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Sun Z, Li G, Shang D, Zhang J, Ai L, Liu M. Identification of microsatellite instability and immune-related prognostic biomarkers in colon adenocarcinoma. Front Immunol 2022; 13:988303. [PMID: 36275690 PMCID: PMC9585257 DOI: 10.3389/fimmu.2022.988303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundColon adenocarcinoma (COAD) is a prevalent malignancy that causes significant mortality. Microsatellite instability plays a pivotal function in COAD development and immunotherapy resistance. However, the detailed underlying mechanism requires further investigation. Consequently, identifying molecular biomarkers with prognostic significance and revealing the role of MSI in COAD is important for addressing key obstacles in the available treatments.MethodsCIBERSORT and ESTIMATE analyses were performed to evaluate immune infiltration in COAD samples, followed by correlation analysis for MSI and immune infiltration. Then, differentially expressed genes (DEGs) in MSI and microsatellite stability (MSS) samples were identified and subjected to weighted gene co-expression network analysis (WGCNA). A prognostic model was established with univariate cox regression and LASSO analyses, then evaluated with Kaplan-Meier analysis. The correlation between the prognostic model and immune checkpoint inhibitor (ICI) response was also analyzed.ResultsIn total, 701 significant DEGs related to MSI status were identified, and WGCNA revealed two modules associated with the immune score. Then, a seven-gene prognostic model was constructed using LASSO and univariate cox regression analyses to predict survival and ICI response. The high-risk score patients in TCGA and GEO cohorts presented a poor prognosis, as well as a high immune checkpoint expression, so they are more likely to benefit from ICI treatment.ConclusionThe seven-gene prognostic model constructed could predict the survival of COAD and ICI response and serve as a reference for immunotherapy decisions.
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Affiliation(s)
- Ziquan Sun
- Colorectal Cancer Surgery Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jinning Zhang
- Colorectal Cancer Surgery Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lianjie Ai
- Colorectal Cancer Surgery Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ming Liu
- Colorectal Cancer Surgery Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Ming Liu,
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Transcriptome Changes in Retinal Pigment Epithelium Post-PNU-282987 Treatment Associated with Adult Retinal Neurogenesis in Mice. J Mol Neurosci 2022; 72:1990-2010. [PMID: 35867327 DOI: 10.1007/s12031-022-02049-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/12/2022] [Indexed: 10/17/2022]
Abstract
PNU-282987, a selective alpha7 nicotinic acetylcholine receptor agonist, has previously been shown to have both neurogenic and broad regenerative effects in the adult murine retina. The objective of this study was to assay the molecular mechanism by which PNU-282987 promotes the production of Muller-derived progenitor cells through signaling via the resident retinal pigment epithelium. These Muller-derived progenitor cells generate a myriad of differentiated neurons throughout the retina that have previously been characterized by morphology. Herein, we demonstrate that topical application of PNU-282987 stimulates production of functional neurons as measured by electroretinograms. Further, we examine the mechanism of how this phenomenon occurs through activation of this atypical receptor using a transcriptomic approach isolated retinal pigment epithelium activated by PNU-282987 and in whole retina. We provide evidence that PNU-282987 causes a bi-modal signaling event in which early activation primes the retina with an inflammatory response and developmental signaling cues, followed by an inhibition of gliotic mechanisms and a decrease in the immune response, ending with upregulation of genes associated with specific retinal neuron generation. Taken together, these data provide evidence that PNU-282987 activates the retinal pigment epithelium to signal to Muller glia to produce Muller-derived progenitor cells, which can differentiate into new, functional neurons in adult mice. These data not only increase our understanding of how adult mammalian retinal regeneration can occur, but also provide therapeutic promise for treating functional vision loss.
