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Chen X, Wei Q, Yang Z, Chen X, Guo S, Jiang M, Wang M. Structural basis for RNA recognition by the C-terminal RRM domain of human RBM45. J Biol Chem 2024; 300:107640. [PMID: 39122006 DOI: 10.1016/j.jbc.2024.107640] [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: 02/08/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024] Open
Abstract
RBM45 is an RNA-binding protein with roles in neural development by regulating RNA splicing. Its dysfunction and aggregation are associated with neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). RBM45 harbors three RRM domains that potentially bind RNA. While the recognitions of RNA by its N-terminal tandem RRM domains (RRM1 and RRM2) have been well understood, the RNA-binding property of its C-terminal RRM (RRM3) remains unclear. In this work, we identified that the RRM3 of the RBM45 sequence specifically binds RNA with a GACG sequence, similar but not identical to those recognized by the RRM1 and RRM2. Further, we determined the crystal structure of RBM45RRM3 in complex with a GACG sequence-containing single-stranded DNA. Our structural results, together with the RNA-binding assays of mutants at key amino acid residues, revealed the molecular mechanism by which RBM45RRM3 recognizes an RNA sequence. Our finding on the RNA-binding property of the individual RRM module of RBM45 provides the foundation for unraveling the RNA-binding characteristics of full-length RBM45 and for understanding the biological functions of RBM45.
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Affiliation(s)
- Xi Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Qinghao Wei
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Zhongmei Yang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiaolei Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Shuoxuan Guo
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Meiyu Jiang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China; School of Life Sciences, Anhui University, Hefei, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China.
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2
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Lv Y, Sun S, Zhang J, Wang C, Chen C, Zhang Q, Zhao J, Qi Y, Zhang W, Wang Y, Li M. Loss of RBM45 inhibits breast cancer progression by reducing the SUMOylation of IRF7 to promote IFNB1 transcription. Cancer Lett 2024; 596:216988. [PMID: 38797234 DOI: 10.1016/j.canlet.2024.216988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Type I interferons exhibit anti-proliferative and anti-cancer activities, but their detailed regulatory mechanisms in cancer have not been fully elucidated yet. RNA binding proteins are master orchestrators of gene regulation, which are closely related to tumor progression. Here we show that the upregulated RNA binding protein RBM45 correlates with poor prognosis in breast cancer. Depletion of RBM45 suppresses breast cancer progression both in cultured cells and xenograft mouse models. Mechanistically, RBM45 ablation inhibits breast cancer progression through regulating type I interferon signaling, particularly by elevating IFN-β production. Importantly, RBM45 recruits TRIM28 to IRF7 and stimulates its SUMOylation, thereby repressing IFNB1 transcription. Loss of RBM45 reduced the SUMOylation of IRF7 by reducing the interaction between TRIM28 and IRF7 to promote IFNB1 transcription, leading to the inhibition of breast cancer progression. Taken together, our finding uncovers a vital role of RBM45 in modulating type I interferon signaling and cancer aggressive progression, implicating RBM45 as a potential therapeutic target in breast cancer.
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Affiliation(s)
- Yuesheng Lv
- Department of Oncology of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116023, China
| | - Siwen Sun
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Chong Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Chaoqun Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Qianyi Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
| | - Yang Wang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116023, China.
| | - Man Li
- Department of Oncology & Sino-US Research Center for Cancer Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
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Sharma H, Koirala S, Chew YL, Konopka A. DNA Damage and Chromatin Rearrangement Work Together to Promote Neurodegeneration. Mol Neurobiol 2024:10.1007/s12035-024-04331-0. [PMID: 38977621 DOI: 10.1007/s12035-024-04331-0] [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: 04/22/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024]
Abstract
Neurodegenerative diseases have a complex origin and are composed of genetic and environmental factors. Both DNA damage and chromatin rearrangement are important processes that occur under pathological conditions and in neurons functioning properly. While numerous studies have demonstrated the inseparable relationship between DNA damage and chromatin organization, understanding of this relationship, especially in neurodegenerative diseases, requires further study. Interestingly, recent studies revealed that known hallmark proteins involved in neurodegenerative diseases function in both DNA damage and chromatin reorganization, and this review discusses the current knowledge of this relationship. This review focused on hallmark proteins involved in various neurodegenerative diseases, such as the microtubule-associated protein tau, TAR DNA/RNA binding protein 43 (TDP-43), superoxide dismutase 1 (SOD1), fused in sarcoma (FUS), huntingtin (HTT), α-synuclein, and β-amyloid precursor protein (APP). Hence, DNA damage and chromatin rearrangement are associated with disease mechanisms in distinct neurodegenerative diseases. Targeting common modulators of DNA repair and chromatin reorganization may lead to promising therapies for treating neurodegeneration.
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Li Z, Liao Y, Tang C, Xu L, Peng B, Xu X. RBM14 promotes DNA end resection during homologous recombination repair. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1864-1873. [PMID: 37559455 PMCID: PMC10753362 DOI: 10.3724/abbs.2023104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 08/11/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) is crucial for the maintenance of genome stability and integrity. In this study, we aim to identify novel RNA binding proteins (RBPs) involved in HR repair because little is known about RBP function in HR. For this purpose, we carry out pulldown assays using a synthetic ssDNA/dsDNA structure coated with replication protein A (RPA) to mimic resected DNA, a crucial intermediate in HR-mediated DSB repair. Using this approach, we identify RNA-binding motif protein 14 (RBM14) as a potential binding partner. We further show that RBM14 interacts with an essential HR repair factor, CtIP. RBM14 is crucial for CtIP recruitment to DSB sites and for subsequent RPA coating and RAD51 replacement, facilitating efficient HR repair. Moreover, inhibition of RBM14 expression sensitizes cancer cells to X-ray irradiation. Together, our results demonstrate that RBM14 promotes DNA end resection to ensure HR repair and may serve as a potential target for cancer therapy.
