tumour growth, but may also paradoxically increase metastasis1,2. Vessel normalization (VN) may resolve this paradox3. VN involves increased pericyte coverage, improved tumour vessel perfusion, reduced vascular permeability, and consequently mitigated hypoxia3. While these processes alter tumour progression, their regulation is poorly understood. Here we show that Type 1 T helper (Th1) cells play a crucial role in VN. Bioinformatic analyses revealed that gene expression features related to VN correlate with immunostimulatory pathways, especially T lymphocyte (TL) infiltration/activities. To delineate the causal relationship, we employed various mouse models with VN or TL deficiencies. While VN disruption reduced TL infiltration as expected4, reciprocal depletion or inactivation of CD4+-TLs decreased VN, indicating a mutually-regulatory loop. Additionally, CD4+-TL activation by immune checkpoint blockade (ICB) increased VN. IFNγ+ Th1 cells are the major population associated with VN. Patient-derived xenograft (PDX) tumours growing in immunodeficient animal hosts exhibited enhanced hypoxia compared to the original tumours in immunocompetent human hosts, which was reduced by adoptive Th1 transfer. Our findings elucidate an unexpected role of Th1 in vasculature and immune reprogramming. Th1 cells may be a marker and a determinant of both ICB and anti-angiogenesis efficacies.
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Affiliation(s)
- Lin Tian
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Amit Goldstein
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Hai Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Hin Ching Lo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Ik Sun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Thomas Welte
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Kuanwei Sheng
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Xiaomei Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Nagireddy Putluri
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Thuy L Phung
- Department of Pathology &Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, Texas 77030, USA
| | - Fabio Stossi
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Arun Sreekumar
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Michael A Mancini
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - William K Decker
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Pathology &Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Chenghang Zong
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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19
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Abstract
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein structure prediction, in particular the development of coarse grained models. We survey results from blind structure prediction. We explore how second generation prediction energy functions can be developed by introducing information from an ensemble of previously simulated structures. This procedure relies on the assumption of a funneled energy landscape keeping with the principle of minimal frustration. First generation simulated structures provide an improved input for associative memory energy functions in comparison to the experimental protein structures chosen on the basis of sequence alignment.
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Affiliation(s)
- Michael C Prentiss
- Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Corey Hardin
- Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Michael P Eastwood
- Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Chenghang Zong
- Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, La Jolla, California 92093, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Department of Physics, University of California, La Jolla, California 92093, and Department of Chemistry, University of Illinois, Urbana [Formula: see text] Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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20
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Lu S, Zong C, Fan W, Yang M, Li J, Chapman AR, Zhu P, Hu X, Xu L, Yan L, Bai F, Qiao J, Tang F, Li R, Xie XS. Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science 2013; 338:1627-30. [PMID: 23258895 DOI: 10.1126/science.1229112] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Meiotic recombination creates genetic diversity and ensures segregation of homologous chromosomes. Previous population analyses yielded results averaged among individuals and affected by evolutionary pressures. We sequenced 99 sperm from an Asian male by using the newly developed amplification method-multiple annealing and looping-based amplification cycles-to phase the personal genome and map recombination events at high resolution, which are nonuniformly distributed across the genome in the absence of selection pressure. The paucity of recombination near transcription start sites observed in individual sperm indicates that such a phenomenon is intrinsic to the molecular mechanism of meiosis. Interestingly, a decreased crossover frequency combined with an increase of autosomal aneuploidy is observable on a global per-sperm basis.
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Affiliation(s)
- Sijia Lu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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Abstract
Kindred cells can have different genomes because of dynamic changes in DNA. Single-cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome amplification bias, resulting in low genome coverage. Here, we report on a new amplification method-multiple annealing and looping-based amplification cycles (MALBAC)-that offers high uniformity across the genome. Sequencing MALBAC-amplified DNA achieves 93% genome coverage ≥1x for a single human cell at 25x mean sequencing depth. We detected digitized copy-number variations (CNVs) of a single cancer cell. By sequencing three kindred cells, we were able to identify individual single-nucleotide variations (SNVs), with no false positives detected. We directly measured the genome-wide mutation rate of a cancer cell line and found that purine-pyrimidine exchanges occurred unusually frequently among the newly acquired SNVs.