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Yu H, Tang D, Wu H, Li C, Lu Y, He F, Zhang X, Yang Y, Shi W, Hu W, Zeng Z, Dai W, Ou M, Dai Y. Integrated single-cell analyses decode the developmental landscape of the human fetal spine. iScience 2022; 25:104679. [PMID: 35832888 PMCID: PMC9272381 DOI: 10.1016/j.isci.2022.104679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
The spine has essential roles in supporting body weight, and passaging the neural elements between the body and the brain. In this study, we used integrated single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing analyses to reveal the cellular heterogeneity, lineage, and transcriptional regulatory network of the developing human spine. We found that EPYC + HAPLN1+ fibroblasts with stem cell characteristics could differentiate into chondrocytes by highly expressing the chondrogenic markers SOX9 and MATN4. Neurons could originate from neuroendocrine cells, and MEIS2 may be an essential transcription factor that promotes spinal neural progenitor cells to selectively differentiate into neurons during early gestation. Furthermore, the interaction of NRP2_SEMA3C and CD74_APP between macrophages and neurons may be essential for spinal cord development. Our integrated map provides a blueprint for understanding human spine development in the early and midgestational stages at single-cell resolution and offers a tool for investigating related diseases. scRNA-seq and scATAC-seq analyses reveal the developmental landscape of the fetal spine Chondrocytes may originate from EPYC + HAPLN1+ fibroblasts with stem cell characteristics Neurons may originate from neuroendocrine cells with regulation by MEIS2
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Affiliation(s)
- Haiyan Yu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China.,Department of Pharmacy, Shenzhen Pingshan District People's Hospital, Pingshan General Hospital of Southern Medical University, Shenzhen, Guangdong 518118, P.R. China
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Hongwei Wu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Chunhong Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yongping Lu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China.,Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Fang He
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China
| | - Xiaogang Zhang
- Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China
| | - Yane Yang
- Shenzhen Far East Women & Children Hospital, Shenzhen 518000, Guangdong, China
| | - Wei Shi
- Department of Obstetrics and Gynecology, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Wenlong Hu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Zhipeng Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX 78721, USA
| | - Minglin Ou
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Lingui District, Guilin 541000, China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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Li J, Sun C, Zheng J, Li J, Yi G, Yang N. Time-Course Transcriptional and Chromatin Accessibility Profiling Reveals Genes Associated With Asymmetrical Gonadal Development in Chicken Embryos. Front Cell Dev Biol 2022; 10:832132. [PMID: 35345851 PMCID: PMC8957256 DOI: 10.3389/fcell.2022.832132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
In birds, male gonads form on both sides whereas most females develop asymmetric gonads. Multiple early lines of evidence suggested that the right gonad fails to develop into a functional ovary, mainly due to differential expression of PITX2 in the gonadal epithelium. Despite some advances in recent years, the molecular mechanisms underlying asymmetric gonadal development remain unclear. Here, using bulk analysis of whole gonads, we established a relatively detailed profile of four representative stages of chicken gonadal development at the transcriptional and chromatin levels. We revealed that many candidate genes were significantly enriched in morphogenesis, meiosis and subcellular structure formation, which may be responsible for asymmetric gonadal development. Further chromatin accessibility analysis suggested that the transcriptional activities of the candidate genes might be regulated by nearby open chromatin regions, which may act as transcription factor (TF) binding sites and potential cis-regulatory elements. We found that LHX9 was a promising TF that bound to the left-biased peaks of many cell cycle-related genes. In summary, this study provides distinctive insights into the potential molecular basis underlying the asymmetric development of chicken gonads.
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Affiliation(s)
- Jianbo Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Aguiar GDM, Ramão A, Plaça JR, Simões SC, Scaraboto NV, Freitas-Castro F, Cardoso C, Sousa JDF, Silva WA. Upregulation of HOX genes promotes cell migration and proliferation in head and neck squamous cell carcinoma. Tumour Biol 2021; 43:263-278. [PMID: 34633333 DOI: 10.3233/tub-211525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Expression dysregulation of HOX homeobox genes has been observed in several cancers, including head and neck squamous cell carcinoma (HNSC). Although characterization of HOX gene roles in HNSC development has been reported, there is still a need to better understand their real contribution to tumorigenesis. OBJECTIVE The present study aimed to evaluate the contribution of the protein-coding HOX genes (HOXA10, HOXC9, HOXC10, and HOXC13) in cellular processes related to carcinogenesis and progression of the HNSC. METHODS Expression of HOX genes was analyzed in HNSC RNA-Seq data from The Cancer Genome Atlas (TCGA) and by RT-qPCR in different tumor cell lines. siRNA-mediated knockdown of HOXA10, HOXC9, HOXC10 or HOXC13 was performed in HNSC cell lines, and predicted transcriptional targets HOX genes was analyzed by bioinformatic. RESULTS Thirty-one out of the 39 mammalian HOX genes were found upregulated in HNSC tissues and cell lines. The HOXC9, HOXC10 or HOXC13 knockdown attenuated cell migration, and lead to downregulation of epithelial-mesenchymal transition (EMT) markers, which were predicted as transcriptional targets of these three HOX genes. Diminished colony formation and cell cycle arrest after HOXC10 or HOXC13 knockdown were also observed, corroborating the fact that there was an enrichment for genes in proliferation/cell cycle pathways. CONCLUSIONS In summary, we revealed roles for HOXC9, HOXC10, and HOXC13 in cell migration and proliferation/cell cycle progression in HNSC cells and suggested that those HOX members contribute to HNSC development possibly by regulating tumor growth and metastasis.