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Affiliation(s)
- Zheng Li
- College of Life SciencesCapital Normal UniversityBeijing100048China
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Yanting Liao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Chen Tang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijing100091China
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM)Dehua HospitalDehua362500China
| | - Linli Xu
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
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Du D, Qin M, Shi L, Liu C, Jiang J, Liao Z, Wang H, Zhang Z, Sun L, Fan H, Liu Z, Yu H, Li H, Peng J, Yuan S, Yang M, Xiong J. RNA binding motif protein 45-mediated phosphorylation enhances protein stability of ASCT2 to promote hepatocellular carcinoma progression. Oncogene 2023; 42:3127-3141. [PMID: 37658192 DOI: 10.1038/s41388-023-02795-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 09/03/2023]
Abstract
Targeting metabolic remodeling represents a potentially promising strategy for hepatocellular carcinoma (HCC) therapy. In-depth understanding on the regulation of the glutamine transporter alanine-serine-cysteine transporter 2 (ASCT2) contributes to the development of novel promising therapeutics. As a developmentally regulated RNA binding protein, RBM45 is capable to shuttle between nucleus and cytoplasm, and directly interacts with proteins. By bioinformatics analysis, we screened out that RBM45 was elevated in the HCC patient specimens and positively correlated with poor prognosis. RBM45 promoted cell proliferation, boosted xenograft tumorigenicity and accelerated HCC progression. Using untargeted metabolomics, it was found that RBM45 interfered with glutamine metabolism. Further results demonstrated that RBM45 positively associated with ASCT2 in human and mouse specimens. Moreover, RBM45 enhanced ASCT2 protein stability by counteracting autophagy-independent lysosomal degradation. Significantly, wild-type ASCT2, instead of phospho-defective mutants, rescued siRBM45-suppressed HCC cell proliferation. Using molecular docking approaches, we found AG-221, a mutant isocitrate dehydrogenase 2 (mIDH2) inhibitor for acute myeloid leukemia therapy, pharmacologically perturbed RBM45-ASCT2 interaction, decreased ASCT2 stability and suppressed HCC progression. These findings provide evidence that RBM45 plays a crucial role in HCC progression via interacting with and counteracting the degradation of ASCT2. Our findings suggest a novel alternative structural sites for the design of ASCT2 inhibitors and the agents interfering with RBM45-ASCT2 interaction may be a potential direction for HCC drug development.
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Affiliation(s)
- Danyu Du
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Mengyao Qin
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Li Shi
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Chan Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Jingwei Jiang
- Shuangyun BioMed Sci & Tech Co., Ltd., Suzhou, 215000, China
| | - Zhengguang Liao
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Hongxv Wang
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhibo Zhang
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Li Sun
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Hui Fan
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengrui Liu
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Hong Yu
- Department of Pathology, Taizhou People's Hospital Affiliated to Dalian Medical University, Taizhou, 225300, Jiangsu, China
| | - Hongyang Li
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, 210042, China
| | - Jun Peng
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China
| | - Shengtao Yuan
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China.
| | - Mei Yang
- Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing, 210009, China.
| | - Jing Xiong
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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Lower expression of NINJ1 (Ninjurin 1), a mediator of plasma membrane rupture, is associated with advanced disease and worse prognosis in serous ovarian cancer. Immunol Res 2023; 71:15-28. [PMID: 36184655 DOI: 10.1007/s12026-022-09323-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/16/2022] [Indexed: 01/20/2023]
Abstract
Gasdermin proteins (GSDMs) form pores in cell membranes upon various stimuli, leading to the release of certain proinflammatory molecules such as IL-1β and IL-18, and this ultimately results in pyroptotic cell death. NINJ1 (Ninjurin 1) has recently been identified as a cell membrane protein responsible for the final complete plasma membrane rupture following lytic cell death mechanisms including pyroptosis, causing the release of relatively larger molecules such as HMGB1 and LDH. In this study, we reported the presence of higher GSDMD and lower GSDME protein levels in ovarian tumors compared to surrounding non-malignant stroma in the tumor microenvironment. GSDME protein levels are also lower in the tumors of the omentum compared to adjacent stromal cells. We found that NINJ1 expression decreases from early to late stage in serous ovarian cancer, and the percentage of NINJ1 copy number loss events is the highest in ovarian cancer among other cancers. Moreover, we showed that low expression of NINJ1 is associated with shorter overall survival of patients with ovarian cancer. In support of the findings showing that low NINJ1 expression contributes to worse prognosis in this most lethal gynecological malignancy, NINJ1 expression was found to be lower in cisplatin-resistant ovarian cancer cells compared to cisplatin-sensitive counterparts in vitro. We suggest that the members of gasdermin family might have distinct functions in serous ovarian cancer, and low levels of NINJ1 might contribute, at least in part, to the progression and poorer prognosis of ovarian cancer. A complete picture of how pyroptosis and subsequent plasma membrane rupture are involved in ovarian cancer will be of high importance in order to identify actionable therapeutic vulnerabilities within this newly identified group of proteins.