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Affiliation(s)
- Chenghang Zong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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22
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Pasqui V, Saint-Bauzel L, Zong C, Clady X, Decq P, Piette F, Michel-Pellegrino V, El Helou A, Carré M, Durand A, Hoang Q, Guiochet J, Rumeau P, Dupourque V, Caquas J. Projet MIRAS : robot d’assistance à la déambulation avec interaction multimodale. Ing Rech Biomed 2012. [DOI: 10.1016/j.irbm.2012.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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So LH, Ghosh A, Zong C, Sepúlveda LA, Segev R, Golding I. General properties of transcriptional time series in Escherichia coli. Nat Genet 2011; 43:554-60. [PMID: 21532574 PMCID: PMC3102781 DOI: 10.1038/ng.821] [Citation(s) in RCA: 265] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 04/05/2011] [Indexed: 11/09/2022]
Abstract
Gene activity is described by the time-series of discrete, stochastic mRNA production events. This transcriptional time-series exhibits intermittent, bursty behavior. One consequence of this temporal intricacy is that gene expression can be tuned by varying different features of the time-series. What schemes for varying the transcriptional time-series are observed in the cell? Are the observed properties of these time-series optimized for cellular function? To address these questions, we characterize mRNA copy-number statistics at single-molecule resolution from multiple Escherichia coli promoters. We find that the degree of burstiness depends only on the gene expression level, while being independent of the details of gene regulation. The observed behavior is explained by the underlying variation in the duration of bursting events. Using information theory, we find that the properties of the transcriptional time series allow the cell to efficiently map the extracellular concentration of inducer molecules to intracellular levels of mRNA and proteins.
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Affiliation(s)
- Lok-Hang So
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
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25
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Zong C, So LH, Sepúlveda LA, Skinner SO, Golding I. Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene. Mol Syst Biol 2011; 6:440. [PMID: 21119634 PMCID: PMC3010116 DOI: 10.1038/msb.2010.96] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 10/19/2010] [Indexed: 11/22/2022] Open
Abstract
Bacterial lysogeny serves as a simple paradigm for cell differentiation. We characterize the activity of the fate-determining genes, cI and cro, with single-molecule resolution. Stability of the lysogenic state is found to depend in a simple manner on the frequency of activity bursts from cI.
The ability of living cells to maintain an inheritable memory of their gene-expression state is key to cellular differentiation. Bacterial lysogeny serves as a simple paradigm for long-term cellular memory. In this study, we address the following question: in the absence of external perturbation, how long will a cell stay in the lysogenic state before spontaneously switching away from that state? We show by direct measurement that lysogen stability exhibits a simple exponential dependence on the frequency of activity bursts from the fate-determining gene, cI. We quantify these gene-activity bursts using single-molecule-resolution mRNA measurements in individual cells, analyzed using a stochastic mathematical model of the gene-network kinetics. The quantitative relation between stability and gene activity is independent of the fine details of gene regulation, suggesting that a quantitative prediction of cell-state stability may also be possible in more complex systems.