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Affiliation(s)
- Graziela de Moura Aguiar
- Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Anelisa Ramão
- Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Sarah Capelupe Simões
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Natália Volgarine Scaraboto
- Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Felipe Freitas-Castro
- Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cibele Cardoso
- Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Josane de Freitas Sousa
- Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Wilson Araújo Silva
- Department of Medical Imaging, Hematology and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center of Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
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Di Persio S, Tekath T, Siebert-Kuss LM, Cremers JF, Wistuba J, Li X, Meyer Zu Hörste G, Drexler HCA, Wyrwoll MJ, Tüttelmann F, Dugas M, Kliesch S, Schlatt S, Laurentino S, Neuhaus N. Single-cell RNA-seq unravels alterations of the human spermatogonial stem cell compartment in patients with impaired spermatogenesis. CELL REPORTS MEDICINE 2021; 2:100395. [PMID: 34622232 PMCID: PMC8484693 DOI: 10.1016/j.xcrm.2021.100395] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/01/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023]
Abstract
Despite the high incidence of male infertility, only 30% of infertile men receive a causative diagnosis. To explore the regulatory mechanisms governing human germ cell function in normal and impaired spermatogenesis (crypto), we performed single-cell RNA sequencing (>30,000 cells). We find major alterations in the crypto spermatogonial compartment with increased numbers of the most undifferentiated spermatogonia (PIWIL4+). We also observe a transcriptional switch within the spermatogonial compartment driven by increased and prolonged expression of the transcription factor EGR4. Intriguingly, the EGR4-regulated chromatin-associated transcriptional repressor UTF1 is downregulated at transcriptional and protein levels. This is associated with changes in spermatogonial chromatin structure and fewer Adark spermatogonia, characterized by tightly compacted chromatin and serving as reserve stem cells. These findings suggest that crypto patients are disadvantaged, as fewer cells safeguard their germline’s genetic integrity. These identified spermatogonial regulators will be highly interesting targets to uncover genetic causes of male infertility. Crypto(zoospermic) men show increased number of PIWIL4+/EGR4+ spermatogonia Crypto undifferentiated spermatogonia over-activate the EGR4 regulatory network The predicted EGR4 target UTF1 is downregulated in crypto spermatogonia Crypto testes show reduced numbers of UTF1+ Adark reserve spermatogonia
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Affiliation(s)
- Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Tobias Tekath
- Institute of Medical Informatics, University Hospital of Münster, 48149 Münster, Germany
| | - Lara Marie Siebert-Kuss
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Jann-Frederik Cremers
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Joachim Wistuba
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Xiaolin Li
- Department of Neurology with Institute of Translational Neurology, University Hospital of Münster, 48149 Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital of Münster, 48149 Münster, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Margot Julia Wyrwoll
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149 Münster, Germany.,Institute of Reproductive Genetics, University of Münster, 48149 Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, 48149 Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital of Münster, 48149 Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Stefan Schlatt
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149 Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149 Münster, Germany
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Cai Z, Zhang F, Chen W, Zhang J, Li H. miRNAs: A Promising Target in the Chemoresistance of Bladder Cancer. Onco Targets Ther 2019; 12:11805-11816. [PMID: 32099386 PMCID: PMC6997227 DOI: 10.2147/ott.s231489] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chemotherapy is an important cancer treatment method. Tumor chemotherapy resistance is one of the main factors leading to tumor progression. Like other malignancies, bladder cancer, especially muscle-invasive bladder cancer, is prone to chemotherapy resistance. Additionally, only approximately 50% of muscle-invasive bladder cancer responds to cisplatin-based chemotherapy. miRNAs are a class of small, endogenous, noncoding RNAs that regulate gene expression at the posttranscriptional level, which results in the inhibition of translation or the degradation of mRNA. In the study of miRNAs and cancer, including gastric cancer, prostate cancer, liver cancer, and colorectal cancer, it has been found that miRNAs can regulate the expression of genes related to tumor resistance, thereby promoting the progression of tumors. In bladder cancer, miRNAs are also closely related to chemotherapy resistance, suggesting that miRNAs can be a new therapeutic target for the chemotherapy resistance of bladder cancer. Therefore, understanding the mechanisms of miRNAs in the chemotherapy resistance of bladder cancer is an important foundation for restoring the chemotherapy sensitivity of bladder cancer and improving the efficacy of chemotherapy and patient survival. In this article, we review the role of miRNAs in the development of chemotherapy-resistant bladder cancer and the various resistance mechanisms that involve apoptosis, the cell cycle, epithelial-mesenchymal transition (EMT), and cancer stem cells (CSCs).