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Lo A, McSharry M, Berger AH. Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer. BMC Cancer 2022; 22:1315. [PMID: 36522653 PMCID: PMC9756471 DOI: 10.1186/s12885-022-10311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Alternative RNA splicing is widely dysregulated in cancers including lung adenocarcinoma, where aberrant splicing events are frequently caused by somatic splice site mutations or somatic mutations of splicing factor genes. However, the majority of mis-splicing in cancers is unexplained by these known mechanisms. We hypothesize that the aberrant Ras signaling characteristic of lung cancers plays a role in promoting the alternative splicing observed in tumors. METHODS We recently performed transcriptome and proteome profiling of human lung epithelial cells ectopically expressing oncogenic KRAS and another cancer-associated Ras GTPase, RIT1. Unbiased analysis of phosphoproteome data identified altered splicing factor phosphorylation in KRAS-mutant cells, so we performed differential alternative splicing analysis using rMATS to identify significantly altered isoforms in lung epithelial cells. To determine whether these isoforms were uniquely regulated by KRAS, we performed a large-scale splicing screen in which we generated over 300 unique RNA sequencing profiles of isogenic A549 lung adenocarcinoma cells ectopically expressing 75 different wild-type or variant alleles across 28 genes implicated in lung cancer. RESULTS Mass spectrometry data showed widespread downregulation of splicing factor phosphorylation in lung epithelial cells expressing mutant KRAS compared to cells expressing wild-type KRAS. We observed alternative splicing in the same cells, with 2196 and 2416 skipped exon events in KRASG12V and KRASQ61H cells, respectively, 997 of which were shared (p < 0.001 by hypergeometric test). In the high-throughput splicing screen, mutant KRAS induced the greatest number of differential alternative splicing events, second only to the RNA binding protein RBM45 and its variant RBM45M126I. We identified ten high confidence cassette exon events across multiple KRAS variants and cell lines. These included differential splicing of the Myc Associated Zinc Finger (MAZ). As MAZ regulates expression of KRAS, this splice variant may be a mechanism for the cell to modulate wild-type KRAS levels in the presence of oncogenic KRAS. CONCLUSION Proteomic and transcriptomic profiling of lung epithelial cells uncovered splicing factor phosphorylation and mRNA splicing events regulated by oncogenic KRAS. These data suggest that in addition to widespread transcriptional changes, the Ras signaling pathway can promote post-transcriptional splicing changes that may contribute to oncogenic processes.
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Affiliation(s)
- April Lo
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Maria McSharry
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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Identification of Novel Circular RNAs of the Human Protein Arginine Methyltransferase 1 (PRMT1) Gene, Expressed in Breast Cancer Cells. Genes (Basel) 2022; 13:genes13071133. [PMID: 35885916 PMCID: PMC9316507 DOI: 10.3390/genes13071133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023] Open
Abstract
Circular RNAs (circRNAs) constitute a type of RNA formed through back-splicing. In breast cancer, circRNAs are implicated in tumor onset and progression. Although histone methylation by PRMT1 is largely involved in breast cancer development and metastasis, the effect of circular transcripts deriving from this gene has not been examined. In this study, total RNA was extracted from four breast cancer cell lines and reversely transcribed using random hexamer primers. Next, first- and second-round PCRs were performed using gene-specific divergent primers. Sanger sequencing followed for the determination of the sequence of each novel PRMT1 circRNA. Lastly, bioinformatics analysis was conducted to predict the functions of the novel circRNAs. In total, nine novel circRNAs were identified, comprising both complete and truncated exons of the PRMT1 gene. Interestingly, we demonstrated that the back-splice junctions consist of novel splice sites of the PRMT1 exons. Moreover, the circRNA expression pattern differed among these four breast cancer cell lines. All the novel circRNAs are predicted to act as miRNA and/or protein sponges, while five circRNAs also possess an open reading frame. In summary, we described the complete sequence of nine novel circRNAs of the PRMT1 gene, comprising distinct back-splice junctions and probably having different molecular properties.
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Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients. NPJ Genom Med 2022; 7:34. [PMID: 35654793 PMCID: PMC9163142 DOI: 10.1038/s41525-022-00305-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
The 3' untranslated region (3'-UTR) is the vital element regulating gene expression, but most studies have focused on variations in RNA-binding proteins (RBPs), miRNAs, alternative polyadenylation (APA) and RNA modifications. To explore the posttranscriptional function of 3'-UTR somatic mutations in tumorigenesis, we collected whole-genome data from 2413 patients across 18 cancer types. Our updated algorithm, PIVar, revealed 25,216 3'-UTR posttranscriptional impairment-related SNVs (3'-UTR piSNVs) spanning 2930 genes; 24 related RBPs were significantly enriched. The somatic 3'-UTR piSNV ratio was markedly increased across all 18 cancer types, which was associated with worse survival for four cancer types. Several cancer-related genes appeared to facilitate tumorigenesis at the protein and posttranscriptional regulation levels, whereas some 3'-UTR piSNV-affected genes functioned mainly via posttranscriptional mechanisms. Moreover, we assessed immune cell and checkpoint characteristics between the high/low 3'-UTR piSNV ratio groups and predicted 80 compounds associated with the 3'-UTR piSNV-affected gene expression signature. In summary, our study revealed the prevalence and clinical relevance of 3'-UTR piSNVs in cancers, and also demonstrates that in addition to affecting miRNAs, 3'-UTR piSNVs perturb RBPs binding, APA and m6A RNA modification, which emphasized the importance of considering 3'-UTR piSNVs in cancer biology.
