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Krishnamoorthy GP, Glover AR, Untch BR, Sigcha-Coello N, Xu B, Vukel D, Liu Y, Tiedje V, Berman K, Tamarapu PP, Acuña-Ruiz A, Saqcena M, de Stanchina E, Boucai L, Ghossein RA, Knauf JA, Abdel-Wahab O, Bradley RK, Fagin JA. RBM10 loss induces aberrant splicing of cytoskeletal and extracellular matrix mRNAs and promotes metastatic fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602730. [PMID: 39026820 PMCID: PMC11257529 DOI: 10.1101/2024.07.09.602730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
RBM10 modulates transcriptome-wide cassette exon splicing. Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon-inclusion events included vinculin (VCL), tenascin C (TNC) and CD44. Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon-inclusion isoforms reduced invasiveness. RAC1-GTP levels were increased in RBM10-null cells. Mouse Hras G12V /Rbm1O KO thyrocytes develop metastases that are reversed by RBM10 or by combined knockdown of VCL, CD44 and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusions in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFkB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers.
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Affiliation(s)
- Gnana P. Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony R. Glover
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian R. Untch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nickole Sigcha-Coello
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dina Vukel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vera Tiedje
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Berman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prasanna P. Tamarapu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrian Acuña-Ruiz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahesh Saqcena
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Boucai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald A. Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James A. Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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52
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Bhatia N, Tiwari JK, Kumari C, Zinta R, Sharma S, Buckseth T, Thakur AK, Singh RK, Kumar V. Transcriptome analysis reveals genes associated with late blight resistance in potato. Sci Rep 2024; 14:15501. [PMID: 38969681 PMCID: PMC11226683 DOI: 10.1038/s41598-024-60608-3] [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: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/07/2024] Open
Abstract
Late blight is a serious disease of potato worldwide. Our study aimed to unveil genes involved in late blight resistance in potato by RNA-seq analysis after artificial inoculation under controlled conditions. In this study, two potato somatic hybrids (P7 and Crd6) and three varieties such as Kufri Girdhari, Kufri Jyoti and Kufri Bahar (control) were used. Transcriptiome analysis revealed statistically significant (p < 0.05) differentially expressed genes (DEGs), which were analysed into up-regulated and down-regulated genes. Further, DEGs were functionally characterized by the Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes pathways. Overall, some of the up-regulated genes in resistant genotypes were disease resistance proteins such as CC-NBS-LRR resistance protein, ankyrin repeat family protein, cytochrome P450, leucine-rich repeat family protein/protein kinase family, and MYB transcription factor. Sequence diversity analysis based on 38 peptide sequences representing 18 genes showed distinct variation and the presence of three motifs in 15 amino acid sequences. Selected genes were also validated by real-time quantitative polymerase chain reaction analysis. Interestingly, gene expression markers were developed for late blight resistant genotypes. Our study elucidates genes involved in imparting late blight resistance in potato, which will be beneficial for its management strategies in the future.
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Affiliation(s)
- Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.
| | - Chandresh Kumari
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay K Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Ke C, Huang B, Xiang J, Liang J, Wu G, Qiu M, Cheng K, Mao L, Lei W, Hu Y, Tang X, Tian Y, Chen G, Luo OJ, Zhang H. Secreted clusterin inhibits tumorigenesis by modulating tumor cells and macrophages in human meningioma. Neuro Oncol 2024; 26:1262-1279. [PMID: 38416702 PMCID: PMC11226886 DOI: 10.1093/neuonc/noae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Meningioma is the most common primary intracranial tumor with a high frequency of postoperative recurrence, yet the biology of the meningioma malignancy process is still obscure. METHODS To identify potential therapeutic targets and tumor suppressors, we performed single-cell transcriptome analysis through meningioma malignancy, which included 18 samples spanning normal meninges, benign and high-grade in situ tumors, and lung metastases, for extensive transcriptome characterization. Tumor suppressor candidate gene and molecular mechanism were functionally validated at the animal model and cellular levels. RESULTS Comprehensive analysis and validation in mice and clinical cohorts indicated clusterin (CLU) had suppressive function for meningioma tumorigenesis and malignancy by inducing mitochondria damage and triggering type 1 interferon pathway dependent on its secreted isoform, and the inhibition effect was enhanced by TNFα as TNFα also induced type 1 interferon pathway. Meanwhile, both intra- and extracellular CLU overexpression enhanced macrophage polarization towards M1 phenotype and TNFα production, thus promoting tumor killing and phagocytosis. CONCLUSIONS CLU might be a key brake of meningioma malignance by synchronously modulating tumor cells and their microenvironment. Our work provides comprehensive insights into meningioma malignancy and a potential therapeutic strategy.
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Affiliation(s)
- Chao Ke
- Department of Neurosurgery, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
| | - Boya Huang
- Department of Systems Biomedical Sciences, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jian Xiang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jinlian Liang
- Department of Biophysics and Biochemistry, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Guangjie Wu
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Minghui Qiu
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Kai Cheng
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Lipeng Mao
- Department of Systems Biomedical Sciences, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Wen Lei
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Yang Hu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Xiaogen Tang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Yizhen Tian
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Hongyi Zhang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
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Li YM, Zhang HX, Tang XS, Wang Y, Cai ZH, Li B, Xie ZS. Abscisic Acid Induces DNA Methylation Alteration in Genes Related to Berry Ripening and Stress Response in Grape ( Vitis vinifera L). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15027-15039. [PMID: 38886897 DOI: 10.1021/acs.jafc.4c02303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Abscisic acid (ABA) is a major regulator of nonclimacteric fruit ripening, with its processes involving epigenetic mechanisms. It remains unclear whether DNA methylation is associated with ABA-regulated ripening. In this study, we investigated the patterns of DNA methylation and gene expression following ABA treatment in grape berries by using whole-genome bisulfite sequencing and RNA-sequencing. ABA application changed global DNA methylation in grapes. The hyper-/hypo-differently methylated regions were enriched in defense-related metabolism, degreening processes, or ripening-related metabolic pathways. Many differentially expressed genes showed an alteration in DNA methylation after ABA treatment. Specifically, ten downregulated genes with hypermethylation in promoters were involved in the ripening process, ABA homeostasis/signaling, and stress response. Nine upregulated genes exhibiting hypo-methylation in promoters were related to the ripening process and stress response. These findings demonstrated ABA-induced DNA alteration of ripening related and stress-responsive genes during grape ripening, which provides new insights of the epigenetic regulation of ABA on fruit ripening.
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Affiliation(s)
- You-Mei Li
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Hong-Xing Zhang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Xuan-Si Tang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Yue Wang
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Zhong-Hui Cai
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Bo Li
- Shandong Academy of Grape, Jinan 250000, China
| | - Zhao-Sen Xie
- College of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
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55
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Rezapour M, Wesolowski R, Gurcan MN. Identifying Key Genes Involved in Axillary Lymph Node Metastasis in Breast Cancer Using Advanced RNA-Seq Analysis: A Methodological Approach with GLMQL and MAS. Int J Mol Sci 2024; 25:7306. [PMID: 39000413 PMCID: PMC11242629 DOI: 10.3390/ijms25137306] [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: 05/29/2024] [Revised: 06/23/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Our study aims to address the methodological challenges frequently encountered in RNA-Seq data analysis within cancer studies. Specifically, it enhances the identification of key genes involved in axillary lymph node metastasis (ALNM) in breast cancer. We employ Generalized Linear Models with Quasi-Likelihood (GLMQLs) to manage the inherently discrete and overdispersed nature of RNA-Seq data, marking a significant improvement over conventional methods such as the t-test, which assumes a normal distribution and equal variances across samples. We utilize the Trimmed Mean of M-values (TMMs) method for normalization to address library-specific compositional differences effectively. Our study focuses on a distinct cohort of 104 untreated patients from the TCGA Breast Invasive Carcinoma (BRCA) dataset to maintain an untainted genetic profile, thereby providing more accurate insights into the genetic underpinnings of lymph node metastasis. This strategic selection paves the way for developing early intervention strategies and targeted therapies. Our analysis is exclusively dedicated to protein-coding genes, enriched by the Magnitude Altitude Scoring (MAS) system, which rigorously identifies key genes that could serve as predictors in developing an ALNM predictive model. Our novel approach has pinpointed several genes significantly linked to ALNM in breast cancer, offering vital insights into the molecular dynamics of cancer development and metastasis. These genes, including ERBB2, CCNA1, FOXC2, LEFTY2, VTN, ACKR3, and PTGS2, are involved in key processes like apoptosis, epithelial-mesenchymal transition, angiogenesis, response to hypoxia, and KRAS signaling pathways, which are crucial for tumor virulence and the spread of metastases. Moreover, the approach has also emphasized the importance of the small proline-rich protein family (SPRR), including SPRR2B, SPRR2E, and SPRR2D, recognized for their significant involvement in cancer-related pathways and their potential as therapeutic targets. Important transcripts such as H3C10, H1-2, PADI4, and others have been highlighted as critical in modulating the chromatin structure and gene expression, fundamental for the progression and spread of cancer.
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Affiliation(s)
- Mostafa Rezapour
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Robert Wesolowski
- Division of Medical Oncology, James Cancer Hospital and the Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Metin Nafi Gurcan
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
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Shekhawat K, Veluchamy A, Fatima A, García-Ramírez GX, Reichheld JP, Artyukh O, Fröhlich K, Polussa A, Parween S, Nagarajan AP, Rayapuram N, Hirt H. Microbe-induced coordination of plant iron-sulfur metabolism enhances high-light-stress tolerance of Arabidopsis. PLANT COMMUNICATIONS 2024:101012. [PMID: 38956873 DOI: 10.1016/j.xplc.2024.101012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/11/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
High-light stress strongly limits agricultural production in subtropical and tropical regions owing to photo-oxidative damage, decreased growth, and decreased yield. Here, we investigated whether beneficial microbes can protect plants under high-light stress. We found that Enterobacter sp. SA187 (SA187) supports the growth of Arabidopsis thaliana under high-light stress by reducing the accumulation of reactive oxygen species and maintaining photosynthesis. Under high-light stress, SA187 triggers dynamic changes in the expression of Arabidopsis genes related to fortified iron metabolism and redox regulation, thereby enhancing the antioxidative glutathione/glutaredoxin redox system of the plant. Genetic analysis showed that the enhancement of iron and sulfur metabolism by SA187 is coordinated by ethylene signaling. In summary, beneficial microbes could be an effective and inexpensive means of enhancing high-light-stress tolerance in plants.
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Affiliation(s)
- Kirti Shekhawat
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Alaguraj Veluchamy
- Department of Computational Biology, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, TN 38105, USA
| | - Anam Fatima
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Gabriel X García-Ramírez
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, 66860 Perpignan, France; Laboratoire Génome et Développement des Plantes, CNRS, 66860 Perpignan, France
| | - Olga Artyukh
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Katja Fröhlich
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Alexander Polussa
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT 06520, USA
| | - Sabiha Parween
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Arun Prasanna Nagarajan
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Naganand Rayapuram
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Heribert Hirt
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.
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Lee DJ, Kim P, Kim HY, Park J, Lee SJ, An H, Heo JS, Lee MJ, Ohshima H, Mizuno S, Takahashi S, Jung HS, Kim SJ. MAST4 regulates stem cell maintenance with DLX3 for epithelial development and amelogenesis. Exp Mol Med 2024; 56:1606-1619. [PMID: 38945953 PMCID: PMC11297042 DOI: 10.1038/s12276-024-01264-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/29/2024] [Accepted: 03/19/2024] [Indexed: 07/02/2024] Open
Abstract
The asymmetric division of stem cells permits the maintenance of the cell population and differentiation for harmonious progress. Developing mouse incisors allows inspection of the role of the stem cell niche to provide specific insights into essential developmental phases. Microtubule-associated serine/threonine kinase family member 4 (Mast4) knockout (KO) mice showed abnormal incisor development with low hardness, as the size of the apical bud was decreased and preameloblasts were shifted to the apical side, resulting in amelogenesis imperfecta. In addition, Mast4 KO incisors showed abnormal enamel maturation, and stem cell maintenance was inhibited as amelogenesis was accelerated with Wnt signal downregulation. Distal-Less Homeobox 3 (DLX3), a critical factor in tooth amelogenesis, is considered to be responsible for the development of amelogenesis imperfecta in humans. MAST4 directly binds to DLX3 and induces phosphorylation at three residues within the nuclear localization site (NLS) that promotes the nuclear translocation of DLX3. MAST4-mediated phosphorylation of DLX3 ultimately controls the transcription of DLX3 target genes, which are carbonic anhydrase and ion transporter genes involved in the pH regulation process during ameloblast maturation. Taken together, our data reveal a novel role for MAST4 as a critical regulator of the entire amelogenesis process through its control of Wnt signaling and DLX3 transcriptional activity.