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Affiliation(s)
- Zhonglin Cai
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Fa Zhang
- Department of Urology, First Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Weijie Chen
- Department of Urology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai Traditional Chinese Medicine University, Shanghai, People's Republic of China
| | - Jianzhong Zhang
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Hongjun Li
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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Veselska R, Jezova M, Kyr M, Mazanek P, Chlapek P, Dobrotkova V, Sterba J. Comparative Analysis of Putative Prognostic and Predictive Markers in Neuroblastomas: High Expression of PBX1 Is Associated With a Poor Response to Induction Therapy. Front Oncol 2019; 9:1221. [PMID: 31803613 PMCID: PMC6872531 DOI: 10.3389/fonc.2019.01221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The survival rate for patients with high-risk neuroblastomas remains poor despite new improvements in available therapeutic modalities. A detailed understanding of the mechanisms underlying clinical responses to multimodal treatment is one of the important aspects that may provide precision in the prediction of a patient's clinical outcome. Our study was designed as a detailed comparative analysis of five selected proteins (DDX39A, HMGA1, HOXC9, NF1, and PBX1) in one cohort of patients using the same methodical approaches. These proteins were already reported separately as related to the resistance or sensitivity to retinoids and as useful prognostic markers of survival probability. In the cohort of 19 patients suffering from high-risk neuroblastomas, we analyzed initial immunohistochemistry samples obtained by diagnostic biopsy and post-induction samples taken after the end of induction therapy. The expression of DDX39A, HMGA1, HOXC9, and NF1 showed varied patterns with almost no differences between responders and non-responders. Nevertheless, we found very interesting results for PBX1: non-responders had significantly higher expression levels of this protein in the initial tumor samples when compared with responders; this expression pattern changed inversely in the post-induction samples, and this change was also statistically significant. Moreover, our results from survival analyses reveal the prognostic value of PBX1, NF1, and HOXC9 expression in neuroblastoma tissue. In addition to the prognostic importance of PBX1, NF1, and HOXC9 proteins, our results demonstrated that PBX1 could be used for the prediction of the clinical response to induction chemotherapy in patients suffering from high-risk neuroblastoma.
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Affiliation(s)
- Renata Veselska
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia.,Department of Pediatric Oncology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Marta Jezova
- Department of Pathology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czechia
| | - Michal Kyr
- Department of Pediatric Oncology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Pavel Mazanek
- Department of Pediatric Oncology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czechia
| | - Petr Chlapek
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Viera Dobrotkova
- Laboratory of Tumor Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Jaroslav Sterba
- Department of Pediatric Oncology, Faculty of Medicine, University Hospital Brno, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
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Molecular profiling of TOX-deficient neoplastic cells in cutaneous T cell lymphoma. Arch Dermatol Res 2019; 312:513-525. [PMID: 31676945 PMCID: PMC7354281 DOI: 10.1007/s00403-019-02000-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 08/28/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
Cutaneous T cell lymphoma (CTCL) is a rare but potentially devastating primary cutaneous lymphoma. CTCL is characterized by localization of neoplastic T lymphocytes to the skin, with mycosis fungoides (MF) and its leukemic form, Sézary syndrome (SS) being the most common variants. Thymocyte selection-associated high-mobility group box (TOX) gene has been found to be highly expressed in MF and SS. It is reported that higher expression levels of TOX in patients will increase risks of disease progression and poor prognosis. However, the molecular events leading to these abnormalities have not been well understood. To better understand the molecular mechanism underlying TOX-mediated differentially expressed genes (DEGs) in CTCL, and to identify DEGs pathways triggered after knockdown of TOX gene in the CTCL cell line Hut78, we employed two shRNA-mediated lentiviruses to knock down TOX gene in the skin lymphoma cell line HuT78. RNA sequencing (RNAseq) analysis was applied to analyze DEGs, DEGs GO and their corresponding pathways. Knockdown of TOX can induce upregulation of 547 genes and downregulation of 649 genes, respectively. HOXC9 was the most significant downregulated gene. Most DEGs are enriched in malignancies and relate to the Wnt and mTOR signaling pathways, and therefore they can regulate cellular processes and induce different biological regulation. Transcriptome analysis of DEGs after knockdown of TOX in our study provides insights into the mechanism of TOX in CTCL and suggests candidate targets for therapy of CTCL.