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Prediction of Response to Radiotherapy by Characterizing the Transcriptomic Features in Clinical Tumor Samples across 15 Cancer Types. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:5443709. [PMID: 35586092 PMCID: PMC9110128 DOI: 10.1155/2022/5443709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022]
Abstract
Purpose Radiotherapy (RT) is one of the major cancer treatments. However, the responses to RT vary among individual patients, partly due to the differences of the status of gene expression and mutation in tumors of patients. Identification of patients who will benefit from RT will improve the efficacy of RT. However, only a few clinical biomarkers were currently used to predict RT response. Our aim is to obtain gene signatures that can be used to predict RT response by analyzing the transcriptome differences between RT responder and nonresponder groups. Materials and Methods We obtained transcriptome data of 1664 patients treated with RT from the TCGA database across 15 cancer types. First, the genes with a significant difference between RT responder (R group) and nonresponder groups (PD group) were identified, and the top 100 genes were used to build the gene signatures. Then, we developed the predictive model based on binary logistic regression to predict patient response to RT. Results We identified a series of differentially expressed genes between the two groups, which are involved in cell proliferation, migration, invasion, EMT, and DNA damage repair pathway. Among them, MDC1, UCP2, and RBM45 have been demonstrated to be involved in DNA damage repair and radiosensitivity. Our analysis revealed that the predictive model was highly specific for distinguishing the R and PD patients in different cancer types with an area under the curve (AUC) ranging from 0.772 to 0.972. It also provided a more accurate prediction than that from a single-gene signature for the overall survival (OS) of patients. Conclusion The predictive model has a potential clinical application as a biomarker to help physicians create optimal treatment plans. Furthermore, some of the genes identified here may be directly involved in radioresistance, providing clues for further studies on the mechanism of radioresistance.
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Wang C, Liu S, Zhang X, Wang Y, Guan P, Bu F, Wang H, Wang D, Fan Y, Hou S, Qiu Z. SKA3 is a prognostic biomarker and associated with immune infiltration in bladder cancer. Hereditas 2022; 159:20. [PMID: 35546682 PMCID: PMC9092687 DOI: 10.1186/s41065-022-00234-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spindle and kinetochore‑associated complex subunit 3 (SKA3) has recently been considered a key regulator of carcinogenesis. However, the connection between SKA3 and immune cell infiltration remains unknown. METHODS The current study investigated the expression mode, prognostic effect, and functional role of SKA3 in different tumors, particularly bladder cancer using numerous databases, comprising TIMER, GEPIA, HPA, UALCAN, PrognoScan, and Kaplan-Meier Plotter. Differentially expressed gene and enrichment analyses were implemented on SKA3 using R packages "edgR" and "clusterProfiler". Immunohistochemistry was further used to validate the expression of SKA3 gene in bladder cancer. Following that, the relevance of SKA3 expression to immune infiltration level in bladder cancer was evaluated using TIMER. RESULTS Overall, the level of SKA3 expression in tumor tissue significantly increased than in normal tissue. In bladder cancer and other tumors, patients with high SKA3 expression levels had worse overall survival (OS) (p = 0.016), disease-specific survival (DSS) (p = 0.00004), and disease-free survival (DFS) (p = 0.032). Additionally, the major molecular functions for SKA3 included nuclear division, mitotic nuclear division, mitotic sister chromatid segregation, humoral immune response, and cell chemotaxis. Additionally, SKA3 expression was found to be positively associated with enhanced M2 macrophage and T helper (Th) 2 cell infiltration in bladder cancer. CONCLUSIONS Our study implies that SKA3 contributes to M2 macrophage and Th2 cell polarization by acting as an oncogene in bladder cancer. SKA3 might be a novel biomarker for evaluating prognosis and immune infiltration in bladder cancer.
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Affiliation(s)
- Chenyang Wang
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Shasha Liu
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Xinhong Zhang
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Yan Wang
- Department of Anesthesiology and Surgery, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Peng Guan
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Fanyou Bu
- Department of Traditional Chinese Medicine, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Hao Wang
- Department of Oncology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Dawen Wang
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Yi Fan
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Sichuan Hou
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China
| | - Zhilei Qiu
- Department of Urology, Qingdao Municipal Hospital, Qingdao University, 266071, Qingdao, Shandong, China.
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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13
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Chen X, Yang Z, Wang W, Qian K, Liu M, Wang J, Wang M. Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45. Nucleic Acids Res 2021; 49:2946-2958. [PMID: 33577684 PMCID: PMC7968997 DOI: 10.1093/nar/gkab075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/16/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
RBM45 is an RNA-binding protein involved in neural development, whose aggregation is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). However, the mechanisms of RNA-binding and aggregation of RBM45 remain unelucidated. Here, we report the crystal structure of the N-terminal tandem RRM domains of human RBM45 in complex with single-stranded DNA (ssDNA). Our structural and biochemical results revealed that both the RRM1 and RRM2 of RBM45 recognized the GAC sequence of RNA/ssDNA. Two aromatic residues and an arginine residue in each RRM were critical for RNA-binding, and the interdomain linker was also involved in RNA-binding. Two RRMs formed a pair of antiparallel RNA-binding sites, indicating that the N-terminal tandem RRM domains of RBM45 bound separate GAC motifs in one RNA strand or GAC motifs in different RNA strands. Our findings will be helpful in the identification of physiologic targets of RBM45 and provide evidence for understanding the physiologic and pathologic functions of RBM45.