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Affiliation(s)
- Dong-Joon Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
- Department of Oral Histology, Dankook University College of Dentistry, Cheonan, 31116, Korea
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, Korea
| | - Pyunggang Kim
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Hyun-Yi Kim
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
- NGeneS Inc., Ansan-si, Gyeonggi-do, 15495, Korea
| | - Jinah Park
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Seung-Jun Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Haein An
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Jin Sun Heo
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Min-Jung Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Hayato Ohshima
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Han-Sung Jung
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea.
| | - Seong-Jin Kim
- GILO Institute, GILO Foundation, Seoul, 06668, Korea.
- Medpacto Inc., Seoul, 06668, Korea.
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Zhao Y, Zhu X, Shi CM, Xu G, Zuo S, Shi Y, Cao W, Kang H, Liu W, Wang R, Ning Y, Wang GL, Wang X. OsEIL2 balances rice immune responses against (hemi)biotrophic and necrotrophic pathogens via the salicylic acid and jasmonic acid synergism. THE NEW PHYTOLOGIST 2024; 243:362-380. [PMID: 38730437 DOI: 10.1111/nph.19809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024]
Abstract
Plants typically activate distinct defense pathways against various pathogens. Heightened resistance to one pathogen often coincides with increased susceptibility to another pathogen. However, the underlying molecular basis of this antagonistic response remains unclear. Here, we demonstrate that mutants defective in the transcription factor ETHYLENE-INSENSITIVE 3-LIKE 2 (OsEIL2) exhibited enhanced resistance to the biotrophic bacterial pathogen Xanthomonas oryzae pv oryzae and to the hemibiotrophic fungal pathogen Magnaporthe oryzae, but enhanced susceptibility to the necrotrophic fungal pathogen Rhizoctonia solani. Furthermore, necrotroph-induced OsEIL2 binds to the promoter of OsWRKY67 with high affinity, leading to the upregulation of salicylic acid (SA)/jasmonic acid (JA) pathway genes and increased SA/JA levels, ultimately resulting in enhanced resistance. However, biotroph- and hemibiotroph-induced OsEIL2 targets OsERF083, resulting in the inhibition of SA/JA pathway genes and decreased SA/JA levels, ultimately leading to reduced resistance. Our findings unveil a previously uncharacterized defense mechanism wherein two distinct transcriptional regulatory modules differentially mediate immunity against pathogens with different lifestyles through the transcriptional reprogramming of phytohormone pathway genes.
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Affiliation(s)
- Yudan Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoying Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cheng-Min Shi
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China
| | - Guojuan Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Yanlong Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenlei Cao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Koenis DS, Evers-van Gogh IJA, van Loenen PB, Zwart W, Kalkhoven E, de Vries CJM. Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages. FEBS Lett 2024; 598:1715-1729. [PMID: 38825601 DOI: 10.1002/1873-3468.14942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/04/2024]
Abstract
Mitochondrial biogenesis requires precise regulation of both mitochondrial-encoded and nuclear-encoded genes. Nuclear receptor Nur77 is known to regulate mitochondrial metabolism in macrophages and skeletal muscle. Here, we compared genome-wide Nur77 binding site and target gene expression in these two cell types, which revealed conserved regulation of mitochondrial genes and enrichment of motifs for the transcription factor Yin-Yang 1 (YY1). We show that Nur77 and YY1 interact, that YY1 increases Nur77 activity, and that their binding sites are co-enriched at mitochondrial ribosomal protein gene loci in macrophages. Nur77 and YY1 co-expression synergistically increases Mrpl1 expression as well as mitochondrial abundance and activity in macrophages but not skeletal muscle. As such, we identify a macrophage-specific Nur77-YY1 interaction that enhances mitochondrial metabolism.
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Affiliation(s)
- Duco S Koenis
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Inkie J A Evers-van Gogh
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pieter B van Loenen
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Carlie J M de Vries
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, Amsterdam, The Netherlands
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60
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Dangoudoubiyam S, Norris JK, Namasivayam S, de Paula Baptista R, Cannes do Nascimento N, Camp J, Schardl CL, Kissinger JC, Howe DK. Temporal gene expression during asexual development of the apicomplexan Sarcocystis neurona. mSphere 2024; 9:e0011124. [PMID: 38809064 PMCID: PMC11332336 DOI: 10.1128/msphere.00111-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
Asexual replication in the apicomplexan Sarcocystis neurona involves two main developmental stages: the motile extracellular merozoite and the sessile intracellular schizont. Merozoites invade host cells and transform into schizonts that undergo replication via endopolygeny to form multiple (64) daughter merozoites that are invasive to new host cells. Given that the capabilities of the merozoite vary significantly from the schizont, the patterns of transcript levels throughout the asexual lifecycle were determined and compared in this study. RNA-Seq data were generated from extracellular merozoites and four intracellular schizont development time points. Of the 6,938 genes annotated in the S. neurona genome, 6,784 were identified in the transcriptome. Of these, 4,111 genes exhibited significant differential expression between the merozoite and at least one schizont development time point. Transcript levels were significantly higher for 2,338 genes in the merozoite and 1,773 genes in the schizont stages. Included in this list were genes encoding the secretory pathogenesis determinants (SPDs), which encompass the surface antigen and SAG-related sequence (SAG/SRS) and the secretory organelle proteins of the invasive zoite stage (micronemes, rhoptries, and dense granules). As anticipated, many of the S. neurona SPD gene transcripts were abundant in merozoites. However, several SPD transcripts were elevated in intracellular schizonts, suggesting roles unrelated to host cell invasion and the initial establishment of the intracellular niche. The hypothetical genes that are potentially unique to the genus Sarcocystis are of particular interest. Their conserved expression patterns are instructive for future investigations into the possible functions of these putative Sarcocystis-unique genes. IMPORTANCE The genus Sarcocystis is an expansive clade within the Apicomplexa, with the species S. neurona being an important cause of neurological disease in horses. Research to decipher the biology of S. neurona and its host-pathogen interactions can be enhanced by gene expression data. This study has identified conserved apicomplexan orthologs in S. neurona, putative Sarcocystis-unique genes, and gene transcripts abundant in the merozoite and schizont stages. Importantly, we have identified distinct clusters of genes with transcript levels peaking during different intracellular schizont development time points, reflecting active gene expression changes across endopolygeny. Each cluster also has subsets of transcripts with unknown functions, and investigation of these seemingly Sarcocystis-unique transcripts will provide insights into the interesting biology of this parasite genus.
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Affiliation(s)
- Sriveny Dangoudoubiyam
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Jamie K. Norris
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Sivaranjani Namasivayam
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Rodrigo de Paula Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Naila Cannes do Nascimento
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Joseph Camp
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | | | - Jessica C. Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Daniel K. Howe
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
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61
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Heijmans N, Wiese KE, Jonkers J, van Amerongen R. Transcriptomic Analysis of Pubertal and Adult Virgin Mouse Mammary Epithelial and Stromal Cell Populations. J Mammary Gland Biol Neoplasia 2024; 29:13. [PMID: 38916673 PMCID: PMC11199289 DOI: 10.1007/s10911-024-09565-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
Conflicting data exist as to how mammary epithelial cell proliferation changes during the reproductive cycle. To study the effect of endogenous hormone fluctuations on gene expression in the mouse mammary gland, we performed bulk RNAseq analyses of epithelial and stromal cell populations that were isolated either during puberty or at different stages of the adult virgin estrous cycle. Our data confirm prior findings that proliferative changes do not occur in every mouse in every cycle. We also show that during the estrous cycle the main gene expression changes occur in adipocytes and fibroblasts. Finally, we present a comprehensive overview of the Wnt gene expression landscape in different mammary gland cell types in pubertal and adult mice. This work contributes to understanding the effects of physiological hormone fluctuations and locally produced signaling molecules on gene expression changes in the mammary gland during the reproductive cycle and should be a useful resource for future studies investigating gene expression patterns in different cell types across different developmental timepoints.
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Affiliation(s)
- Nika Heijmans
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Katrin E Wiese
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
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62
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Jiang G, Zheng JY, Ren SN, Yin W, Xia X, Li Y, Wang HL. A comprehensive workflow for optimizing RNA-seq data analysis. BMC Genomics 2024; 25:631. [PMID: 38914930 PMCID: PMC11197194 DOI: 10.1186/s12864-024-10414-y] [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: 02/26/2024] [Accepted: 05/15/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge. RESULTS By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz. CONCLUSION The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.
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Affiliation(s)
- Gao Jiang
- School of Information Science and Technology, School of Artificial Intelligence, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Juan-Yu Zheng
- School of Information Science and Technology, School of Artificial Intelligence, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Shu-Ning Ren
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Weilun Yin
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Xinli Xia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yun Li
- School of Information Science and Technology, School of Artificial Intelligence, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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Yuan Y, Zhong T, Wang Y, Yang J, Gui L, Shen Y, Zhou J, Chung-Davidson YW, Li W, Xu J, Li J, Li M, Ren J. Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus. Sci Data 2024; 11:653. [PMID: 38906919 PMCID: PMC11192953 DOI: 10.1038/s41597-024-03504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024] Open
Abstract
Acrossocheilus fasciatus is a stream-dwelling fish species of the Barbinae subfamily. It is valued for its colorfully striped appearance and delicious meat. This species is also characterized by apparent sexual dimorphism and toxic ovum. Biology and aquaculture researches of A. fasciatus are hindered by the lack of a high-quality reference genome. Here, we report chromosome-level genome assemblies of the male and female A. fasciatus. The HiFi-only genome assemblies for both female and male individuals were 899.13 Mb (N50 length of 32.58 Mb) and 885.68 Mb (N50 length of 33.06 Mb), respectively. Notably, a substantial proportion of the assembled sequences, accounting for 96.15% and 98.35% for female and male genomes, respectively, were successfully anchored onto 25 chromosomes utilizing Hi-C data. We annotated the female assembly as a reference genome and identified a total of 400.62 Mb (44.56%) repetitive sequences, 27,392 protein-coding genes, and 35,869 ncRNAs. The high-quality male and female reference genomes will provide genomic resources for developing sex-specific molecular markers, inform single-sex breeding, and elucidate genetic mechanisms of sexual dimorphism.
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Affiliation(s)
- Yixin Yuan
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Tianxing Zhong
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Yifei Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinquan Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Lang Gui
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiajun Zhou
- Zhejiang Forest Resource Monitoring Center, Hangzhou, 310020, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Jinkai Xu
- Huangshan Dingxin Ecological Agriculture Co., Ltd, Huangshan, 245431, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Mingyou Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jianfeng Ren
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
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Bang JH, Kim EH, Kim HJ, Chung JW, Seo WK, Kim GM, Lee DH, Kim H, Bang OY. Machine Learning-Based Etiologic Subtyping of Ischemic Stroke Using Circulating Exosomal microRNAs. Int J Mol Sci 2024; 25:6761. [PMID: 38928481 PMCID: PMC11203849 DOI: 10.3390/ijms25126761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Ischemic stroke is a major cause of mortality worldwide. Proper etiological subtyping of ischemic stroke is crucial for tailoring treatment strategies. This study explored the utility of circulating microRNAs encapsulated in extracellular vesicles (EV-miRNAs) to distinguish the following ischemic stroke subtypes: large artery atherosclerosis (LAA), cardioembolic stroke (CES), and small artery occlusion (SAO). Using next-generation sequencing (NGS) and machine-learning techniques, we identified differentially expressed miRNAs (DEMs) associated with each subtype. Through patient selection and diagnostic evaluation, a cohort of 70 patients with acute ischemic stroke was classified: 24 in the LAA group, 24 in the SAO group, and 22 in the CES group. Our findings revealed distinct EV-miRNA profiles among the groups, suggesting their potential as diagnostic markers. Machine-learning models, particularly logistic regression models, exhibited a high diagnostic accuracy of 92% for subtype discrimination. The collective influence of multiple miRNAs was more crucial than that of individual miRNAs. Additionally, bioinformatics analyses have elucidated the functional implications of DEMs in stroke pathophysiology, offering insights into the underlying mechanisms. Despite limitations like sample size constraints and retrospective design, our study underscores the promise of EV-miRNAs coupled with machine learning for ischemic stroke subtype classification. Further investigations are warranted to validate the clinical utility of the identified EV-miRNA biomarkers in stroke patients.