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10
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Coughlan E, Garside VC, Wong SFL, Liang H, Kraus D, Karmakar K, Maheshwari U, Rijli FM, Bourne J, McGlinn E. A Hox Code Defines Spinocerebellar Neuron Subtype Regionalization. Cell Rep 2019; 29:2408-2421.e4. [DOI: 10.1016/j.celrep.2019.10.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/12/2019] [Accepted: 10/10/2019] [Indexed: 11/25/2022] Open
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Luo Z, Rhie SK, Farnham PJ. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel) 2019; 11:cancers11030323. [PMID: 30866492 PMCID: PMC6468460 DOI: 10.3390/cancers11030323] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
Homeobox genes (HOX) are a large family of transcription factors that direct the formation of many body structures during early embryonic development. There are 39 genes in the subgroup of homeobox genes that constitute the human HOX gene family. Correct embryonic development of flies and vertebrates is, in part, mediated by the unique and highly regulated expression pattern of the HOX genes. Disruptions in these fine-tuned regulatory mechanisms can lead to developmental problems and to human diseases such as cancer. Unfortunately, the molecular mechanisms of action of the HOX family of transcription factors are severely under-studied, likely due to idiosyncratic details of their structure, expression, and function. We suggest that a concerted and collaborative effort to identify interacting protein partners, produce genome-wide binding profiles, and develop HOX network inhibitors in a variety of human cell types will lead to a deeper understanding of human development and disease. Within, we review the technological challenges and possible approaches needed to achieve this goal.
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Affiliation(s)
- Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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12
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Yang L, Zha Y, Ding J, Ye B, Liu M, Yan C, Dong Z, Cui H, Ding HF. Histone demethylase KDM6B has an anti-tumorigenic function in neuroblastoma by promoting differentiation. Oncogenesis 2019; 8:3. [PMID: 30631055 PMCID: PMC6328563 DOI: 10.1038/s41389-018-0112-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/19/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023] Open
Abstract
Induction of differentiation is a therapeutic strategy in high-risk neuroblastoma, a childhood cancer of the sympathetic nervous system. Neuroblastoma differentiation requires transcriptional upregulation of neuronal genes. How this process is regulated at epigenetic levels is not well understood. Here we report that the histone H3 lysine 27 demethylase KDM6B is an epigenetic activator of neuroblastoma cell differentiation. KDM6B mRNA expression is downregulated in poorly differentiated high-risk neuroblastomas and upregulated in differentiated tumors, and high KDM6B expression is prognostic for better survival in neuroblastoma patients. In neuroblastoma cell lines, KDM6B depletion promotes cell proliferation, whereas KDM6B overexpression induces neuronal differentiation and inhibits cell proliferation and tumorgenicity. Mechanistically, KDM6B epigenetically activates the transcription of neuronal genes by removing the repressive chromatin marker histone H3 lysine 27 trimethylation. In addition, we show that KDM6B functions downstream of the retinoic acid-HOXC9 axis in inducing neuroblastoma cell differentiation: KDM6B expression is upregulated by retinoic acid via HOXC9, and KDM6B is required for HOXC9-induced neuroblastoma cell differentiation. Finally, we present evidence that KDM6B interacts with HOXC9 to target neuronal genes for epigenetic activation. These findings identify a KDM6B-dependent epigenetic mechanism in the control of neuroblastoma cell differentiation, providing a rationale for reducing histone H3 lysine 27 trimethylation as a strategy for enhancing differentiation-based therapy in high-risk neuroblastoma.
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Affiliation(s)
- Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Jane Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Bingwei Ye
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Mengling Liu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA.,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Charlie Norwood VA Medical Center, Augusta, GA, 30904, USA
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
| | - Han-Fei Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA. .,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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13
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Transcriptional Profiling Reveals a Common Metabolic Program in High-Risk Human Neuroblastoma and Mouse Neuroblastoma Sphere-Forming Cells. Cell Rep 2017; 17:609-623. [PMID: 27705805 DOI: 10.1016/j.celrep.2016.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/04/2016] [Accepted: 09/08/2016] [Indexed: 01/02/2023] Open
Abstract
High-risk neuroblastoma remains one of the deadliest childhood cancers. Identification of metabolic pathways that drive or maintain high-risk neuroblastoma may open new avenues of therapeutic interventions. Here, we report the isolation and propagation of neuroblastoma sphere-forming cells with self-renewal and differentiation potential from tumors of the TH-MYCN mouse, an animal model of high-risk neuroblastoma with MYCN amplification. Transcriptional profiling reveals that mouse neuroblastoma sphere-forming cells acquire a metabolic program characterized by transcriptional activation of the cholesterol and serine-glycine synthesis pathways, primarily as a result of increased expression of sterol regulatory element binding factors and Atf4, respectively. This metabolic reprogramming is recapitulated in high-risk human neuroblastomas and is prognostic for poor clinical outcome. Genetic and pharmacological inhibition of the metabolic program markedly decreases the growth and tumorigenicity of both mouse neuroblastoma sphere-forming cells and human neuroblastoma cell lines. These findings suggest a therapeutic strategy for targeting the metabolic program of high-risk neuroblastoma.