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Affiliation(s)
- Chenghang Zong
- Department of Physics, University of Illinois, Urbana, IL, USA
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26
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Oklejas V, Zong C, Papoian GA, Wolynes PG. Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice? Methods 2010; 52:84-90. [PMID: 20561998 DOI: 10.1016/j.ymeth.2010.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 05/17/2010] [Accepted: 05/20/2010] [Indexed: 11/16/2022] Open
Abstract
The many-body physics of hydrogen bond formation in alpha-helices of globular proteins was investigated using a simple physics-based model. Specifically, a context-sensitive hydrogen bond potential, which depends on residue identity and degree of solvent exposure, was used in the framework of the Associated Memory Hamiltonian codes developed previously but without using local-sequence structure matches ("memories"). Molecular dynamics simulations employing the energy function using the context-sensitive hydrogen bond potential alone (the "amnesiac" model) were used to generate low energy structures for three alpha-helical test proteins. The resulting structures were compared to both the X-ray crystal structures of the test proteins and the results obtained using the full Associated Memory Hamiltonian previously used. Results show that the amnesiac Hamiltonian was able to generate structures with reasonably high structural similarity (Q approximately 0.4) to that of the native protein but only with the use of predicted secondary structure information encoding local steric signals. Low energy structures obtained using the amnesiac Hamiltonian without any a priori secondary structure information had considerably less similarity to the native protein structures (Q approximately 0.3). Both sets of results utilizing the amnesiac Hamiltonian are poorer than when local-sequence structure matches are used.
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Affiliation(s)
- Vanessa Oklejas
- Department of Chemistry and Biochemistry, University of California, La Jolla, CA 92093-0371, United States.
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27
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Zong C, Golding I. The Energy Landscape of an Epigenetic System. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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28
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Shen T, Zong C, Portman JJ, Wolynes PG. Variationally determined free energy profiles for structural models of proteins: characteristic temperatures for folding and trapping. J Phys Chem B 2008; 112:6074-82. [PMID: 18376882 DOI: 10.1021/jp076280n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Characterizing the phase diagram for proteins is important both for laboratory studies and for the development of structure prediction algorithms. Using a variational scheme, we calculated the generic features of the protein thermostability over a large range of temperatures for a set of more than 50 different proteins using a model based on native structure alone. Focusing on a specific system, protein G, we further examined, using a more realistic model that includes the nonnative interaction, the thermostability of both the native state and a collection of trap structures. By surveying the native structures for many proteins and by paying closer attention to the various trap structures of protein G, we obtained an overall understanding of the folding dynamics far from the conditions usually focused on; namely, those near the folding temperature alone. Two characteristic temperatures (shown to scale with folding temperature in general) signal drastic changes in the folding mechanism. The variational calculations suggest that most proteins would, indeed, fold in a barrierless manner below a critical temperature analogous to a spinodal in crystallization. For fixed interaction strengths, this temperature, however, seems to be generally very low, approximately 50% of the equilibrium folding temperature. Likewise, native proteins, in general, would unfold in a completely barrierless way at a temperature 25% above folding temperature according to these variational calculations. We also studied the distribution of free energy profiles for escape from a set of trap structures generated by simulations.
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Affiliation(s)
- Tongye Shen
- Department of Chemistry & Biochemistry, University of California at San Diego, and Center for Theoretical Biological Physics, La Jolla, California 92093-0371, USA
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29
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Zong C, Wilson CJ, Shen T, Wittung-Stafshede P, Mayo SL, Wolynes PG. Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin. Proc Natl Acad Sci U S A 2007; 104:3159-64. [PMID: 17301232 PMCID: PMC1805512 DOI: 10.1073/pnas.0611149104] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting this issue are provided by electron transfer proteins. The environment provided by the folded protein to the cofactor tunes the metal's electron transport capabilities as envisioned in the entatic hypothesis. To see how the entatic state is achieved one must study how the folding landscape affects and in turn is affected by the metal. Here, we develop a coarse-grained functional to explicitly model how the coordination of the metal (which results in a so-called entatic or rack-induced state) modifies the folding of the metallated Pseudomonas aeruginosa azurin. Our free-energy functional-based approach directly yields the proper nonlinear extra-thermodynamic free energy relationships for the kinetics of folding the wild type and several point-mutated variants of the metallated protein. The results agree quite well with corresponding laboratory experiments. Moreover, our modified free-energy functional provides a sufficient level of detail to explicitly model how the geometric entatic state of the metal modifies the dynamic folding nucleus of azurin.