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Affiliation(s)
- Xiaolei Chen
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Zhongmei Yang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Wenfeng Wang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Kaiyue Qian
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Mingjie Liu
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Junchao Wang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China.,Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China
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14
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Klingl YE, Pakravan D, Van Den Bosch L. Opportunities for histone deacetylase inhibition in amyotrophic lateral sclerosis. Br J Pharmacol 2021; 178:1353-1372. [PMID: 32726472 PMCID: PMC9327724 DOI: 10.1111/bph.15217] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease. ALS patients suffer from a progressive loss of motor neurons, leading to respiratory failure within 3 to 5 years after diagnosis. Available therapies only slow down the disease progression moderately or extend the lifespan by a few months. Epigenetic hallmarks have been linked to the disease, creating an avenue for potential therapeutic approaches. Interference with one class of epigenetic enzymes, histone deacetylases, has been shown to affect neurodegeneration in many preclinical models. Consequently, it is crucial to improve our understanding about histone deacetylases and their inhibitors in (pre)clinical models of ALS. We conclude that selective inhibitors with high tolerability and safety and sufficient blood-brain barrier permeability will be needed to interfere with both epigenetic and non-epigenetic targets of these enzymes. LINKED ARTICLES: This article is part of a themed issue on Neurochemistry in Japan. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.6/issuetoc.
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Affiliation(s)
- Yvonne E. Klingl
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI)KU Leuven‐University of LeuvenLeuvenBelgium
- Laboratory of NeurobiologyVIB, Center for Brain & Disease ResearchLeuvenBelgium
| | - Donya Pakravan
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI)KU Leuven‐University of LeuvenLeuvenBelgium
- Laboratory of NeurobiologyVIB, Center for Brain & Disease ResearchLeuvenBelgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI)KU Leuven‐University of LeuvenLeuvenBelgium
- Laboratory of NeurobiologyVIB, Center for Brain & Disease ResearchLeuvenBelgium
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15
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de Oliveira RTG, Cordeiro JVA, Vitoriano BF, de Lima Melo MM, Sampaio LR, de Paula Borges D, Magalhães SMM, Pinheiro RF. ERVs-TLR3-IRF axis is linked to myelodysplastic syndrome pathogenesis. Med Oncol 2021; 38:27. [PMID: 33594613 DOI: 10.1007/s12032-021-01466-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022]
Abstract
Toll-like receptors are mutated or overexpressed in up to 50% of patients with myelodysplastic syndrome (MDS). Endogenous retroviruses (ERV) trigger TLR3 leading to interferon regulatory genes (IRFs) activation. We evaluated if the ERVs-TLR3-IRF axis activation would be linked to MDS pathogenesis and we also conducted a detailed cancer analysis of the ERVs, TLR3 and IRFs gene expression in 30 cancer types using GEPIA database. Seventy-nine bone marrow samples from patients with MDS were evaluated for cytogenetics and quantitative real‑time PCR of TLR3, ERVK6, ERVW-1, ERV3-1, IRF3 and IRF7. Patients with dyserythropoiesis showed higher TLR3 (p = 0.035), ERVK6 (p = 0.001), ERVW1 (p = 0.045) and ERV3-1 (p = 0.016) expression than patients without dyserythropoiesis. Upregulation of Interferon Regulatory Factors, IRF3 and IRF7, was associated with poor prognostic markers in MDS such as > 10% of blasts (p = 0.003-IRF3; p = 0.009-IRF7), low platelets count (< 50.000/mm3) (p = 0.001-IRF3; p = 0.021-IRF7), transfusion dependence (p = 0.014-IRF3) and chromosomal abnormalities (p = 0.036-IRF7). We found strong correlations between ERVK6-ERVW1 (r = 0.800; r2 = 0.640; p = 0.000), ERVW1-ERV3-1 (r = 0.715; r2 = 0.511; p = 0.000), and IRF7-IRF3 (r = 0.567; r2 = 0.321; p = 0.000) and moderate correlation between ERVK6-ERV3-1(r = 0.485; r2 = 0.235; p = 0.000), ERVW1-IRF7 (r = 0.389; r2 = 0.151; p = 0.001), ERVW1-IRF3 (r = 0.357; r2 = 0.127; p = 0.004), ERV3-1-IRF7 (r = 0.314; r2 = 0.098; p = 0.009), and ERV3-1-IRF3 (r = 0.324; r2 = 0.104; p = 0.007). Using GEPIA Database in 30 cancer types, we detected a typical pattern of upregulation as here presented in MDS. We suggest TLR3 activation by ERVs is linked to MDS pathogenesis leading to bone marrow failure. Abnormal double-stranded RNA (dsRNA) expression of Endogenous Retroviruses (ERV) triggers TLR3 hyperactivation. This induces IRF3, IRF7, and NF-kB to translocate to the nucleus and activate transcription of IFNα/β which binds to the type I-IFN receptor promoting interferon response. Thus, just as TLR4 induces a crucial myeloid shift, the ERVs-TLR3 axis may play an important role in establishing one of the most striking characteristics in MDS, dyserythropoiesis.
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Affiliation(s)
- Roberta Taiane Germano de Oliveira
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil.,Post-Graduate Program in Medical Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - João Victor Alves Cordeiro
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil.,Post-Graduate Program in Medical Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Bruna Ferreira Vitoriano
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil.,Post-Graduate Program in Pathology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Mayara Magna de Lima Melo
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil.,Post-Graduate Program in Medical Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Letícia Rodrigues Sampaio
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil
| | - Daniela de Paula Borges
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil.,Post-Graduate Program in Medical Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Silvia Maria Meira Magalhães
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Clinical Medicine Department, Federal University of Ceará, Fortaleza, Ceará, Brazil.,Post-Graduate Program in Medical Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Ronald Feitosa Pinheiro
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil. .,Center for Research and Drug Development (NPDM), Fortaleza, Ceará, Brazil. .,Clinical Medicine Department, Federal University of Ceará, Fortaleza, Ceará, Brazil. .,Post-Graduate Program in Medical Science, Federal University of Ceará, Fortaleza, Ceará, Brazil. .,Post-Graduate Program in Pathology, Federal University of Ceará, Fortaleza, Ceará, Brazil. .,Center for Research and Drug Development (NPDM), Federal University of Ceará, 1000 Coronel Nunes de Melo St. Rodolfo Teófilo, Fortaleza, Ceará, 60430-275, Brazil.