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14
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Bhosale PG, Cristea S, Ambatipudi S, Desai RS, Kumar R, Patil A, Kane S, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB. Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer. Transl Oncol 2017; 10:396-409. [PMID: 28433800 PMCID: PMC5403767 DOI: 10.1016/j.tranon.2017.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 12/11/2022] Open
Abstract
We present an integrative genome-wide analysis that can be used to predict the risk of progression from leukoplakia to oral squamous cell carcinoma (OSCC) arising in the gingivobuccal complex (GBC). We find that the genomic and transcriptomic profiles of leukoplakia resemble those observed in later stages of OSCC and that several changes are associated with this progression, including amplification of 8q24.3, deletion of 8p23.2, and dysregulation of DERL3, EIF5A2, ECT2, HOXC9, HOXC13, MAL, MFAP5 and NELL2. Comparing copy number profiles of primary tumors with and without lymph-node metastasis, we identify alterations associated with metastasis, including amplifications of 3p26.3, 8q24.21, 11q22.1, 11q22.3 and deletion of 8p23.2. Integrative analysis reveals several biomarkers that have never or rarely been reported in previous OSCC studies, including amplifications of 1p36.33 (attributable to MXRA8), 3q26.31 (EIF5A2), 9p24.1 (CD274), and 12q13.2 (HOXC9 and HOXC13). Additionally, we find that amplifications of 1p36.33 and 11q22.1 are strongly correlated with poor clinical outcome. Overall, our findings delineate genomic changes that can be used in treatment management for patients with potentially malignant leukoplakia and OSCC patients with higher risk of lymph-node metastasis.
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Affiliation(s)
- Priyanka G Bhosale
- Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Navi Mumbai, 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, India
| | - Simona Cristea
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Srikant Ambatipudi
- Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Navi Mumbai, 410210, India; MRC Integrative Epidemiology Unit, University of Bristol, BS8 1TH, UK
| | - Rajiv S Desai
- Department of Oral Pathology & Microbiology, Nair Hospital Dental College, Mumbai, 400 008, India
| | - Rajiv Kumar
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre (TMC), Parel, Mumbai, 400012, India
| | - Asawari Patil
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre (TMC), Parel, Mumbai, 400012, India
| | - Shubhada Kane
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre (TMC), Parel, Mumbai, 400012, India
| | - Anita M Borges
- Department of Pathology & Laboratory Medicine, S. L. Raheja Hospital, Mumbai, 400016, India
| | - Alejandro A Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, National Institute of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, MD, 20894, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Manoj B Mahimkar
- Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Navi Mumbai, 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, India.
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15
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Rezsohazy R, Saurin AJ, Maurel-Zaffran C, Graba Y. Cellular and molecular insights into Hox protein action. Development 2016; 142:1212-27. [PMID: 25804734 DOI: 10.1242/dev.109785] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hox genes encode homeodomain transcription factors that control morphogenesis and have established functions in development and evolution. Hox proteins have remained enigmatic with regard to the molecular mechanisms that endow them with specific and diverse functions, and to the cellular functions that they control. Here, we review recent examples of Hox-controlled cellular functions that highlight their versatile and highly context-dependent activity. This provides the setting to discuss how Hox proteins control morphogenesis and organogenesis. We then summarise the molecular modalities underlying Hox protein function, in particular in light of current models of transcription factor function. Finally, we discuss how functional divergence between Hox proteins might be achieved to give rise to the many facets of their action.