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Affiliation(s)
- Chenghang Zong
- *Department of Chemistry and Biochemistry
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
- To whom correspondence may be addressed. E-mail: , , or
| | - Corey J. Wilson
- Division of Biology, California Institute of Technology, Mail Code 147-75, Pasadena, CA 91125; and
- To whom correspondence may be addressed. E-mail: , , or
| | - Tongye Shen
- *Department of Chemistry and Biochemistry
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
| | - Pernilla Wittung-Stafshede
- Departments of Biochemistry and Cell Biology and Chemistry, Rice University, 6100 Main Street, Houston, TX 77251
| | - Steven L. Mayo
- Division of Biology, California Institute of Technology, Mail Code 147-75, Pasadena, CA 91125; and
| | - Peter G. Wolynes
- *Department of Chemistry and Biochemistry
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
- To whom correspondence may be addressed. E-mail: , , or
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Lu T, Shen T, Zong C, Hasty J, Wolynes PG. Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space. Proc Natl Acad Sci U S A 2006; 103:16752-7. [PMID: 17071742 PMCID: PMC1636527 DOI: 10.1073/pnas.0607698103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular signal transduction often involves a reaction network of phosphorylation and transport events arranged with a ladder topology. If we keep track of the location of the phosphate groups describing an abstract state space, a simple model of signal transduction involving enzymes can be mapped on to a problem of how multiple biased random walkers compete to reach their target in the nucleus yielding a signal. Here, the first passage time probability and the survival probability for multiple walkers can be used to characterize the response of the network. The statistics of the first passage through the network has an asymmetric distribution with a long tail arising from the hierarchical structure of the network. This distribution implies a significant difference between the mean and the most probable signal transduction time. The response patterns for various external inputs generated by our model agree with recent experiments. In addition, the model predicts that there is an optimal phosphorylation enzyme concentration for rapid signal transduction.
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Affiliation(s)
- Ting Lu
- Departments of *Physics
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
| | - Tongye Shen
- Chemistry and Biochemistry, and
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
| | - Chenghang Zong
- Chemistry and Biochemistry, and
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
| | - Jeff Hasty
- Bioengineering
- Institute for Nonlinear Science, and
| | - Peter G. Wolynes
- Departments of *Physics
- Chemistry and Biochemistry, and
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093
- To whom correspondence should be addressed. E-mail:
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31
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Zong C, Wilson CJ, Shen T, Wolynes PG, Wittung-Stafshede P. Phi-value analysis of apo-azurin folding: comparison between experiment and theory. Biochemistry 2006; 45:6458-66. [PMID: 16700556 DOI: 10.1021/bi060025w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa azurin is a 128-residue beta-sandwich metalloprotein; in vitro kinetic experiments have shown that it folds in a two-state reaction. Here, we used a variational free energy functional to calculate the characteristics of the transition state ensemble (TSE) for folding of the apo-form of P. aeruginosa azurin and investigate how it responds to thermal and mutational changes. The variational method directly yields predicted chevron plots for wild-type and mutant apo-forms of azurin. In parallel, we performed in vitro kinetic-folding experiments on the same set of azurin variants using chemical perturbation. Like the wild-type protein, all apo-variants fold in apparent two-state reactions both in calculations and in stopped-flow mixing experiments. Comparisons of phi (phi) values determined from the experimental and theoretical chevron parameters reveal an excellent agreement for most positions, indicating a polarized, highly structured TSE for folding of P. aeruginosa apo-azurin. We also demonstrate that careful analysis of side-chain interactions is necessary for appropriate theoretical description of core mutants.