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16
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Sun Y, Curle AJ, Haider AM, Balmus G. The role of DNA damage response in amyotrophic lateral sclerosis. Essays Biochem 2020; 64:847-861. [PMID: 33078197 PMCID: PMC7588667 DOI: 10.1042/ebc20200002] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly disabling and fatal neurodegenerative disease. Due to insufficient disease-modifying treatments, there is an unmet and urgent need for elucidating disease mechanisms that occur early and represent common triggers in both familial and sporadic ALS. Emerging evidence suggests that impaired DNA damage response contributes to age-related somatic accumulation of genomic instability and can trigger or accelerate ALS pathological manifestations. In this review, we summarize and discuss recent studies indicating a direct link between DNA damage response and ALS. Further mechanistic understanding of the role genomic instability is playing in ALS disease pathophysiology will be critical for discovering new therapeutic avenues.
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Affiliation(s)
- Yu Sun
- UK Dementia Research Institute at University of Cambridge, Cambridge CB2 0AH, U.K
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Annabel J Curle
- UK Dementia Research Institute at University of Cambridge, Cambridge CB2 0AH, U.K
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Arshad M Haider
- UK Dementia Research Institute at University of Cambridge, Cambridge CB2 0AH, U.K
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Cambridge CB2 0AH, U.K
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, U.K
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17
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Konopka A, Whelan DR, Jamali MS, Perri E, Shahheydari H, Toth RP, Parakh S, Robinson T, Cheong A, Mehta P, Vidal M, Ragagnin AMG, Khizhnyak I, Jagaraj CJ, Galper J, Grima N, Deva A, Shadfar S, Nicholson GA, Yang S, Cutts SM, Horejsi Z, Bell TDM, Walker AK, Blair IP, Atkin JD. Impaired NHEJ repair in amyotrophic lateral sclerosis is associated with TDP-43 mutations. Mol Neurodegener 2020; 15:51. [PMID: 32907630 PMCID: PMC7488163 DOI: 10.1186/s13024-020-00386-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background Pathological forms of TAR DNA-binding protein 43 (TDP-43) are present in motor neurons of almost all amyotrophic lateral sclerosis (ALS) patients, and mutations in TDP-43 are also present in ALS. Loss and gain of TDP-43 functions are implicated in pathogenesis, but the mechanisms are unclear. While the RNA functions of TDP-43 have been widely investigated, its DNA binding roles remain unclear. However, recent studies have implicated a role for TDP-43 in the DNA damage response. Methods We used NSC-34 motor neuron-like cells and primary cortical neurons expressing wildtype TDP-43 or TDP-43 ALS associated mutants (A315T, Q331K), in which DNA damage was induced by etoposide or H2O2 treatment. We investigated the consequences of depletion of TDP-43 on DNA repair using small interfering RNAs. Specific non homologous end joining (NHEJ) reporters (EJ5GFP and EJ2GFP) and cells lacking DNA-dependent serine/threonine protein kinase (DNA-PK) were used to investigate the role of TDP-43 in DNA repair. To investigate the recruitment of TDP-43 to sites of DNA damage we used single molecule super-resolution microscopy and a co-immunoprecipitation assay. We also investigated DNA damage in an ALS transgenic mouse model, in which TDP-43 accumulates pathologically in the cytoplasm. We also examined fibroblasts derived from ALS patients bearing the TDP-43 M337V mutation for evidence of DNA damage. Results We demonstrate that wildtype TDP-43 is recruited to sites of DNA damage where it participates in classical NHEJ DNA repair. However, ALS-associated TDP-43 mutants lose this activity, which induces DNA damage. Furthermore, DNA damage is present in mice displaying TDP-43 pathology, implying an active role in neurodegeneration. Additionally, DNA damage triggers features typical of TDP-43 pathology; cytoplasmic mis-localisation and stress granule formation. Similarly, inhibition of NHEJ induces TDP-43 mis-localisation to the cytoplasm. Conclusions This study reveals that TDP-43 functions in DNA repair, but loss of this function triggers DNA damage and is associated with key pathological features of ALS.
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Affiliation(s)
- Anna Konopka
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Donna R Whelan
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Md Shafi Jamali
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Emma Perri
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Hamideh Shahheydari
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Reka P Toth
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Sonam Parakh
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Tina Robinson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Alison Cheong
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Prachi Mehta
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Marta Vidal
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Audrey M G Ragagnin
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Ivan Khizhnyak
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Cyril J Jagaraj
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Jasmin Galper
- Brain and Mind Centre, Central Clinical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Natalie Grima
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Anand Deva
- Department of Plastic and Reconstructive Surgery, Macquarie University, and The Integrated Specialist Healthcare Education and Research Foundation, Sydney, Australia
| | - Sina Shadfar
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Garth A Nicholson
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia.,ANZAC Research Institute, Concord Hospital, University of Sydney, Sydney, NSW, Australia
| | - Shu Yang
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Suzanne M Cutts
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Zuzana Horejsi
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Toby D M Bell
- School of Chemistry, Monash University, Wellington Road, Clayton, VIC, Australia
| | - Adam K Walker
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia.,Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Ian P Blair
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia
| | - Julie D Atkin
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, 75 Talavera Road NSW, North Ryde, NSW, 2109, Australia. .,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia.