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Affiliation(s)
- Ji Hoon Bang
- Global School of Media, College of IT, Soongsil University, Seoul 06978, Republic of Korea;
| | - Eun Hee Kim
- S&E Bio, Inc., Seoul 05855, Republic of Korea
| | - Hyung Jun Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jong-Won Chung
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Woo-Keun Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Gyeong-Moon Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Dong-Ho Lee
- Calth, Inc., Seongnam-si 13449, Republic of Korea
| | - Heewon Kim
- Global School of Media, College of IT, Soongsil University, Seoul 06978, Republic of Korea;
| | - Oh Young Bang
- S&E Bio, Inc., Seoul 05855, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Seoul 06351, Republic of Korea
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Fan S, Li Y, Wang Q, Jin M, Yu M, Zhao H, Zhou C, Xu J, Li B, Li X. The role of cis-zeatin in enhancing high-temperature resistance and fucoxanthin biosynthesis in Phaeodactylum tricornutum. Appl Environ Microbiol 2024; 90:e0206823. [PMID: 38786362 PMCID: PMC11218622 DOI: 10.1128/aem.02068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Phaeodactylum tricornutum a prominent source of industrial fucoxanthin production, faces challenges in its application due to its tolerance to high-temperature environments. This study investigates the physiological responses of P. tricornutum to high-temperature stress and its impact on fucoxanthin content, with a specific focus on the role of cis-zeatin. The results reveal that high-temperature stress inhibits P. tricornutum's growth and photosynthetic activity, leading to a decrease in fucoxanthin content. Transcriptome analysis shows that high temperature suppresses the expression of genes related to photosynthesis (e.g., psbO, psbQ, and OEC) and fucoxanthin biosynthesis (e.g., PYS, PDS1, and PSD2), underscoring the negative effects of high temperature on P. tricornutum. Interestingly, genes associated with cis-zeatin biosynthesis and cytokinesis signaling pathways exhibited increased expression under high-temperature conditions, indicating a potential role of cis-zeatin signaling in response to elevated temperatures. Content measurements confirm that high temperature enhances cis-zeatin content. Furthermore, the exogenous addition of cytokinesis mimetics or inhibitors significantly affected P. tricornutum's high-temperature resistance. Overexpression of the cis-zeatin biosynthetic enzyme gene tRNA DMATase enhanced P. tricornutum's resistance to high-temperature stress, while genetic knockout of tRNA DMATase reduced its resistance to high temperatures. Therefore, this research not only uncovers a novel mechanism for high-temperature resistance in P. tricornutum but also offers a possible alga species that can withstand high temperatures for the industrial production of fucoxanthin, offering valuable insights for practical utilization.IMPORTANCEThis study delves into Phaeodactylum tricornutum's response to high-temperature stress, specifically focusing on cis-zeatin. We uncover inhibited growth, reduced fucoxanthin, and significant cis-zeatin-related gene expression under high temperatures, highlighting potential signaling mechanisms. Crucially, genetic engineering and exogenous addition experiments confirm that the change in cis-zeatin levels could influence P. tricornutum's resistance to high-temperature stress. This breakthrough deepens our understanding of microalgae adaptation to high temperatures and offers an innovative angle for industrial fucoxanthin production. This research is a pivotal step toward developing heat-resistant microalgae for industrial use.
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Affiliation(s)
- Sizhe Fan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yixuan Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Qi Wang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Mengjie Jin
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Mange Yu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hejing Zhao
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jilin Xu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Bing Li
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China, Ningbo, China
| | - Xiaohui Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
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Noonan HR, Thornock AM, Barbano J, Xifaras ME, Baron CS, Yang S, Koczirka K, McConnell AM, Zon LI. A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma. eLife 2024; 13:e83527. [PMID: 38874379 PMCID: PMC11178360 DOI: 10.7554/elife.83527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 04/15/2024] [Indexed: 06/15/2024] Open
Abstract
Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this TGFb Induced Enhancer driving green fluorescent protein (TIE:EGFP). TIE:EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of advanced melanomas. Single-cell RNA-sequencing revealed that TIE:EGFP+ melanoma cells down-regulated interferon response while up-regulating a novel set of chronic TGFb target genes. ChIP-sequencing demonstrated that AP-1 factor binding is required for activation of chronic TGFb response. Overexpression of SATB2, a chromatin remodeler associated with tumor spreading, showed activation of TGFb signaling in early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages localize to TIE:EGFP+ regions and preferentially phagocytose TIE:EGFP+ melanoma cells compared to TIE:EGFP- melanoma cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors.
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Affiliation(s)
- Haley R Noonan
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
- Biological and Biomedical Sciences Program, Harvard Medical SchoolBostonUnited States
| | - Alexandra M Thornock
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
- Biological and Biomedical Sciences Program, Harvard Medical SchoolBostonUnited States
| | - Julia Barbano
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
| | - Michael E Xifaras
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
- Immunology Program, Harvard Medical SchoolBostonUnited States
| | - Chloe S Baron
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
| | - Katherine Koczirka
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
| | - Alicia M McConnell
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical InstituteBostonUnited States
- Stem Cell and Regenerative Biology Department, Harvard UniversityCambridgeUnited States
- Harvard Medical SchoolBostonUnited States
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67
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Taya M, Hou X, Veneris JT, Kazi N, Larson MC, Maurer MJ, Heinzen EP, Chen H, Lastra R, Oberg AL, Weroha SJ, Fleming GF, Conzen SD. Investigation of selective glucocorticoid receptor modulation in high-grade serous ovarian cancer PDX models. J Gynecol Oncol 2024; 36:36.e4. [PMID: 38909640 DOI: 10.3802/jgo.2025.36.e4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/18/2024] [Accepted: 05/07/2024] [Indexed: 06/25/2024] Open
Abstract
OBJECTIVE In ovarian cancer (OvCa), tumor cell high glucocorticoid receptor (GR) has been associated with poor patient prognosis. In vitro, GR activation inhibits chemotherapy-induced OvCa cell death in association with transcriptional upregulation of genes encoding anti-apoptotic proteins. A recent randomized phase II study demonstrated improvement in progression-free survival (PFS) for heavily pre-treated OvCa patients randomized to receive therapy with a selective GR modulator (SGRM) plus chemotherapy compared to chemotherapy alone. We hypothesized that SGRM therapy would improve carboplatin response in OvCa patient-derived xenograft (PDX). METHODS Six high-grade serous (HGS) OvCa PDX models expressing GR mRNA (NR3C1) and protein were treated with chemotherapy +/- SGRM. Tumor size was measured longitudinally by peritoneal transcutaneous ultrasonography. RESULTS One of the 6 GR-positive PDX models showed a significant improvement in PFS with the addition of a SGRM. Interestingly, the single model with an improved PFS was least carboplatin sensitive. Possible explanations for the modest SGRM activity include the high carboplatin sensitivity of 5 of the PDX tumors and the potential that SGRMs activate the tumor invasive immune cells in patients (absent from immunocompromised mice). The level of tumor GR protein expression alone appears insufficient for predicting SGRM response. CONCLUSION The significant improvement in PFS shown in 1 of the 6 models after treatment with a SGRM plus chemotherapy underscores the need to determine predictive biomarkers for SGRM therapy in HGS OvCa and to better identify patient subgroups that are most likely to benefit from adding GR modulation to chemotherapy.
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Affiliation(s)
- Manisha Taya
- Division of Hematology and Oncology, UT Southwestern, Dallas, TX, USA
| | - Xiaonan Hou
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer T Veneris
- Department of Medicine, Section of Hematology and Oncology, The University of Chicago, Chicago, IL, USA
| | - Nina Kazi
- Division of Hematology and Oncology, UT Southwestern, Dallas, TX, USA
| | - Melissa C Larson
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Maurer
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Ethan P Heinzen
- Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
| | - Hao Chen
- Department of Pathology, UT Southwestern, Dallas, TX, USA
| | - Ricardo Lastra
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Ann L Oberg
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - S John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Gini F Fleming
- Department of Medicine, Section of Hematology and Oncology, The University of Chicago, Chicago, IL, USA
| | - Suzanne D Conzen
- Division of Hematology and Oncology, UT Southwestern, Dallas, TX, USA.
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Martinez-Terroba E, Plasek-Hegde LM, Chiotakakos I, Li V, de Miguel FJ, Robles-Oteiza C, Tyagi A, Politi K, Zamudio JR, Dimitrova N. Overexpression of Malat1 drives metastasis through inflammatory reprogramming of the tumor microenvironment. Sci Immunol 2024; 9:eadh5462. [PMID: 38875320 DOI: 10.1126/sciimmunol.adh5462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/23/2024] [Indexed: 06/16/2024]
Abstract
Expression of the long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) correlates with tumor progression and metastasis in many tumor types. However, the impact and mechanism of action by which MALAT1 promotes metastatic disease remain elusive. Here, we used CRISPR activation (CRISPRa) to overexpress MALAT1/Malat1 in patient-derived lung adenocarcinoma (LUAD) cell lines and in the autochthonous K-ras/p53 LUAD mouse model. Malat1 overexpression was sufficient to promote the progression of LUAD to metastatic disease in mice. Overexpression of MALAT1/Malat1 enhanced cell mobility and promoted the recruitment of protumorigenic macrophages to the tumor microenvironment through paracrine secretion of CCL2/Ccl2. Ccl2 up-regulation was the result of increased global chromatin accessibility upon Malat1 overexpression. Macrophage depletion and Ccl2 blockade counteracted the effects of Malat1 overexpression. These data demonstrate that a single lncRNA can drive LUAD metastasis through reprogramming of the tumor microenvironment.
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Affiliation(s)
- Elena Martinez-Terroba
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Leah M Plasek-Hegde
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ioannis Chiotakakos
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Vincent Li
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | | | - Camila Robles-Oteiza
- Departments of Pathology and Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT 06511, USA
| | - Antariksh Tyagi
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06516, USA
| | - Katerina Politi
- Yale Cancer Center, Yale University, New Haven, CT 06511, USA
- Departments of Pathology and Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT 06511, USA
| | - Jesse R Zamudio
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Cancer Center, Yale University, New Haven, CT 06511, USA
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69
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Chen M, Li Z, He X, Zhang Z, Wang D, Cui L, Xie M, Zhao Z, Sun Q, Wang D, Dai J, Gong D. Comparative transcriptome analysis reveals genes involved in trichome development and metabolism in tobacco. BMC PLANT BIOLOGY 2024; 24:541. [PMID: 38872084 DOI: 10.1186/s12870-024-05265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The glandular trichomes of tobacco (Nicotiana tabacum) can efficiently produce secondary metabolites. They act as natural bioreactors, and their natural products function to protect plants against insect-pests and pathogens and are also components of industrial chemicals. To clarify the molecular mechanisms of tobacco glandular trichome development and secondary metabolic regulation, glandular trichomes and glandless trichomes, as well as other different developmental tissues, were used for RNA sequencing and analysis. RESULTS By comparing glandless and glandular trichomes with other tissues, we obtained differentially expressed genes. They were obviously enriched in KEGG pathways, such as cutin, suberine, and wax biosynthesis, flavonoid and isoflavonoid biosynthesis, terpenoid biosynthesis, and plant-pathogen interaction. In particular, the expression levels of genes related to the terpenoid, flavonoid, and wax biosynthesis pathway mainly showed down-regulation in glandless trichomes, implying that they lack the capability to synthesize certain exudate compounds. Among the differentially expressed genes, 234 transcription factors were found, including AP2-ERFs, MYBs, bHLHs, WRKYs, Homeoboxes (HD-ZIP), and C2H2-ZFs. These transcription factor and genes that highly expressed in trichomes or specially expressed in GT or GLT. Following the overexpression of R2R3-MYB transcription factor Nitab4.5_0011760g0030.1 in tobacco, an increase in the number of branched glandular trichomes was observed. CONCLUSIONS Our data provide comprehensive gene expression information at the transcriptional level and an understanding of the regulatory pathways involved in glandular trichome development and secondary metabolism.