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Affiliation(s)
- Chenghang Zong
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0371, USA
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Abstract
Many of the large structures of cells are constructed from fibers. These fibers self-assemble from individual proteins in a far-from-equilibrium fashion. Nonequilibrium self-assembly results in a highly dynamic process at the subcellular level that can be regulated and tuned to carry out many of the biological functions of the cell: growth, division and locomotion. We construct and analyze a nonequilibrium model of the dynamic end of a biological fiber that possesses site-resolved resolution. We solve for the steady states of this nonequilibrium system using a variational method. The results are compared to exact numerical solutions for systems with modest size. Using an effective reaction coordinate, we construct an effective potential from the steady-state distribution. The stochastic transitions of the system can be analyzed in this representation. We then apply this method to model microtubule systems. Predictions for macroscopic catastrophe, rescue and dynamic instability in the steady states are analyzed. We find that the length of the cap of the microtubule is small. The relations between the catastrophe/rescue rate and the growth rate are also discussed.
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Affiliation(s)
- Chenghang Zong
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0371, USA
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33
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Zong C, Papoian GA, Ulander J, Wolynes PG. Role of Topology, Nonadditivity, and Water-Mediated Interactions in Predicting the Structures of α/β Proteins. J Am Chem Soc 2006; 128:5168-76. [PMID: 16608353 DOI: 10.1021/ja058589v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The folding of alpha/beta proteins involves most of the commonly known structural and dynamic complexities of the protein energy landscapes. Thus, the interplay among different structural components, taking into account the cooperative interactions, is important in determining the success of protein structure prediction. In this work we present further developments of our knowledge-based force field for alpha/beta proteins, introducing more realistic modeling of many-body interactions governing the folding of beta-sheets. The model's innovations highlight both specific topological characteristics of secondary structures and the generic nonadditive interactions that are mediated by water. We also investigate how a coarse biasing of the protein morphology can be used to understand the role of heterogeneity in protein collapse. Analysis of the simulation results for three test alpha/beta proteins indicates that the addition of the topological and many-body ingredients to the model helps to greatly reduce the roughness in the energy landscape. Consequently, high quality candidate structures for alpha/beta proteins can be generated from simulated annealing runs, using very modest amounts of computer time.
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Affiliation(s)
- Chenghang Zong
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0371, USA.
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34
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Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB J 2006; 19:1389-95. [PMID: 16126906 DOI: 10.1096/fj.04-3590hyp] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An energy landscape approach predicts the conformational changes of the configurations of the regulatory domain of the protein nuclear factor of activated T cells (NFAT) caused by phosphorylation of specific multiple sites. Structurally local effects and secondary structural changes are modeled using all-atom Brownian dynamics to investigate the changes of the backbone torsional distributions upon phosphorylation. For tertiary and global changes, we employ a coarse-grained model to sample ensembles of conformations both with and without phosphorylation. At the secondary structure level, phosphorylation moderately increases the helical propensity and gives a more rigid local backbone conformation. The tertiary effects of phosphorylation caused by the extensive charge modification are more pronounced and collectively change the conformation of the regulatory domain of NFAT from a flexible globular ensemble to a rather rigid helical bundle, blocking access to the nuclear localization sequence. These studies give computational support to one scenario conjectured from experiments.
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Affiliation(s)
- Tongye Shen
- Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, La Jolla, California, USA
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35
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Weinkam P, Zong C, Wolynes PG. A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proc Natl Acad Sci U S A 2005; 102:12401-6. [PMID: 16116080 PMCID: PMC1194935 DOI: 10.1073/pnas.0505274102] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteins fold through a variety of mechanisms. For a given protein, folding routes largely depend on the protein's stability and its native-state geometry, because the landscape is funneled. These ideas are corroborated for cytochrome c by using a coarse-grained topology-based model with a perfect funnel landscape that includes explicit modeling of the heme. The results show the importance of the heme as a nucleation site and explain the observed hydrogen exchange patterns of cytochrome c within the context of energy landscape theory.