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18
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Shukla A, Srivastava S, Darokar J, Kulshreshtha R. HIF1α and p53 Regulated MED30, a Mediator Complex Subunit, is Involved in Regulation of Glioblastoma Pathogenesis and Temozolomide Resistance. Cell Mol Neurobiol 2020; 41:1521-1535. [PMID: 32705436 DOI: 10.1007/s10571-020-00920-4] [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] [Received: 03/04/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
Glioblastoma (GBM) is the most common, malignant, and aggressive form of glial cell cancer with unfavorable clinical outcomes. It is believed that a better understanding of the mechanisms of gene deregulation may lead to novel therapeutic approaches for this yet incurable cancer. Mediator complex is a crucial component of enhancer-based gene expression and works as a transcriptional co-activator. Many of the mediator complex subunits are found to be deregulated/mutated in various malignancies; however, their status and role in GBM remains little studied. We report that MED30, a core subunit of the head module, is overexpressed in GBM tissues and cell lines. MED30 was found to be induced by conditions present in the tumor microenvironment such as hypoxia, serum, and glucose deprivation. MED30 harbors hypoxia response elements (HREs) and p53 binding site in its promoter and is induced in a HIF1α and p53 dependent manner. Further, MED30 levels also significantly positively correlated with p53 and HIF1α levels in GBM tissues. Using both MED30 overexpression and knockdown approach, we show that MED30 promotes cell proliferation while reduces the migration capabilities in GBM cell lines. Notably, MED30 was also found to confer sensitivity to chemodrug, temozolomide, in GBM cells and modulate the level of p53 in vitro. Overall, this is the first report showing MED30 overexpression in GBM and its involvement in GBM pathogenesis suggesting its diagnostic and therapeutic potential urging the need for further systematic exploration of MED30 interactome and target networks.
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Affiliation(s)
- Anubha Shukla
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Srishti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Jayant Darokar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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19
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Wu CC, Jin LW, Wang IF, Wei WY, Ho PC, Liu YC, Tsai KJ. HDAC1 dysregulation induces aberrant cell cycle and DNA damage in progress of TDP-43 proteinopathies. EMBO Mol Med 2020; 12:e10622. [PMID: 32449313 PMCID: PMC7278561 DOI: 10.15252/emmm.201910622] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) has been implicated in frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-TDP) and amyotrophic lateral sclerosis. Histone deacetylase 1 (HDAC1) is involved in DNA repair and neuroprotection in numerous neurodegenerative diseases. However, the pathological mechanisms of FTLD-TDP underlying TDP-43 proteinopathies are unclear, and the role of HDAC1 is also poorly understood. Here, we found that aberrant cell cycle activity and DNA damage are important pathogenic factors in FTLD-TDP transgenic (Tg) mice, and we further identified these pathological features in the frontal cortices of patients with FTLD-TDP. TDP-43 proteinopathies contributed to pathogenesis by inducing cytosolic mislocalization of HDAC1 and reducing its activity. Pharmacological recovery of HDAC1 activity in FTLD-TDP Tg mice ameliorated their cognitive and motor impairments, normalized their aberrant cell cycle activity, and attenuated their DNA damage and neuronal loss. Thus, HDAC1 deregulation is involved in the pathogenesis of TDP-43 proteinopathies, and HDAC1 is a potential target for therapeutic interventions in FTLD-TDP.
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Affiliation(s)
- Cheng-Chun Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - I-Fang Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Yen Wei
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Chuan Ho
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chih Liu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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20
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Sanna S, Esposito S, Masala A, Sini P, Nieddu G, Galioto M, Fais M, Iaccarino C, Cestra G, Crosio C. HDAC1 inhibition ameliorates TDP-43-induced cell death in vitro and in vivo. Cell Death Dis 2020; 11:369. [PMID: 32409664 PMCID: PMC7224392 DOI: 10.1038/s41419-020-2580-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
TDP-43 pathology is a disease hallmark that characterizes both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). TDP-43 undergoes several posttranslational modifications that can change its biological activities and its aggregative propensity, which is a common hallmark of different neurodegenerative conditions. New evidence is provided by the current study pointing at TDP-43 acetylation in ALS cellular models. Using both in vitro and in vivo approaches, we demonstrate that TDP-43 interacts with histone deacetylase 1 (HDAC1) via RRM1 and RRM2 domains, that are known to contain the two major TDP-43 acetylation sites, K142 and K192. Moreover, we show that TDP-43 is a direct transcriptional activator of CHOP promoter and this activity is regulated by acetylation. Finally and most importantly, we observe both in cell culture and in Drosophila that a HDCA1 reduced level (genomic inactivation or siRNA) or treatment with pan-HDAC inhibitors exert a protective role against WT or pathological mutant TDP-43 toxicity, suggesting TDP-43 acetylation as a new potential therapeutic target. HDAC inhibition efficacy in neurodegeneration has long been debated, but future investigations are warranted in this area. Selection of more specific HDAC inhibitors is still a promising option for neuronal protection especially as HDAC1 appears as a downstream target of both TDP- 43 and FUS, another ALS-related gene.
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Affiliation(s)
- Simona Sanna
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Sonia Esposito
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Alessandra Masala
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Paola Sini
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Gabriele Nieddu
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Manuela Galioto
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Milena Fais
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy
| | - Gianluca Cestra
- Istitute of Molecular Biology and Pathology-National Research Council at Department of Biology and Biotechnology-Charles Darwin, Sapienza University of Rome, P.Le A.Moro 5, I-00185, Rome, Italy
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Via Muroni 25, I-07100, Sassari, Italy.