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Affiliation(s)
- Mingli Chen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhiyuan Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xinxi He
- China Tobacco Hunan Industry Co., Ltd, Changsha, China
| | - Zhe Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Graduate School of the Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Wang
- China Tobacco Hunan Industry Co., Ltd, Changsha, China
| | - Luying Cui
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Minmin Xie
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zeyu Zhao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Quan Sun
- College of Bioinformation, Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Dahai Wang
- Shandong Weifang Tobacco Co., Ltd, Weifang, China
| | - Jiameng Dai
- Yunnan Key Laboratory of Tobacco Chemistry, China , Tobacco Yunnan Industrial Co., Ltd, Kunming, China.
| | - Daping Gong
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China.
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Margalit S, Tulpová Z, Detinis Zur T, Michaeli Y, Deek J, Nifker G, Haldar R, Gnatek Y, Omer D, Dekel B, Feldman HB, Grunwald A, Ebenstein Y. Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587463. [PMID: 38915648 PMCID: PMC11195078 DOI: 10.1101/2024.03.31.587463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping and nanopore sequencing are attractive technologies that bridge this resolution gap and offer enhanced performance for cytogenetic applications. These methods profile native, individual DNA molecules, thus capturing epigenetic information. We applied both techniques to characterize a clear cell renal cell carcinoma (ccRCC) tumor's structural and copy number landscape, highlighting the relative strengths of each method in the context of variant size and average read length. Additionally, we assessed their utility for methylome and hydroxymethylome profiling, emphasizing differences in epigenetic analysis applicability.
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Affiliation(s)
- Sapir Margalit
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpová
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Tahir Detinis Zur
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Jasline Deek
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Gil Nifker
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Rita Haldar
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yehudit Gnatek
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Dorit Omer
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- Pediatric Nephrology Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagit Baris Feldman
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Assaf Grunwald
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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Alami MM, Shu S, Liu S, Ouyang Z, Zhang Y, Lv M, Sang Y, Gong D, Yang G, Feng S, Mei Z, Xie DY, Wang X. Chromosome-scale genome assembly of medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family. Sci Data 2024; 11:610. [PMID: 38866889 PMCID: PMC11169364 DOI: 10.1038/s41597-024-03315-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 06/14/2024] Open
Abstract
Tinospora sagittata (Oliv.) Gagnep. is an important medicinal tetraploid plant in the Menispermaceae family. Its tuber, Radix Tinosporae, used in traditional Chinese medicine, is rich in diterpenoids and benzylisoquinoline alkaloids (BIAs). To enhance our understanding of medicinal compounds' biosynthesis and Menispermaceae's evolution, we herein report assembling a high-quality chromosome-scale genome with both PacBio HiFi and Illumina sequencing technologies. PacBio Sequel II generated 2.5 million circular consensus sequencing (CCS) reads, and a hybrid assembly strategy with Illumina sequencing resulted in 4483 contigs. The assembled genome size was 2.33 Gb, consisting of 4070 scaffolds (N50 = 42.06 Mb), of which 92.05% were assigned to 26 pseudochromosomes. T. sagittata's chromosomal-scale genome assembly, the first species in Menispermaceae, aids Menispermaceae evolution and T. sagittata's secondary metabolites biosynthesis understanding.
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Affiliation(s)
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sanbo Liu
- China Resources Sanjiu (Huangshi) Pharmaceutical Co., Ltd., Huangshi, 435000, Hubei, China
| | - Zhen Ouyang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yipeng Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meijia Lv
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yonghui Sang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dalin Gong
- China Resources Sanjiu (Huangshi) Pharmaceutical Co., Ltd., Huangshi, 435000, Hubei, China
| | - Guozheng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengqiu Feng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhinan Mei
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xuekui Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Kashyap MK, Karathia H, Kumar D, Vera Alvarez R, Forero-Forero JV, Moreno E, Lujan JV, Amaya-Chanaga CI, Vidal NM, Yu Z, Ghia EM, Lengerke-Diaz PA, Achinko D, Choi MY, Rassenti LZ, Mariño-Ramírez L, Mount SM, Hannenhalli S, Kipps TJ, Castro JE. Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102202. [PMID: 38846999 PMCID: PMC11154714 DOI: 10.1016/j.omtn.2024.102202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Splicing factor 3b subunit 1 (SF3B1) is the largest subunit and core component of the spliceosome. Inhibition of SF3B1 was associated with an increase in broad intron retention (IR) on most transcripts, suggesting that IR can be used as a marker of spliceosome inhibition in chronic lymphocytic leukemia (CLL) cells. Furthermore, we separately analyzed exonic and intronic mapped reads on annotated RNA-sequencing transcripts obtained from B cells (n = 98 CLL patients) and healthy volunteers (n = 9). We measured intron/exon ratio to use that as a surrogate for alternative RNA splicing (ARS) and found that 66% of CLL-B cell transcripts had significant IR elevation compared with normal B cells (NBCs) and that correlated with mRNA downregulation and low expression levels. Transcripts with the highest IR levels belonged to biological pathways associated with gene expression and RNA splicing. A >2-fold increase of active pSF3B1 was observed in CLL-B cells compared with NBCs. Additionally, when the CLL-B cells were treated with macrolides (pladienolide-B), a significant decrease in pSF3B1, but not total SF3B1 protein, was observed. These findings suggest that IR/ARS is increased in CLL, which is associated with SF3B1 phosphorylation and susceptibility to SF3B1 inhibitors. These data provide additional support to the relevance of ARS in carcinogenesis and evidence of pSF3B1 participation in this process.
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Affiliation(s)
- Manoj Kumar Kashyap
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Gurugram (HR) 122413, India
| | - Hiren Karathia
- Advanced Biomedical Computational Science and National Center for Advancing Translational Sciences, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Greenwood Genetic Center, Greenwood, SC, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Deepak Kumar
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Eider Moreno
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Juliana Velez Lujan
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | | | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhe Yu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Emanuela M. Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Paula A. Lengerke-Diaz
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Daniel Achinko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Y. Choi
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M. Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
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Dunn-Davies H, Dudnakova T, Nogara A, Rodor J, Thomas AC, Parish E, Gautier P, Meynert A, Ulitsky I, Madeddu P, Caporali A, Baker A, Tollervey D, Mitić T. Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102173. [PMID: 38617973 PMCID: PMC11015509 DOI: 10.1016/j.omtn.2024.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Epigenetic processes involving long non-coding RNAs regulate endothelial gene expression. However, the underlying regulatory mechanisms causing endothelial dysfunction remain to be elucidated. Enhancer of zeste homolog 2 (EZH2) is an important rheostat of histone H3K27 trimethylation (H3K27me3) that represses endothelial targets, but EZH2 RNA binding capacity and EZH2:RNA functional interactions have not been explored in post-ischemic angiogenesis. We used formaldehyde/UV-assisted crosslinking ligation and sequencing of hybrids and identified a new role for maternally expressed gene 3 (MEG3). MEG3 formed the predominant RNA:RNA hybrid structures in endothelial cells. Moreover, MEG3:EZH2 assists recruitment onto chromatin. By EZH2-chromatin immunoprecipitation, following MEG3 depletion, we demonstrated that MEG3 controls recruitment of EZH2/H3K27me3 onto integrin subunit alpha4 (ITGA4) promoter. Both MEG3 knockdown or EZH2 inhibition (A-395) promoted ITGA4 expression and improved endothelial cell migration and adhesion to fibronectin in vitro. The A-395 inhibitor re-directed MEG3-assisted chromatin remodeling, offering a direct therapeutic benefit by increasing endothelial function and resilience. This approach subsequently increased the expression of ITGA4 in arterioles following ischemic injury in mice, thus promoting arteriogenesis. Our findings show a context-specific role for MEG3 in guiding EZH2 to repress ITGA4. Novel therapeutic strategies could antagonize MEG3:EZH2 interaction for pre-clinical studies.
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Affiliation(s)
- Hywel Dunn-Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tatiana Dudnakova
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Antonella Nogara
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Anita C. Thomas
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Elisa Parish
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann-UK Building rm. 007, Weizmann Institute of Science Rehovot 76100, Israel
| | - Paolo Madeddu
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrew Baker
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tijana Mitić
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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Sudo R, Asakura T, Ishikawa T, Hatakeyama R, Fujiwara A, Inoue K, Mochida K, Nomura K. Transcriptome analysis of the Japanese eel (Anguilla japonica) during larval metamorphosis. BMC Genomics 2024; 25:585. [PMID: 38862878 PMCID: PMC11165803 DOI: 10.1186/s12864-024-10459-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Anguillid eels spend their larval period as leptocephalus larvae that have a unique and specialized body form with leaf-like and transparent features, and they undergo drastic metamorphosis to juvenile glass eels. Less is known about the transition of leptocephali to the glass eel stage, because it is difficult to catch the metamorphosing larvae in the open ocean. However, recent advances in rearing techniques for the Japanese eel have made it possible to study the larval metamorphosis of anguillid eels. In the present study, we investigated the dynamics of gene expression during the metamorphosis of Japanese eel leptocephali using RNA sequencing. RESULTS During metamorphosis, Japanese eels were classified into 7 developmental stages according to their morphological characteristics, and RNA sequencing was used to collect gene expression data from each stage. A total of 354.8 million clean reads were generated from the body and 365.5 million from the head, after the processing of raw reads. For filtering of genes that characterize developmental stages, a classification model created by a Random Forest algorithm was built. Using the importance of explanatory variables feature obtained from the created model, we identified 46 genes selected in the body and 169 genes selected in the head that were defined as the "most characteristic genes" during eel metamorphosis. Next, network analysis and subsequently gene clustering were conducted using the most characteristic genes and their correlated genes, and then 6 clusters in the body and 5 clusters in the head were constructed. Then, the characteristics of the clusters were revealed by Gene Ontology (GO) enrichment analysis. The expression patterns and GO terms of each stage were consistent with previous observations and experiments during the larval metamorphosis of the Japanese eel. CONCLUSION Genome and transcriptome resources have been generated for metamorphosing Japanese eels. Genes that characterized metamorphosis of the Japanese eel were identified through statistical modeling by a Random Forest algorithm. The functions of these genes were consistent with previous observations and experiments during the metamorphosis of anguillid eels.
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Affiliation(s)
- Ryusuke Sudo
- Fisheries Technology Institute, Minamiizu Field Station, Japan Fisheries Research and Education Agency, Minamiizu, Kamo, Shizuoka, 415-0156, Japan.
| | - Taiga Asakura
- Fisheries Resources Institute, Yokohama Field Station, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, 236-8648, Japan
| | - Takashi Ishikawa
- Fisheries Technology Institute, Nansei Field Station, Japan Fisheries Research and Education Agency, Minamiise, Mie, 516-0193, Japan
| | - Rui Hatakeyama
- Fisheries Technology Institute, Minamiizu Field Station, Japan Fisheries Research and Education Agency, Minamiizu, Kamo, Shizuoka, 415-0156, Japan
| | - Atushi Fujiwara
- Fisheries Technology Institute, Nansei Field Station, Japan Fisheries Research and Education Agency, Minamiise, Mie, 516-0193, Japan
| | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-Ku, Yokohama, 230-0045, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-Ku, Yokohama, 230-0045, Japan
- School of Information and Data Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
- RIKEN Baton Zone Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazuharu Nomura
- Fisheries Technology Institute, Nansei Field Station, Japan Fisheries Research and Education Agency, Minamiise, Mie, 516-0193, Japan.