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Affiliation(s)
- Patrick Weinkam
- Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
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36
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Georgescu MM, Kirsch KH, Shishido T, Zong C, Hanafusa H. Biological effects of c-Mer receptor tyrosine kinase in hematopoietic cells depend on the Grb2 binding site in the receptor and activation of NF-kappaB. Mol Cell Biol 1999; 19:1171-81. [PMID: 9891051 PMCID: PMC116046 DOI: 10.1128/mcb.19.2.1171] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The c-Mer receptor tyrosine kinase (RTK) is most closely related to chicken c-Eyk and belongs to the Axl RTK subfamily. Although not detected in normal lymphocytes, c-Mer is expressed in B- and T-cell leukemia cell lines, suggesting an association with lymphoid malignancies. To gain an understanding of the role of this receptor in lymphoid cells, we expressed in murine interleukin-3 (IL-3)-dependent Ba/F3 pro-B-lymphocyte cells a constitutively active receptor, CDMer, formed from the CD8 extracellular domain and the c-Mer intracellular domain. Cells transfected with a plasmid encoding the CDMer receptor became IL-3 independent. When tyrosine (Y)-to-phenylalanine (F) mutations were introduced into c-Mer, only the Y867 change significantly reduced the IL-3-independent cell proliferation. The Y867 residue in the CDMer receptor mediated the binding of Grb2, which recruited the p85 phosphatidylinositol 3-kinase (PI 3-kinase). Despite the difference in promotion of proliferation, both the CDMer and mutant F867 receptors activated Erk in transfected cells. On the other hand, we found that both transcriptional activation of NF-kappaB and activation of PI 3-kinase were significantly suppressed with the F867 mutant receptor, suggesting that the activation of antiapoptotic pathways is the major mechanism for the observed phenotypic difference. Consistent with this notion, apoptosis induced by IL-3 withdrawal was strongly prevented by CDMer but not by the F867 mutant receptor.
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Affiliation(s)
- M M Georgescu
- Laboratory of Molecular Oncology, The Rockefeller University, New York, New York 10021, USA
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37
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Nagata K, Ohashi K, Nakano T, Arita H, Zong C, Hanafusa H, Mizuno K. Identification of the product of growth arrest-specific gene 6 as a common ligand for Axl, Sky, and Mer receptor tyrosine kinases. J Biol Chem 1996; 271:30022-7. [PMID: 8939948 DOI: 10.1074/jbc.271.47.30022] [Citation(s) in RCA: 373] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Axl, Sky, and Mer, members of an Axl/Sky receptor tyrosine kinase subfamily, are typified by the cell adhesion molecule-related extracellular domain. The product of growth arrest-specific gene 6 (Gas6), structurally homologous to the anticoagulant protein S, was recently identified as the ligand for Axl and Sky, but the ligand for Mer remained unknown. We have now obtained evidence that Gas6 can also function as a ligand for Mer. Co-precipitation analysis, using soluble receptors of Axl, Sky, and Mer (Axl-Fc, Sky-Fc, and Mer-Fc) composed of the extracellular domain of receptors fused to the Fc domain of immunoglobulin G1, clearly showed that Gas6, but not protein S, specifically bound to Axl-Fc, Sky-Fc, and Mer-Fc fusion proteins. Quantitative kinetic analyses using a BIAcore biosensor instrument revealed dissociation constants (Kd) of the binding of rat Gas6 to Axl-Fc, Sky-Fc, and Mer-Fc are 0.4, 2.7, and 29 nM, respectively. We also found that Gas6 stimulated tyrosine phosphorylation of Axl, Sky, and Mer receptors ectopically expressed in Chinese hamster ovary cells. Taken together, these findings suggest that Gas6 is a common ligand for Axl, Sky, and Mer, all known members of an Axl/Sky receptor subfamily.