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Affiliation(s)
- René Rezsohazy
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve B-1348, Belgium
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
| | | | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
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16
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Zhao E, Ding J, Xia Y, Liu M, Ye B, Choi JH, Yan C, Dong Z, Huang S, Zha Y, Yang L, Cui H, Ding HF. KDM4C and ATF4 Cooperate in Transcriptional Control of Amino Acid Metabolism. Cell Rep 2016; 14:506-519. [PMID: 26774480 DOI: 10.1016/j.celrep.2015.12.053] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 11/10/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022] Open
Abstract
The histone lysine demethylase KDM4C is often overexpressed in cancers primarily through gene amplification. The molecular mechanisms of KDM4C action in tumorigenesis are not well defined. Here, we report that KDM4C transcriptionally activates amino acid biosynthesis and transport, leading to a significant increase in intracellular amino acid levels. Examination of the serine-glycine synthesis pathway reveals that KDM4C epigenetically activates the pathway genes under steady-state and serine deprivation conditions by removing the repressive histone modification H3 lysine 9 (H3K9) trimethylation. This action of KDM4C requires ATF4, a transcriptional master regulator of amino acid metabolism and stress responses. KDM4C activates ATF4 transcription and interacts with ATF4 to target serine pathway genes for transcriptional activation. We further present evidence for KDM4C in transcriptional coordination of amino acid metabolism and cell proliferation. These findings suggest a molecular mechanism linking KDM4C-mediated H3K9 demethylation and ATF4-mediated transactivation in reprogramming amino acid metabolism for cancer cell proliferation.
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Affiliation(s)
- Erhu Zhao
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and System Biology, Southwest University, Chongqing 400715, China; Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Jane Ding
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Yingfeng Xia
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Insititute of Translational Neuroscience and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang 443000, China
| | - Mengling Liu
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Insititute of Translational Neuroscience and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang 443000, China
| | - Bingwei Ye
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Jeong-Hyeon Choi
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Chunhong Yan
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Shuang Huang
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL 32611, USA
| | - Yunhong Zha
- Insititute of Translational Neuroscience and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang 443000, China
| | - Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and System Biology, Southwest University, Chongqing 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and System Biology, Southwest University, Chongqing 400715, China.
| | - Han-Fei Ding
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
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17
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Xuan F, Huang M, Liu W, Ding H, Yang L, Cui H. Homeobox C9 suppresses Beclin1-mediated autophagy in glioblastoma by directly inhibiting the transcription of death-associated protein kinase 1. Neuro Oncol 2015; 18:819-29. [PMID: 26582930 DOI: 10.1093/neuonc/nov281] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/16/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The transcription factor homeobox C9 (HOXC9) plays a crucial role in developmental regulatory systems, where it determines the specific positional identities of cells along the anteroposterior axis. The expression of HOXC9 has been found to be dysregulated in some cancers such as lung cancer, breast cancer, and neuroblastoma. Here, we report for the first time that HOXC9 is a novel autophagy regulator and reveal its oncogenic role in cell survival and its usefulness as a prognostic marker in glioblastoma patients. METHODS Kaplan-Meier analysis was performed to evaluate the possible prognostic value of HOXC9 in glioblastoma. Growth curve assays, subcutaneous, and orthotopic implantations were used to analyze cell viability and tumor formation, respectively. Luciferase and chromatin immunoprecipitation assays were employed to explore the mechanisms involved in the association between HOXC9 and its downstream effector, death-associated protein kinase 1 (DAPK1). RESULTS High expression of HOXC9 was found to be an indicator of a poor prognosis in glioblastoma. HOXC9 knockdown resulted in a significant reduction of cell viability, migration, invasion, and tumorigenicity and a marked increase in autophagy. During the autophagy process, HOXC9 inhibited DAPK1 transcription by directly binding to its promoter. The downregulation of HOXC9 releases its transcriptional inhibition of DAPK1, resulting in the activation of the DAPK1-Beclin1 pathway, which induces autophagy in glioblastoma cells. CONCLUSIONS Collectively, our data indicate that HOXC9 is an oncogene in glioblastoma. We have revealed its role in the control of autophagy, and we suggest that HOXC9 is a novel and promising therapeutic target.
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Affiliation(s)
- Fan Xuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China (F.X., M.H., W.L., L.Y., H.C.); Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia (H.D.)
| | - Mengying Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China (F.X., M.H., W.L., L.Y., H.C.); Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia (H.D.)
| | - Wen Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China (F.X., M.H., W.L., L.Y., H.C.); Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia (H.D.)
| | - Hanfei Ding
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China (F.X., M.H., W.L., L.Y., H.C.); Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia (H.D.)
| | - Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China (F.X., M.H., W.L., L.Y., H.C.); Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia (H.D.)
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China (F.X., M.H., W.L., L.Y., H.C.); Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia (H.D.)