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Robertson AL, Yue L, Choudhuri A, Kubaczka C, Wattrus SJ, Mandelbaum J, Avagyan S, Yang S, Freeman RJ, Chan V, Blair MC, Daley GQ, Zon LI. Hematopoietic stem cell division is governed by distinct RUNX1 binding partners. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.596542. [PMID: 38895208 PMCID: PMC11185638 DOI: 10.1101/2024.06.07.596542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A defined number of hematopoietic stem cell (HSC) clones are born during development and expand to form the pool of adult stem cells. An intricate balance between self-renewal and differentiation of these HSCs supports hematopoiesis for life. HSC fate is determined by complex transcription factor networks that drive cell-type specific gene programs. The transcription factor RUNX1 is required for definitive hematopoiesis, and mutations in Runx1 have been shown to reduce clonal diversity. The RUNX1 cofactor, CBFý, stabilizes RUNX1 binding to DNA, and disruption of their interaction alters downstream gene expression. Chemical screening for modulators of Runx1 and HSC expansion in zebrafish led us to identify a new mechanism for the RUNX1 inhibitor, Ro5-3335. We found that Ro5-3335 increased HSC divisions in zebrafish, and animals transplanted with Ro5-3335 treated cells had enhanced chimerism compared to untreated cells. Using human CD34+ cells, we show that Ro5-3335 remodels the RUNX1 transcription complex by binding to ELF1, independent of CBFý. This allows specific expression of cell cycle and hematopoietic genes that enhance HSC self-renewal and prevent differentiation. Furthermore, we provide the first evidence to show that it is possible to pharmacologically increase the number of stem cell clones in vivo , revealing a previously unknown mechanism for enhancing clonal diversity. Our studies have revealed a mechanism by which binding partners of RUNX1 determine cell fate, with ELF transcription factors guiding cell division. This information could lead to treatments that enhance clonal diversity for blood diseases.
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Lohmaneeratana K, Leetanasaksakul K, Thamchaipenet A. Transcriptomic Profiling of Sugarcane White Leaf (SCWL) Canes during Maturation Phase. PLANTS (BASEL, SWITZERLAND) 2024; 13:1551. [PMID: 38891358 PMCID: PMC11174868 DOI: 10.3390/plants13111551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, results in the most damage to sugarcane plantations. Some SCWL canes can grow unnoticed through the maturation phase, subsequently resulting in an overall low sugar yield, or they can be used accidentally as seed canes. In this work, 12-month-old SCWL and asymptomatic canes growing in the same field were investigated. An abundance of phytoplasma in SCWL canes affected growth and sugar content as well as alterations of transcriptomic profiles corresponding to several pathways that responded to the infection. Suppression of photosynthesis, porphyrin and chlorophyll metabolism, coupled with an increase in the expression of chlorophyllase, contributed to the reduction in chlorophyll levels and photosynthesis. Blockage of sucrose transport plausibly occurred due to the expression of sugar transporters in leaves but suppression in stalks, resulting in low sugar content in canes. Increased expression of genes associated with MAPK cascades, plant hormone signaling transduction, callose plug formation, the phenylpropanoid pathway, and calcium cascades positively promoted defense mechanisms against phytoplasma colonization by an accumulation of lignin and calcium in response to plant immunity. Significant downregulation of CPK plausibly results in a reduction in antioxidant enzymes and likely facilitates pathogen invasion, while expression of sesquiterpene biosynthesis possibly attracts the insect vectors for transmission, thereby enabling the spread of phytoplasma. Moreover, downregulation of flavonoid biosynthesis potentially intensifies the symptoms of SCWL upon challenge by phytoplasma. These SCWL sugarcane transcriptomic profiles describe the first comprehensive sugarcane-phytoplasma interaction during the harvesting stage. Understanding molecular mechanisms will allow for sustainable management and the prevention of SCWL disease-a crucial benefit to the sugar industry.
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Affiliation(s)
- Karan Lohmaneeratana
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Kantinan Leetanasaksakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand;
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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77
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Regunath K, Fomin V, Liu Z, Wang P, Hoque M, Tian B, Rabadan R, Prives C. Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types. Mol Cancer Res 2024; 22:555-571. [PMID: 38393317 DOI: 10.1158/1541-7786.mcr-23-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
The p53 tumor suppressor protein, a sequence-specific DNA binding transcription factor, regulates the expression of a large number of genes, in response to various forms of cellular stress. Although the protein coding target genes of p53 have been well studied, less is known about its role in regulating long noncoding genes and their functional relevance to cancer. Here we report the genome-wide identification of a large set (>1,000) of long noncoding RNAs (lncRNA), which are putative p53 targets in a colon cancer cell line and in human patient datasets from five different common types of cancer. These lncRNAs have not been annotated by other studies of normal unstressed systems. In the colon cancer cell line, a high proportion of these lncRNAs are uniquely induced by different chemotherapeutic agents that activate p53, whereas others are induced by more than one agent tested. Further, subsets of these lncRNAs independently predict overall and disease-free survival of patients across the five different common cancer types. Interestingly, both genetic alterations and patient survival associated with different lncRNAs are unique to each cancer tested, indicating extraordinary tissue-specific variability in the p53 noncoding response. The newly identified noncoding p53 target genes have allowed us to construct a classifier for tumor diagnosis and prognosis. IMPLICATIONS Our results not only identify myriad p53-regulated long noncoding (lncRNA), they also reveal marked drug-induced, as well as tissue- and tumor-specific heterogeneity in these putative p53 targets and our findings have enabled the construction of robust classifiers for diagnosis and prognosis.
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Affiliation(s)
- Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, New York
| | - Vitalay Fomin
- Department of Biological Sciences, Columbia University, New York, New York
| | - Zhaoqi Liu
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Pingzhang Wang
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York
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78
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Pineda JMB, Bradley RK. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers. eLife 2024; 12:RP89017. [PMID: 38829686 PMCID: PMC11147511 DOI: 10.7554/elife.89017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Cancer immune evasion contributes to checkpoint immunotherapy failure in many patients with metastatic cancers. The embryonic transcription factor DUX4 was recently characterized as a suppressor of interferon-γ signaling and antigen presentation that is aberrantly expressed in a small subset of primary tumors. Here, we report that DUX4 expression is a common feature of metastatic tumors, with ~10-50% of advanced bladder, breast, kidney, prostate, and skin cancers expressing DUX4. DUX4 expression is significantly associated with immune cell exclusion and decreased objective response to PD-L1 blockade in a large cohort of urothelial carcinoma patients. DUX4 expression is a significant predictor of survival even after accounting for tumor mutational burden and other molecular and clinical features in this cohort, with DUX4 expression associated with a median reduction in survival of over 1 year. Our data motivate future attempts to develop DUX4 as a biomarker and therapeutic target for checkpoint immunotherapy resistance.
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Affiliation(s)
- Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Medical Scientist Training Program, University of WashingtonSeattleUnited States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
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79
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Tang M, Liu Y, Zhang H, Sun L, Lü P, Chen K. Comprehensive transcriptome sequencing of silkworm Midguts: Uncovering extensive isoform diversity and alternative splicing in BmNPV-Sensitive and BmNPV-resistant strains. J Invertebr Pathol 2024; 204:108104. [PMID: 38608751 DOI: 10.1016/j.jip.2024.108104] [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: 12/05/2023] [Revised: 03/06/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
The silkworm, Bombyx mori, stands out as one of the few economically valuable insects within the realm of model organisms. However, Bombyx mori nucleopolyhedrovirus (BmNPV) poses a significant threat, decreasing the quality and quantity of silkworm cocoons. Over the past few decades, a multitude of researchers has delved into the mechanisms that underlie silkworm resistance to BmNPV, employing diverse methodologies and approaching the problem from various angles. Despite this extensive research, the role of alternative splicing (AS) in the silkworm's response to BmNPV infection has been largely unexplored. This study leveraged both third-generation (Oxford Nanopore Technologies) and second-generation (Illumina) high-throughput sequencing technologies to meticulously identify and analyze AS patterns in the context of BmNPV response, utilizing two distinct silkworm strains-the susceptible strain 306 and the resistant strain NB. Consequently, we identified five crucial genes (Dsclp, LOC692903, LOC101743583, LOC101742498, LOC101743809) that are linked to the response to BmNPV infection through AS and differential expression. Additionally, a thorough comparative analysis was conducted on their diverse transcriptomic expression profiles, including alternative polyadenylation, simple sequence repeats, and transcription factors.
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Affiliation(s)
- Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Lindan Sun
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
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80
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Caudal É, Loegler V, Dutreux F, Vakirlis N, Teyssonnière É, Caradec C, Friedrich A, Hou J, Schacherer J. Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast. Nat Genet 2024; 56:1278-1287. [PMID: 38778243 PMCID: PMC11176082 DOI: 10.1038/s41588-024-01769-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.
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Affiliation(s)
- Élodie Caudal
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Victor Loegler
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | | | | | - Claudia Caradec
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Jing Hou
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France.
| | - Joseph Schacherer
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France.
- Institut Universitaire de France (IUF), Paris, France.
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81
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Huang K, Wang Y, Li Y, Zhang B, Zhang L, Duan P, Xu R, Wang D, Liu L, Zhang G, Zhang H, Wang C, Guo N, Hao J, Luo Y, Zhu X, Li Y. Modulation of histone acetylation enables fully mechanized hybrid rice breeding. NATURE PLANTS 2024; 10:954-970. [PMID: 38831046 DOI: 10.1038/s41477-024-01720-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024]
Abstract
Hybrid rice has achieved high grain yield and greatly contributes to food security, but the manual-labour-intensive hybrid seed production process limits fully mechanized hybrid rice breeding. For next-generation hybrid seed production, the use of small-grain male sterile lines to mechanically separate small hybrid seeds from mixed harvest is promising. However, it is difficult to find ideal grain-size genes for breeding ideal small-grain male sterile lines without penalties in the number of hybrid seeds and hybrid rice yield. Here we report that the use of small-grain alleles of the ideal grain-size gene GSE3 in male sterile lines enables fully mechanized hybrid seed production and dramatically increases hybrid seed number in three-line and two-line hybrid rice systems. The GSE3 gene encodes a histone acetyltransferase that binds histones and influences histone acetylation levels. GSE3 is recruited by the transcription factor GS2 to the promoters of their co-regulated grain-size genes and influences the histone acetylation status of their co-regulated genes. Field trials demonstrate that genome editing of GSE3 can be used to immediately improve current elite male sterile lines of hybrid rice for fully mechanized hybrid rice breeding, providing a new perspective for mechanized hybrid breeding in other crops.
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Affiliation(s)
- Ke Huang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Hainan Seed Industry Laboratory, Sanya, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yingjie Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Hainan Seed Industry Laboratory, Sanya, China
| | - Baolan Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Limin Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Penggen Duan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ran Xu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dekai Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lijie Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - Guozheng Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hao Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - Chenjie Wang
- School of Breeding and Multiplication, Hainan University, Sanya, China
| | - Nian Guo
- School of Breeding and Multiplication, Hainan University, Sanya, China
| | - Jianqin Hao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuehua Luo
- School of Breeding and Multiplication, Hainan University, Sanya, China
| | - Xudong Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
| | - Yunhai Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China.