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21
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RNA Binding Motif Protein RBM45 Regulates Expression of the 11-Kilodalton Protein of Parvovirus B19 through Binding to Novel Intron Splicing Enhancers. mBio 2020; 11:mBio.00192-20. [PMID: 32156816 PMCID: PMC7064759 DOI: 10.1128/mbio.00192-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human parvovirus B19 (B19V) is a human pathogen that causes severe hematological disorders in immunocompromised individuals. B19V infection has a remarkable tropism with respect to human erythroid progenitor cells (EPCs) in human bone marrow and fetal liver. During B19V infection, only one viral precursor mRNA (pre-mRNA) is transcribed by a single promoter of the viral genome and is alternatively spliced and alternatively polyadenylated, a process which plays a key role in expression of viral proteins. Our studies revealed that a cellular RNA binding protein, RBM45, binds to two intron splicing enhancers and is essential for the maturation of the small nonstructural protein 11-kDa-encoding mRNA. The 11-kDa protein plays an important role not only in B19V infection-induced apoptosis but also in viral DNA replication. Thus, the identification of the RBM45 protein and its cognate binding site in B19V pre-mRNA provides a novel target for antiviral development to combat B19V infection-caused severe hematological disorders. During infection of human parvovirus B19 (B19V), one viral precursor mRNA (pre-mRNA) is transcribed by a single promoter and is alternatively spliced and alternatively polyadenylated. Here, we identified a novel cis-acting sequence (5′-GUA AAG CUA CGG GAC GGU-3′), intronic splicing enhancer 3 (ISE3), which lies 72 nucleotides upstream of the second splice acceptor (A2-2) site of the second intron that defines the exon of the mRNA encoding the 11-kDa viral nonstructural protein. RNA binding motif protein 45 (RBM45) specifically binds to ISE3 with high affinity (equilibrium dissociation constant [KD] = 33 nM) mediated by its RNA recognition domain and 2-homo-oligomer assembly domain (RRM2-HOA). Knockdown of RBM45 expression or ectopic overexpression of RRM2-HOA in human erythroid progenitor cells (EPCs) expanded ex vivo significantly decreased the level of viral mRNA spliced at the A2-2 acceptor but not that of the mRNA spliced at A2-1 that encodes VP2. Moreover, silent mutations of ISE3 in an infectious DNA of B19V significantly reduced 11-kDa expression. Notably, RBM45 also specifically interacts in vitro with ISE2, which shares the octanucleotide (GGGACGGU) with ISE3. Taken together, our results suggest that RBM45, through binding to both ISE2 and ISE3, is an essential host factor for maturation of 11-kDa-encoding mRNA.
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Abstract
All organisms must protect their genome from constantly occurring DNA damage. To this end, cells have evolved complex pathways for repairing sites of DNA lesions, and multiple in vitro and in vivo techniques have been developed to study these processes. In this review, we discuss the commonly used laser microirradiation method for monitoring the accumulation of repair proteins at DNA damage sites in cells, and we outline several strategies for deriving kinetic models from such experimental data. We discuss an example of how in vitro measurements and in vivo microirradation experiments complement each other to provide insight into the mechanism of PARP1 recruitment to DNA lesions. We also discuss a strategy to combine data obtained for the recruitment of many different proteins in a move toward fully quantitating the spatiotemporal relationships between various damage responses, and we outline potential venues for future development in the field.
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23
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Borroni B, Alberici A, Buratti E. Review: Molecular pathology of frontotemporal lobar degenerations. Neuropathol Appl Neurobiol 2019; 45:41-57. [DOI: 10.1111/nan.12534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023]
Affiliation(s)
- B. Borroni
- Neurology Clinic; Department of Clinical and Experimental Sciences; University of Brescia; Brescia Italy
| | - A. Alberici
- Neurology Clinic; Department of Clinical and Experimental Sciences; University of Brescia; Brescia Italy
| | - E. Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB); Trieste Italy
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24
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Anufrieva KS, Shender VO, Arapidi GP, Lagarkova MA, Govorun VM. The Diverse Roles of Spliceosomal Proteins in the Regulation of Cell Processes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Konopka A, Atkin JD. The Emerging Role of DNA Damage in the Pathogenesis of the C9orf72 Repeat Expansion in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2018; 19:ijms19103137. [PMID: 30322030 PMCID: PMC6213462 DOI: 10.3390/ijms19103137] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, rapidly progressing neurodegenerative disease affecting motor neurons, and frontotemporal dementia (FTD) is a behavioural disorder resulting in early-onset dementia. Hexanucleotide (G4C2) repeat expansions in the gene encoding chromosome 9 open reading frame 72 (C9orf72) are the major cause of familial forms of both ALS (~40%) and FTD (~20%) worldwide. The C9orf72 repeat expansion is known to form abnormal nuclei acid structures, such as hairpins, G-quadruplexes, and R-loops, which are increasingly associated with human diseases involving microsatellite repeats. These configurations form during normal cellular processes, but if they persist they also damage DNA, and hence are a serious threat to genome integrity. It is unclear how the repeat expansion in C9orf72 causes ALS, but recent evidence implicates DNA damage in neurodegeneration. This may arise from abnormal nucleic acid structures, the greatly expanded C9orf72 RNA, or by repeat-associated non-ATG (RAN) translation, which generates toxic dipeptide repeat proteins. In this review, we detail recent advances implicating DNA damage in C9orf72-ALS. Furthermore, we also discuss increasing evidence that targeting these aberrant C9orf72 confirmations may have therapeutic value for ALS, thus revealing new avenues for drug discovery for this disorder.
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Affiliation(s)
- Anna Konopka
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Julie D Atkin
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- La Trobe Institute for Molecular Science, Melbourne, VIC 3086, Australia.
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