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18
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Wang X, Yang L, Choi JH, Kitamura E, Chang CS, Ding J, Lee EJ, Cui H, Ding HF. Genome-wide analysis of HOXC9-induced neuronal differentiation of neuroblastoma cells. GENOMICS DATA 2014; 2:50-52. [PMID: 25013753 PMCID: PMC4084856 DOI: 10.1016/j.gdata.2014.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Induction of differentiation is a therapeutic strategy in neuroblastoma, a common pediatric cancer of the sympathetic nervous system. The homeobox protein HOXC9 is a key regulator of neuroblastoma differentiation. To gain a molecular understanding of the function of HOXC9 in promoting differentiation of neuroblastoma cells, we conducted a genome-wide analysis of the HOXC9-induced differentiation program by microarray gene expression profiling and chromatin immunoprecipitation in combination with massively parallel sequencing (ChIP-seq). Here we describe in detail the experimental system, methods, and quality control for the generation of the microarray and ChIP-seq data associated with our recent publication [1].
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19
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Lv L, Li Y, Deng H, Zhang C, Pu Y, Qian L, Xiao J, Zhao W, Liu Q, Zhang D, Wang Y, Zhang H, He Y, Zhu J. MiR-193a-3p promotes the multi-chemoresistance of bladder cancer by targeting the HOXC9 gene. Cancer Lett 2014; 357:105-113. [PMID: 25444900 DOI: 10.1016/j.canlet.2014.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 01/15/2023]
Abstract
Chemoresistance prevents the curative cancer chemotherapy and presents a formidable challenge for both cancer researchers and clinicians. We have previously shown that miR-193a-3p promotes the multi-chemoresistance of bladder cancer cells via repressing its three target genes: SRSF2, PLAU and HIC2. Here, we showed that as a new direct target, the homeobox C9 (HOXC9) gene also executes the promoting effect of miR-193a-3p on the bladder cancer chemoresistance from a systematic study of multi-chemosensitive (5637) and resistant (H-bc) bladder cancer cell lines in both cell culture and tumor-xenograft/nude mice system. Paralleled with the changes in the drug-triggered cell death, the activities of both DNA damage response and oxidative stress pathways were drastically altered by a forced reversal of miR-193a-3p or HOXC9 levels in bladder cancer cells. In addition to a new mechanistic insight, our results provide a set of the essential genes in the miR-193a-3p/HOXC9/DNA damage response/oxidative stress pathway axis as the diagnostic targets for the guided anti-bladder cancer chemotherapy.
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Affiliation(s)
- Lei Lv
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Yang Li
- Department of Biology, School of Life Science, Anhui Medical University, Hefei, Anhui 230031, China
| | - Hui Deng
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Youguang Pu
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Liting Qian
- Department of Radiotherapy, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Jun Xiao
- Department of Urology, Anhui Provincial Hospital, Hefei, Anhui, China
| | - Weidong Zhao
- Department of Gynecologic Cancer, Anhui Cancer Hospital, Hefei, Anhui 230031, China
| | - Qi Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Daming Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yingwei Wang
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hongyu Zhang
- Cancer Epigenetics Program, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University, Shanghai 200032, China
| | - Yinghua He
- Cancer Epigenetics Program, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University, Shanghai 200032, China
| | - Jingde Zhu
- Cancer Epigenetics Program, Anhui Cancer Hospital, Hefei, Anhui 230031, China; Cancer Epigenetics Program, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University, Shanghai 200032, China.
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20
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MEIS2 is essential for neuroblastoma cell survival and proliferation by transcriptional control of M-phase progression. Cell Death Dis 2014; 5:e1417. [PMID: 25210800 PMCID: PMC4540202 DOI: 10.1038/cddis.2014.370] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/14/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023]
Abstract
MEIS2 has an important role in development and organogenesis, and is implicated in the pathogenesis of human cancer. The molecular basis of MEIS2 action in tumorigenesis is not clear. Here, we show that MEIS2 is highly expressed in human neuroblastoma cell lines and is required for neuroblastoma cell survival and proliferation. Depletion of MEIS2 in neuroblastoma cells leads to M-phase arrest and mitotic catastrophe, whereas ectopic expression of MEIS2 markedly enhances neuroblastoma cell proliferation, anchorage-independent growth, and tumorigenicity. Gene expression profiling reveals an essential role of MEIS2 in maintaining the expression of a large number of late cell-cycle genes, including those required for DNA replication, G2-M checkpoint control and M-phase progression. Importantly, we identify MEIS2 as a transcription activator of the MuvB-BMYB-FOXM1 complex that functions as a master regulator of cell-cycle gene expression. Further, we show that FOXM1 is a direct target gene of MEIS2 and is required for MEIS2 to upregulate mitotic genes. These findings link a developmentally important gene to the control of cell proliferation and suggest that high MEIS2 expression is a molecular mechanism for high expression of mitotic genes that is frequently observed in cancers of poor prognosis.
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