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82
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Wang Y, Li Y, Wu W, Shao S, Fang Q, Xu S, Guo Z, Shi S, He Z. The evolution history of an allotetraploid mangrove tree analysed with a new tool Allo4D. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1491-1503. [PMID: 38157253 PMCID: PMC11123425 DOI: 10.1111/pbi.14281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Mangrove species are broadly classified as true mangroves and mangrove associates. The latter are amphibious plants that can survive in the intertidal zone and reproduce naturally in terrestrial environments. Their widespread distribution and extensive adaptability make them ideal research materials for exploring adaptive evolution. In this study, we de novo assembled two genomes of mangrove associates (the allotetraploid Barringtonia racemosa (2n = 4x = 52) and diploid Barringtonia asiatica (2n = 2x = 26)) to investigate the role of allopolyploidy in the evolutionary history of mangrove species. We developed a new allotetraploid-dividing tool Allo4D to distinguish between allotetraploid scaffold-scale subgenomes and verified its accuracy and reliability using real and simulated data. According to the two subgenomes of allotetraploid B. racemosa divided using Allo4D, the allopolyploidization event was estimated to have occurred approximately one million years ago (Mya). We found that B. racemosa, B. asiatica, and Diospyros lotus shared a whole genome duplication (WGD) event during the K-Pg (Cretaceous-Paleozoic) period. K-Pg WGD and recent allopolyploidization events contributed to the speciation of B. racemosa and its adaptation to coastal habitats. We found that genes in the glucosinolates (GSLs) pathway, an essential pathway in response to various biotic and abiotic stresses, expanded rapidly in B. racemosa during polyploidization. In summary, this study provides a typical example of the adaptation of allopolyploid plants to extreme environmental conditions. The newly developed tool, Allo4D, can effectively divide allotetraploid subgenomes and explore the evolutionary history of polyploid plants, especially for species whose ancestors are unknown or extinct.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yulong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- School of EcologySun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Qi Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- School of EcologySun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
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83
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Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024; 291:2423-2448. [PMID: 38451841 DOI: 10.1111/febs.17112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
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Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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Tsung K, Liu KQ, Han JS, Deshpande K, Doan T, Loh YHE, Ding L, Yang W, Neman J, Dou Y, Attenello FJ. CRISPRi screen of long non-coding RNAs identifies LINC03045 regulating glioblastoma invasion. PLoS Genet 2024; 20:e1011314. [PMID: 38857306 PMCID: PMC11192328 DOI: 10.1371/journal.pgen.1011314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/21/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
INTRODUCTION Glioblastoma (GBM) invasion studies have focused on coding genes, while few studies evaluate long non-coding RNAs (lncRNAs), transcripts without protein-coding potential, for role in GBM invasion. We leveraged CRISPR-interference (CRISPRi) to evaluate invasive function of GBM-associated lncRNAs in an unbiased functional screen, characterizing and exploring the mechanism of identified candidates. METHODS We implemented a CRISPRi lncRNA loss-of-function screen evaluating association of lncRNA knockdown (KD) with invasion capacity in Matrigel. Top screen candidates were validated using CRISPRi and oligonucleotide(ASO)-mediated knockdown in three tumor lines. Clinical relevance of candidates was assessed via The Cancer Genome Atlas(TCGA) and Genotype-Tissue Expression(GTEx) survival analysis. Mediators of lncRNA effect were identified via differential expression analysis following lncRNA KD and assessed for tumor invasion using knockdown and rescue experiments. RESULTS Forty-eight lncRNAs were significantly associated with 33-83% decrease in invasion (p<0.01) upon knockdown. The top candidate, LINC03045, identified from effect size and p-value, demonstrated 82.7% decrease in tumor cell invasion upon knockdown, while LINC03045 expression was significantly associated with patient survival and tumor grade(p<0.0001). RNAseq analysis of LINC03045 knockdown revealed that WASF3, previously implicated in tumor invasion studies, was highly correlated with lncRNA expression, while WASF3 KD was associated with significant decrease in invasion. Finally, WASF3 overexpression demonstrated rescue of invasive function lost with LINC03045 KD. CONCLUSION CRISPRi screening identified LINC03045, a previously unannotated lncRNA, as critical to GBM invasion. Gene expression is significantly associated with tumor grade and survival. RNA-seq and mechanistic studies suggest that this novel lncRNA may regulate invasion via WASF3.
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Affiliation(s)
- Kathleen Tsung
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kristie Q. Liu
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jane S. Han
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Krutika Deshpande
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Tammy Doan
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yong-Hwee Eddie Loh
- USC Libraries Bioinformatics Services, University of Southern California, Los Angeles, California, United States of America
| | - Li Ding
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Wentao Yang
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Josh Neman
- Department of Neurological Surgery, Physiology and Neuroscience, USC Brain Tumor Center, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yali Dou
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Frank J. Attenello
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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Kwak S, Song CL, Lee J, Kim S, Nam S, Park YJ, Lee J. Development of pluripotent stem cell-derived epidermal organoids that generate effective extracellular vesicles in skin regeneration. Biomaterials 2024; 307:122522. [PMID: 38428092 DOI: 10.1016/j.biomaterials.2024.122522] [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: 09/28/2023] [Revised: 02/03/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Cellular skin substitutes such as epidermal constructs have been developed for various applications, including wound healing and skin regeneration. These cellular models are mostly derived from primary cells such as keratinocytes and fibroblasts in a two-dimensional (2D) state, and further development of three-dimensional (3D) cultured organoids is needed to provide insight into the in vivo epidermal phenotype and physiology. Here, we report the development of epidermal organoids (EpiOs) generated from induced pluripotent stem cells (iPSCs) as a novel epidermal construct and its application as a source of secreted biomolecules recovered by extracellular vesicles (EVs) that can be utilized for cell-free therapy of regenerative medicine. Differentiated iPSC-derived epidermal organoids (iEpiOs) are easily cultured and expanded through multiple organoid passages, while retaining molecular and functional features similar to in vivo epidermis. These mature iEpiOs contain epidermal stem cell populations and retain the ability to further differentiate into other skin compartment lineages, such as hair follicle stem cells. By closely recapitulating the epidermal structure, iEpiOs are expected to provide a more relevant microenvironment to influence cellular processes and therapeutic response. Indeed, iEpiOs can generate high-performance EVs containing high levels of the angiogenic growth factor VEGF and miRNAs predicted to regulate cellular processes such as proliferation, migration, differentiation, and angiogenesis. These EVs contribute to target cell proliferation, migration, and angiogenesis, providing a promising therapeutic tool for in vivo wound healing. Overall, the newly developed iEpiOs strategy as an organoid-based approach provides a powerful model for studying basic and translational skin research and may also lead to future therapeutic applications using iEpiOs-secreted EVs.
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Affiliation(s)
- Sojung Kwak
- Developmental Biology Laboratory, Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Cho Lok Song
- Developmental Biology Laboratory, Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jinhyuk Lee
- Department of Bioscience, KRIBB School, University of Science and Technology, Daejeon 34141, Republic of Korea; Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sungyeon Kim
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea; Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
| | - Young-Jun Park
- Department of Bioscience, KRIBB School, University of Science and Technology, Daejeon 34141, Republic of Korea; Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jungwoon Lee
- Developmental Biology Laboratory, Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea; Department of Bioscience, KRIBB School, University of Science and Technology, Daejeon 34141, Republic of Korea.
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86
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Goto S, Kojima N, Komori M, Kawade N, Oshima K, Nadano D, Sasaki N, Horio F, Matsuda T, Miyata S. Vitamin C deficiency alters the transcriptome of the rat brain in a glucocorticoid-dependent manner, leading to microglial activation and reduced neurogenesis. J Nutr Biochem 2024; 128:109608. [PMID: 38458474 DOI: 10.1016/j.jnutbio.2024.109608] [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: 07/19/2023] [Revised: 02/20/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
Vitamin C (VitC) is maintained at high concentrations in the brain and is an essential micronutrient for brain function. VitC deficiency leads to neuropsychiatric scurvy, which is characterized by depression and cognitive impairment. However, the molecular mechanism by which mild VitC deficiency impairs brain function is currently unknown. In the present study, we conducted RNA sequencing analysis and found that a short-term VitC deficiency altered the brain transcriptome in ODS rats, which cannot synthesize VitC. Bioinformatic analysis indicated that VitC deficiency affected the expression of genes controlled by the glucocorticoid receptor in the brain. We confirmed an increased secretion of glucocorticoids from the adrenal gland during VitC deficiency. We found that non-neuronal cells, including microglia, which are resident immune cells in the brain, changed their transcriptional patterns in response to VitC deficiency. Immunohistochemical analysis revealed that the quiescent ramified microglia transform into the activated amoeboid microglia during three weeks of VitC deficiency. The morphological activation of microglia was accompanied by increased expression of proinflammatory cytokines such as interleukin-6 in the hippocampus. Furthermore, VitC deficiency decreased the number of newly born neurons in the dentate gyrus of the hippocampus, suggesting that VitC was required for adult neurogenesis that plays a crucial role in learning and memory. Our findings may provide insights into the molecular mechanisms underlying the maintenance of normal brain function by adequate levels of VitC.
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Affiliation(s)
- Shunta Goto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Natsuki Kojima
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Miyu Komori
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Noe Kawade
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Kenzi Oshima
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Daita Nadano
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Nobumitsu Sasaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Fumihiko Horio
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan; Department of Life Studies and Environmental Science, Nagoya Women's University, Nagoya, Japan
| | - Tsukasa Matsuda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan; Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Shinji Miyata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan; Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan.
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87
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Li M, Deng A, He C, Yao Z, Zhuo Z, Wang XY, Wang Z. Genome sequencing, comparative analysis, and gene expression responses of cytochrome P450 genes in Oryzias curvinotus provide insights into environmental adaptation. Ecol Evol 2024; 14:e11565. [PMID: 38895576 PMCID: PMC11184212 DOI: 10.1002/ece3.11565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The mangrove fish (Oryzias curvinotus) serves as a model for researching environmental adaptation and sexual development. To further such research, we sequenced and assembled a high-quality 842 Mb reference genome for O. curvinotus. Comparative genomic analysis revealed 891 expanded gene families, including significantly expanded cytochrome P450 (CYP) detoxification genes known to be involved in xenobiotic defense. We identified 69 O. curvinotus CYPs (OcuCYPs) across 18 families and 10 clans using multiple methods. Extensive RNA-seq and qPCR analysis demonstrated diverse spatiotemporal expression patterns of OcuCYPs by developmental stage, tissue type, sex, and pollutant exposure (17β-estradiol (E2) and testosterone (MT)). Many OcuCYPs exhibited sexual dimorphism in gonads, suggesting reproductive roles in steroidogenesis, while their responsiveness to model toxicants indicates their importance in environmental adaptation through enhanced detoxification. Pathway analysis highlighted expanded CYP genes in arachidonic acid metabolism, drug metabolism, and steroid hormone biosynthesis. This chromosome-level genomic resource provides crucial biological insights to elucidate the functional roles of expanded CYPs in environmental adaptation, sexual development, early life history, and conservation in the anthropogenically impacted mangrove habitats of O. curvinotus. It also enables future ecotoxicology research leveraging O. curvinotus as a pollution sentinel species.
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Affiliation(s)
- Ming Li
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Aiping Deng
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Chuanmeng He
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Zebin Yao
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Zixuan Zhuo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Xiu yue Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries College, Guangdong Ocean UniversityZhanjiangChina
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy CultureFisheries College, Guangdong Ocean UniversityZhanjiangChina
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88
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Tan J, Zhang J, Hu C, Wang G, Ren Q, Wang C, Dan J, Zeng Z, Hu J, Zhu W, Liang J, Cai J, Liu Y, Yan G, Lin Y. Pharmacokinetic enhancement of oncolytic virus M1 by inhibiting JAK‒STAT pathway. Acta Pharm Sin B 2024; 14:2554-2566. [PMID: 38828147 PMCID: PMC11143530 DOI: 10.1016/j.apsb.2024.03.007] [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: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 06/05/2024] Open
Abstract
Oncolytic viruses (OVs), a group of replication-competent viruses that can selectively infect and kill cancer cells while leaving healthy cells intact, are emerging as promising living anticancer agents. Unlike traditional drugs composed of non-replicating compounds or biomolecules, the replicative nature of viruses confer unique pharmacokinetic properties that require further studies. Despite some pharmacokinetics studies of OVs, mechanistic insights into the connection between OV pharmacokinetics and antitumor efficacy remain vague. Here, we characterized the pharmacokinetic profile of oncolytic virus M1 (OVM) in immunocompetent mouse tumor models and identified the JAK‒STAT pathway as a key modulator of OVM pharmacokinetics. By suppressing the JAK‒STAT pathway, early OVM pharmacokinetics are ameliorated, leading to enhanced tumor-specific viral accumulation, increased AUC and Cmax, and improved antitumor efficacy. Rather than compromising antitumor immunity after JAK‒STAT inhibition, the improved pharmacokinetics of OVM promotes T cell recruitment and activation in the tumor microenvironment, providing an optimal opportunity for the therapeutic outcome of immune checkpoint blockade, such as anti-PD-L1. Taken together, this study advances our understanding of the pharmacokinetic-pharmacodynamic relationship in OV therapy.