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Affiliation(s)
- K Nagata
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 812-81, Japan
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38
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Zong C, Yan R, August A, Darnell JE, Hanafusa H. Unique signal transduction of Eyk: constitutive stimulation of the JAK-STAT pathway by an oncogenic receptor-type tyrosine kinase. EMBO J 1996. [DOI: 10.1002/j.1460-2075.1996.tb00829.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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39
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Zong C, Yan R, August A, Darnell JE, Hanafusa H. Unique signal transduction of Eyk: constitutive stimulation of the JAK-STAT pathway by an oncogenic receptor-type tyrosine kinase. EMBO J 1996; 15:4515-25. [PMID: 8887543 PMCID: PMC452181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The proto-oncogene c-eyk, the cellular counterpart of a transforming oncogene, v-eyk, encodes a receptor protein tyrosine kinase with a distinctive extracellular region. We now demonstrate that c-Eyk can be constitutively activated through dimerization, and that the active Eyk displays a unique signaling pattern. When the kinase domain of c-Eyk was fused to the extracellular and transmembrane domains of CD8, the resulting chimera showed elevated kinase activity and caused cellular transformation. We found that the activated Eyk kinases, both v- and c-Eyk, constitutively stimulate the JAK-STAT pathway, while exerting little effect on other signaling routes such as the Ras-MAP kinase and the JNK pathways. The activated Eyk kinases specifically stimulate tyrosine phosphorylation of STAT1, STAT3 and JAK1. These downstream molecules also co-immunoprecipitate with the constitutively dimerized form of Eyk. The Eyk kinase activity is required for STAT1 stimulation. We found that the activation of STAT1 but not STAT3 correlates well with cellular transformation. In constitutively stimulating the JAK-STAT pathway, particularly STAT1, Eyk is unique in its downstream signaling and may be dependent on this pathway for cellular transformation.
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Affiliation(s)
- C Zong
- Laboratory of Molecular Oncology, The Rockefeller University, New York, NY 10021-6399, USA
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40
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Abstract
Monoclonal antibodies were raised against a specific human sperm protein and designated as the YWK-II mAb. The partial cDNA encoding the protein was isolated from a rat testis lambda gt11 expression library and the amino acid sequence of the protein was deduced. The cytoplasmic-transmembrane domains of the deduced protein had high homology with the A4 amyloid precursor protein of Alzheimer's disease. To evaluate the stage of spermatogenesis when the gene was expressed, single-stranded 35S-labeled RNA probes were prepared from the cDNA. By an in situ hybridization technique the mRNA for the antigen was detected in germ cells at all stages of spermatogenesis. The finding that the gene is expressed in spermatogonia suggests possible involvement in the initiation of germ cell differentiation or in the detachment of spermatogonia from the basement membrane.
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Affiliation(s)
- Y C Yan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing
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Wang LF, Miao SY, Yan YC, Li YH, Zong C, Koide SS. Expression of a sperm protein gene during spermatogenesis in mammalian testis: an in situ hybridization study. Mol Reprod Dev 1990; 26:1-5. [PMID: 1693279 DOI: 10.1002/mrd.1080260102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In previous work a specific membrane protein with an estimated Mr of 20.1 kDa was purified from rabbit sperm tails and designated as rSMP-B protein. Antibodies were raised against rSMP-B protein and used to isolate and identify the cDNA coding the rSMP-B protein from a rat testis lambda gt11 expression library. The nucleotide sequence of the cDNA was determined in a previous study. Single-stranded 35S-labeled RNA probes were prepared. With the techniques of in situ hybridization, rSMP-B mRNA was detected in spermatids of rat and rabbit testis. The present results support our previous observation that immunization of male rabbits with the rSMP-B protein results in the arrest of spermatogenesis at the spermatid stage. Overall, rSMP-B protein appears to be involved in spermiogenesis, and the synthesis of the mRNA encoding the protein occurs in germ cells during the postmeiotic haploid phase of spermatogenesis.
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Affiliation(s)
- L F Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing
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