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Affiliation(s)
- Jingyi Tan
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiayu Zhang
- The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Cheng Hu
- Department of Urology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Gongwei Wang
- Department of Urology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Qianyao Ren
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Chaoqun Wang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jia Dan
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Advanced Medical Technology Center, the First Affiliated Hospital-Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zexin Zeng
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jun Hu
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenbo Zhu
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiankai Liang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jing Cai
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Ying Liu
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Guangmei Yan
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuan Lin
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Advanced Medical Technology Center, the First Affiliated Hospital-Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Human Microbiome and Elderly Chronic Diseases, Ministry of Education, Guangzhou 510655, China
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Wang H, Fang T, Li X, Xie Y, Wang W, Hu T, Kudrna D, Amombo E, Yin Y, Fan S, Gong Z, Huang Y, Xia C, Zhang J, Wu Y, Fu J. Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2068-2084. [PMID: 38531629 DOI: 10.1111/tpj.16729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/06/2024] [Accepted: 03/09/2024] [Indexed: 03/28/2024]
Abstract
Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.
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Affiliation(s)
- Huan Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao City, Shandong Province, 266109, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Tilin Fang
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Yan Xie
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province, 430074, China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Tao Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, Gansu Province, 730020, China
| | - David Kudrna
- School of Plant Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Erick Amombo
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Zhiyun Gong
- Agricultural Department, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Yicheng Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chunjiao Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Jinmin Fu
- College of Grassland Science, Qingdao Agricultural University, Qingdao City, Shandong Province, 266109, China
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
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Xu WQ, Ren CQ, Zhang XY, Comes HP, Liu XH, Li YG, Kettle CJ, Jalonen R, Gaisberger H, Ma YZ, Qiu YX. Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1372-1387. [PMID: 38343032 DOI: 10.1111/tpj.16675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/31/2024]
Abstract
Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values.
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Affiliation(s)
- Wu-Qin Xu
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Chao-Qian Ren
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xin-Yi Zhang
- Systematic & Evolutionary Botany and Biodiversity Group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Hans-Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, Austria
| | - Xin-Hong Liu
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Yin-Gang Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | | | - Riina Jalonen
- Bioversity International, Regional Office for Asia, Penang, Malaysia
| | | | - Ya-Zhen Ma
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Ying-Xiong Qiu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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91
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Yang Y, Liu JF, Jiang XF. A chromosome-level genome assembly of Chinese quince ( Pseudocydonia sinensis). FRONTIERS IN PLANT SCIENCE 2024; 15:1368861. [PMID: 38887462 PMCID: PMC11180997 DOI: 10.3389/fpls.2024.1368861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
Abstract
Introduction Pseudocydonia sinensis, also known as Chinese quince, is a perennial shrub or small tree highly valued for its edibility and medicinal properties. Method This study presents the first chromosome-level genome assembly of P. sinensis, achieved using HiFi sequencing and Hi-C scaffolding technology. Results The assembly resulted in a high-quality genome of 576.39 Mb in size. The genome was anchored to 17 pseudo-chromosomes, with a contig N50 of 27.6 Mb and a scaffold N50 of 33.8 Mb. Comprehensive assessment using BUSCO, CEGMA and BWA tools indicates the high completeness and accuracy of the genome assembly. Our analysis identified 116 species-specific genes, 1196 expanded genes and 1109 contracted genes. Additionally, the distribution of 4DTv values suggests that the most recent duplication event occurred before the divergence of P. sinensis from both Chaenomeles pinnatifida and Pyrus pyrifolia. Discussion The assembly of this high-quality genome provides a valuable platform for the genetic breeding and cultivation of P. sinensis, as well as for the comparison of the genetic complexity of P. sinensis with other important crops in the Rosaceae family.
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Affiliation(s)
- Ying Yang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
| | - Jin Feng Liu
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
| | - Xian Feng Jiang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yunnan, China
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Ng AYE, Chan SN, Pek JW. Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA. Cell Rep 2024; 43:114228. [PMID: 38735045 DOI: 10.1016/j.celrep.2024.114228] [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: 03/01/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. Here, we report a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, our study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes.
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive Singapore 117543, Singapore.
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93
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Sayed IM, Vo DT, Alcantara J, Inouye KM, Pranadinata RF, Luo L, Boland CR, Goyal NP, Kuo DJ, Huang SC, Sahoo D, Ghosh P, Das S. Molecular Signatures for Microbe-Associated Colorectal Cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595902. [PMID: 38853996 PMCID: PMC11160670 DOI: 10.1101/2024.05.26.595902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Genetic factors and microbial imbalances play crucial roles in colorectal cancers (CRCs), yet the impact of infections on cancer initiation remains poorly understood. While bioinformatic approaches offer valuable insights, the rising incidence of CRCs creates a pressing need to precisely identify early CRC events. We constructed a network model to identify continuum states during CRC initiation spanning normal colonic tissue to pre-cancer lesions (adenomatous polyps) and examined the influence of microbes and host genetics. Methods A Boolean network was built using a publicly available transcriptomic dataset from healthy and adenoma affected patients to identify an invariant Microbe-Associated Colorectal Cancer Signature (MACS). We focused on Fusobacterium nucleatum ( Fn ), a CRC-associated microbe, as a model bacterium. MACS-associated genes and proteins were validated by RT-qPCR, RNA seq, ELISA, IF and IHCs in tissues and colon-derived organoids from genetically predisposed mice ( CPC-APC Min+/- ) and patients (FAP, Lynch Syndrome, PJS, and JPS). Results The MACS that is upregulated in adenomas consists of four core genes/proteins: CLDN2/Claudin-2 (leakiness), LGR5/leucine-rich repeat-containing receptor (stemness), CEMIP/cell migration-inducing and hyaluronan-binding protein (epithelial-mesenchymal transition) and IL8/Interleukin-8 (inflammation). MACS was induced upon Fn infection, but not in response to infection with other enteric bacteria or probiotics. MACS induction upon Fn infection was higher in CPC-APC Min+/- organoids compared to WT controls. The degree of MACS expression in the patient-derived organoids (PDOs) generally corresponded with the known lifetime risk of CRCs. Conclusions Computational prediction followed by validation in the organoid-based disease model identified the early events in CRC initiation. MACS reveals that the CRC-associated microbes induce a greater risk in the genetically predisposed hosts, suggesting its potential use for risk prediction and targeted cancer prevention.
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94
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Ebrahimi B, Viswanadhapalli S, Pratap UP, Rahul G, Yang X, Pitta Venkata P, Drel V, Santhamma B, Konda S, Li X, Sanchez ALR, Yan H, Sareddy GR, Xu Z, Singh BB, Valente PT, Chen Y, Lai Z, Rao M, Kost ER, Curiel T, Tekmal RR, Nair HB, Vadlamudi RK. Pharmacological inhibition of the LIF/LIFR autocrine loop reveals vulnerability of ovarian cancer cells to ferroptosis. NPJ Precis Oncol 2024; 8:118. [PMID: 38789520 PMCID: PMC11126619 DOI: 10.1038/s41698-024-00612-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Of all gynecologic cancers, epithelial-ovarian cancer (OCa) stands out with the highest mortality rates. Despite all efforts, 90% of individuals who receive standard surgical and cytotoxic therapy experience disease recurrence. The precise mechanism by which leukemia inhibitory factor (LIF) and its receptor (LIFR) contribute to the progression of OCa remains unknown. Analysis of cancer databases revealed that elevated expression of LIF or LIFR was associated with poor progression-free survival of OCa patients and a predictor of poor response to chemotherapy. Using multiple primary and established OCa cell lines or tissues that represent five subtypes of epithelial-OCa, we demonstrated that LIF/LIFR autocrine signaling is active in OCa. Moreover, treatment with LIFR inhibitor, EC359 significantly reduced OCa cell viability and cell survival with an IC50 ranging from 5-50 nM. Furthermore, EC359 diminished the stemness of OCa cells. Mechanistic studies using RNA-seq and rescue experiments unveiled that EC359 primarily induced ferroptosis by suppressing the glutathione antioxidant defense system. Using multiple in vitro, ex vivo and in vivo models including cell-based xenografts, patient-derived explants, organoids, and xenograft tumors, we demonstrated that EC359 dramatically reduced the growth and progression of OCa. Additionally, EC359 therapy considerably improved tumor immunogenicity by robust CD45+ leukocyte tumor infiltration and polarizing tumor-associated macrophages (TAMs) toward M1 phenotype while showing no impact on normal T-, B-, and other immune cells. Collectively, our findings indicate that the LIF/LIFR autocrine loop plays an essential role in OCa progression and that EC359 could be a promising therapeutic agent for OCa.
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Affiliation(s)
- Behnam Ebrahimi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Suryavathi Viswanadhapalli
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
| | - Uday P Pratap
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Gopalam Rahul
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Xue Yang
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Department of Obstetrics and Gynecology, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
| | - Prabhakar Pitta Venkata
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Viktor Drel
- Department of Periodontics, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | | | | | - Xiaonan Li
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | | | - Hui Yan
- Department of microbiology and immunology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Gangadhara R Sareddy
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Zhenming Xu
- Department of microbiology and immunology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Brij B Singh
- Department of Periodontics, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Philip T Valente
- Department of Pathology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yidong Chen
- Department of Population Sciences, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Manjeet Rao
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Edward R Kost
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Tyler Curiel
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth, NH, 03755, USA
| | - Rajeshwar R Tekmal
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | | | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
- Audie L. Murphy Division, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
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95
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Choi KH, Lee DK, Jeong J, Ahn Y, Go DM, Kim DY, Lee CK. Inhibition of BMP-mediated SMAD pathway supports the pluripotency of pig embryonic stem cells in the absence of feeder cells. Theriogenology 2024; 225:67-80. [PMID: 38795512 DOI: 10.1016/j.theriogenology.2024.05.027] [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: 03/18/2024] [Revised: 05/18/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
Here, we examined the effects of the BMP signaling pathway inhibitor LDN-193189 on the pluripotency of porcine embryonic stem cells (ESCs) in the absence of feeder cells using molecular and transcriptomic techniques. Additionally, the effects of some extracellular matrix components on porcine ESC pluripotency were evaluated to develop an optimized and sustainable feeder-free culture system for porcine ESCs. Feeder cells were found to play an important role in supporting the pluripotency of porcine ESCs by blocking trophoblast and mesodermal differentiation through the inhibition of the BMP pathway. Additionally, treatment with LDN-193189, an inhibitor of the BMP pathway, maintained the pluripotency and homogeneity of porcine ESCs for an extended period in the absence of feeder cells by stimulating the secretion of chemokines and suppressing differentiation, based on transcriptome analysis. Conclusively, these results suggest that LDN-193189 could be a suitable replacement for feeder cells in the maintenance of porcine ESC pluripotency during culture. Additionally, these findings contribute to the understanding of pluripotency gene networks and comparative embryogenesis.
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Affiliation(s)
- Kwang-Hwan Choi
- Research and Development Center, Space F Corporation, Hwaseong, Gyeonggi-do, 18471, Republic of Korea; Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Dong-Kyung Lee
- Research and Development Center, Space F Corporation, Hwaseong, Gyeonggi-do, 18471, Republic of Korea; Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinsol Jeong
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yelim Ahn
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Du-Min Go
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Yong Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Pyeong Chang, 25354, Republic of Korea.
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96
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Moore J, Gkantalis J, Guix I, Chou W, Yuen K, Lazar AA, Spitzer M, Combes AJ, Barcellos-Hoff MH. Lack of TGFβ signaling competency predicts immune poor cancer conversion to immune rich and response to checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583752. [PMID: 38496519 PMCID: PMC10942434 DOI: 10.1101/2024.03.06.583752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Transforming growth factor beta (TGFβ) is well-recognized as an immunosuppressive player in the tumor microenvironment but also has a significant impact on cancer cell phenotypes. Loss of TGFβ signaling impairs DNA repair competency, which is described by a transcriptomic score, βAlt. Cancers with high βAlt have more genomic damage and are more responsive to genotoxic therapy. The growing appreciation that cancer DNA repair deficits are important determinants of immune response prompted us to investigate the association of βAlt with response to immune checkpoint blockade (ICB). We predicted that high βAlt tumors would be infiltrated with lymphocytes because of DNA damage burden and hence responsive to ICB. Methods We analyzed public transcriptomic data from clinical trials and preclinical models using transcriptomic signatures of TGFβ targets, DNA repair genes, tumor educated immune cells and interferon. A high βAlt, immune poor mammary tumor derived transplant model resistant to programmed death ligand 1 (PD-L1) antibodies was studied using multispectral flow cytometry to interrogate the immune system. Results Metastatic bladder patients in IMvigor 210 who responded to ICB had significantly increased βAlt scores and experienced significantly longer overall survival compared to those with low βAlt scores (hazard ratio 0.62, P=0.011) . Unexpectedly, 75% of high βAlt cancers were immune poor as defined by low expression of tumor educated immune cell and interferon signatures. The association of high βAlt with immune poor cancer was also evident in TCGA and preclinical cancer models. We used a high βAlt, immune poor cancer to test therapeutic strategies to overcome its inherent anti-PD-L1 resistance. Combination treatment with radiation and TGFβ inhibition were necessary for lymphocytic infiltration and activated NK cells were required for ICB response. Bioinformatic analysis identified high βAlt, immune poor B16 and CT26 preclinical models and paired biopsies of cancer patients that also demonstrated NK cell activation upon response to ICB. Conclusions Our studies support βAlt as a biomarker that predicts response to ICB albeit in immune poor cancers, which has implications for the development of therapeutic strategies to increase the number of cancer patients who will benefit from immunotherapy.
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Affiliation(s)
- Jade Moore
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Jim Gkantalis
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ines Guix
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - William Chou
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Kobe Yuen
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Ann A Lazar
- Division of Oral Epidemiology and Division of Biostatistics, University of California, San Francisco, CA, USA
| | - Mathew Spitzer
- Parker Institute for Cancer Immunotherapy, Department of Otolaryngology- Head and Neck Surgery, Department of Microbiology and Immunology, University of California, San Francisco, CA USA
- A member of the imCORE Network
| | - Alexis J Combes
- Department of Pathology, CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- A member of the imCORE Network
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97
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Lee JY, Bae K, Kim JH, Han HJ, Yoon HY, Yoon KA. Establishment and characterization of six canine hepatocellular carcinoma cell lines. Front Vet Sci 2024; 11:1392728. [PMID: 38840628 PMCID: PMC11150866 DOI: 10.3389/fvets.2024.1392728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/23/2024] [Indexed: 06/07/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common malignant liver tumor in dogs. Although surgical resection is a major treatment option for canine HCC, there are no distinct strategies for unresectable tumor subtypes or adjuvant chemotherapy for tumors with positive margins. We aimed to establish and characterize novel HCC cell lines from canine patients. Methods The cellular morphology, general growth features and tumorigenicity of the established cell lines were evaluated. We also examined the sensitivity of the cell lines to multi-target tyrosine kinase inhibitors (TKIs). Results We established novel canine HCC cell lines from hepatic tumors and an additional kidney tumor of six canine patients. All cell lines showed colony forming and migratory ability. KU-cHCC-001 and KU-cHCC-001-Kidney, two cell lines exhibiting high epithelial-mesenchymal transition characteristics, showed tumorigenicity in xenografted mice. Toceranib, a veterinary TKI that targets vascular endothelial growth factor (VEGFR)/platelet-derived growth factor receptor (PDGFR)/c-kit, effectively inhibited the mitogen-activated protein kinase pathway and induced apoptosis. The established canine HCC cell lines showed greater sensitivity to toceranib than to sorafenib, a first-line treatment for human HCC targeting RAF/VEGFR/PDGFR. Sorafenib showed improved anti-tumor effects when co-treated with SCH772984, an extracellular signal-regulated kinase inhibitor. Conclusion Our study suggests new therapeutic strategies for canine HCC, and these cell lines are valuable research materials for understanding HCC tumor biology in both humans and dogs.
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Affiliation(s)
- Ja Young Lee
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Kieun Bae
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
- KU Animal Cancer Center, Konkuk University Veterinary Medical Teaching Hospital, Seoul, Republic of Korea
| | - Jung-Hyun Kim
- KU Animal Cancer Center, Konkuk University Veterinary Medical Teaching Hospital, Seoul, Republic of Korea
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hyun-Jung Han
- KU Animal Cancer Center, Konkuk University Veterinary Medical Teaching Hospital, Seoul, Republic of Korea
- Department of Veterinary Emergency and Critical Care, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hun-Young Yoon
- KU Animal Cancer Center, Konkuk University Veterinary Medical Teaching Hospital, Seoul, Republic of Korea
- Department of Veterinary Surgery, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Kyong-Ah Yoon
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
- KU Animal Cancer Center, Konkuk University Veterinary Medical Teaching Hospital, Seoul, Republic of Korea
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98
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Zhang P, Li F, Tian Y, Wang D, Fu J, Rong Y, Wu Y, Gao T, Zhang H. Transcriptome Analysis of Sesame ( Sesamum indicum L.) Reveals the LncRNA and mRNA Regulatory Network Responding to Low Nitrogen Stress. Int J Mol Sci 2024; 25:5501. [PMID: 38791539 PMCID: PMC11122487 DOI: 10.3390/ijms25105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Nitrogen is one of the important factors restricting the development of sesame planting and industry in China. Cultivating sesame varieties tolerant to low nitrogen is an effective way to solve the problem of crop nitrogen deficiency. To date, the mechanism of low nitrogen tolerance in sesame has not been elucidated at the transcriptional level. In this study, two sesame varieties Zhengzhi HL05 (ZZ, nitrogen efficient) and Burmese prolific (MD, nitrogen inefficient) in low nitrogen were used for RNA-sequencing. A total of 3964 DEGs (differentially expressed genes) and 221 DELs (differentially expressed lncRNAs) were identified in two sesame varieties at 3d and 9d after low nitrogen stress. Among them, 1227 genes related to low nitrogen tolerance are mainly located in amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and participate in the process of transporter activity and antioxidant activity. In addition, a total of 209 pairs of lncRNA-mRNA were detected, including 21 pairs of trans and 188 cis. WGCNA (weighted gene co-expression network analysis) analysis divided the obtained genes into 29 modules; phenotypic association analysis identified three low-nitrogen response modules; through lncRNA-mRNA co-expression network, a number of hub genes and cis/trans-regulatory factors were identified in response to low-nitrogen stress including GS1-2 (glutamine synthetase 1-2), PAL (phenylalanine ammonia-lyase), CHS (chalcone synthase, CHS), CAB21 (chlorophyll a-b binding protein 21) and transcription factors MYB54, MYB88 and NAC75 and so on. As a trans regulator, lncRNA MSTRG.13854.1 affects the expression of some genes related to low nitrogen response by regulating the expression of MYB54, thus responding to low nitrogen stress. Our research is the first to provide a more comprehensive understanding of DEGs involved in the low nitrogen stress of sesame at the transcriptome level. These results may reveal insights into the molecular mechanisms of low nitrogen tolerance in sesame and provide diverse genetic resources involved in low nitrogen tolerance research.
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Affiliation(s)
- Pengyu Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feng Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yuan Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Dongyong Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Jinzhou Fu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yasi Rong
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yin Wu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
| | - Tongmei Gao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
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99
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Benbarche S, Pineda JMB, Galvis LB, Biswas J, Liu B, Wang E, Zhang Q, Hogg SJ, Lyttle K, Dahi A, Lewis AM, Sarchi M, Rahman J, Fox N, Ai Y, Mehta S, Garippa R, Ortiz-Pacheco J, Li Z, Monetti M, Stanley RF, Doulatov S, Bradley RK, Abdel-Wahab O. GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies. Mol Cell 2024; 84:1886-1903.e10. [PMID: 38688280 PMCID: PMC11102302 DOI: 10.1016/j.molcel.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Mutations in the RNA splicing factor gene SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing, yet there is currently no therapeutic means to correct this mis-splicing. Here, we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain-containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis. GPATCH8 is involved in quality control of branchpoint selection, interacts with the RNA helicase DHX15, and functionally opposes SURP and G-patch domain containing 1 (SUGP1), a G-patch protein recently implicated in SF3B1-mutant diseases. Silencing of GPATCH8 corrected one-third of mutant SF3B1-dependent splicing defects and was sufficient to improve dysfunctional hematopoiesis in SF3B1-mutant mice and primary human progenitors. These data identify GPATCH8 as a novel splicing factor required for mis-splicing by mutant SF3B1 and highlight the therapeutic impact of correcting aberrant splicing in SF3B1-mutant cancers.
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Affiliation(s)
- Salima Benbarche
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Laura Baquero Galvis
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jeetayu Biswas
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qian Zhang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kadeen Lyttle
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariana Dahi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lewis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Sarchi
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nina Fox
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuxi Ai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Juliana Ortiz-Pacheco
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Mara Monetti
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergei Doulatov
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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100
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Desai PB, Karve AS, Zawit M, Arora P, Dave N, Awosika J, Li N, Fuhrman B, Medvedovic M, Sallans L, Kendler A, DasGupta B, Plas D, Curry R, Zuccarello M, Chaudhary R, Sengupta S, Wise-Draper TM. A Phase 0/I Pharmacokinetic and Pharmacodynamics and Safety and Tolerability Study of Letrozole in Combination with Standard Therapy in Recurrent High-Grade Gliomas. Clin Cancer Res 2024; 30:2068-2077. [PMID: 38530160 DOI: 10.1158/1078-0432.ccr-23-3341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
PURPOSE High-grade gliomas (HGG) carry a poor prognosis, with glioblastoma accounting for almost 50% of primary brain malignancies in the elderly. Unfortunately, despite the use of multiple treatment modalities, the prognosis remains poor in this population. Our preclinical studies suggest that the presence of aromatase expression, encoded by CYP19A1, is significantly upregulated in HGGs. Remarkably, we find that letrozole (LTZ), an FDA-approved aromatase inhibitor, has marked activity against HGGs. PATIENTS AND METHODS We conducted a phase 0/I single-center clinical trial (NCT03122197) to assess the tumoral availability, pharmacokinetics (PK), safety, and tolerability of LTZ in recurrent patients with HGG. Planned dose cohorts included 2.5, 5, 10, 12.5, 15, 17.5, and 20 mg of LTZ administered daily pre- and postsurgery or biopsy. Tumor samples were assayed for LTZ content and relevant biomarkers. The recommended phase 2 dose (R2PD) was determined as the dose that resulted in predicted steady-state tumoral extracellular fluid (ECF; Css,ecf) >2 μmol/L and did not result in ≥33% dose-limiting adverse events (AE) assessed using CTCAE v5.0. RESULTS Twenty-one patients were enrolled. Common LTZ-related AEs included fatigue, nausea, musculoskeletal, anxiety, and dysphoric mood. No DLTs were observed. The 15 mg dose achieved a Css,ecf of 3.6 ± 0.59 μmol/L. LTZ caused dose-dependent inhibition of estradiol synthesis and modulated DNA damage pathways in tumor tissues as evident using RNA-sequencing analysis. CONCLUSIONS On the basis of safety, brain tumoral PK, and mechanistic data, 15 mg daily is identified as the RP2D for future trials.
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Affiliation(s)
- Pankaj B Desai
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Aniruddha S Karve
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Misam Zawit
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio
| | - Priyanka Arora
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Nimita Dave
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Joy Awosika
- National Institute of Health, Bethesda, Maryland
| | - Ningjing Li
- Division of Oncology, University of Texas Health Science Center at Houston, Houston, Texas
| | | | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Larry Sallans
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - Ady Kendler
- Department of Pathology, University of Cincinnati, Cincinnati, Ohio
| | - Biplab DasGupta
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio
| | | | - Mario Zuccarello
- Department of Neurosurgery, University of Cincinnati, Cincinnati, Ohio
| | - Rekha Chaudhary
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio
| | - Soma Sengupta
- Department of Neurology & Neurosurgery & the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Trisha M Wise-Draper
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio
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