1
|
Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [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: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
Collapse
Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
| |
Collapse
|
2
|
Mensah IK, Gowher H. Epigenetic Regulation of Mammalian Cardiomyocyte Development. EPIGENOMES 2024; 8:25. [PMID: 39051183 PMCID: PMC11270418 DOI: 10.3390/epigenomes8030025] [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: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
The heart is the first organ formed during mammalian development and functions to distribute nutrients and oxygen to other parts of the developing embryo. Cardiomyocytes are the major cell types of the heart and provide both structural support and contractile function to the heart. The successful differentiation of cardiomyocytes during early development is under tight regulation by physical and molecular factors. We have reviewed current studies on epigenetic factors critical for cardiomyocyte differentiation, including DNA methylation, histone modifications, chromatin remodelers, and noncoding RNAs. This review also provides comprehensive details on structural and morphological changes associated with the differentiation of fetal and postnatal cardiomyocytes and highlights their differences. A holistic understanding of all aspects of cardiomyocyte development is critical for the successful in vitro differentiation of cardiomyocytes for therapeutic purposes.
Collapse
Affiliation(s)
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
3
|
Su H, Zhi D, Song Y, Yang Y, Wang D, Li X, Cao G. Exploring the formation mechanism of short-tailed phenotypes in animals using mutant mice with the TBXT gene c.G334T developed by CRISPR/Cas9. Gene 2024; 910:148310. [PMID: 38401832 DOI: 10.1016/j.gene.2024.148310] [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: 09/03/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
With the change in diet structure, individuals prefer to consume mutton with less fat. However, sheep tail has a lot of fat. We identified a breed of low-fat short-tailed sheep (i.e., Hulunbuir short-tailed sheep). It is necessary to develop an animal model that can promote research on the potential mechanisms of the short-tail phenotype in sheep, which results from the TBXT gene c.G334T mutation. To create animal models, we selected mice as experimental animals. Mouse embryos lacking the TBXT protein, which crucially regulates mouse embryonic development, cannot develop normally. We utilized CRISPR/Cas9 gene editing technology to generate site-specific mutation (c.G334T) in the TBXT gene of mice, and found that the mouse TBXT mutation (c.G334T) leads to a short-tail phenotype. Furthermore, we investigated the interaction between TBXT and Wnt signaling pathways. The expressions of TBXT, Axin2, Dkk1, Wnt3, Wnt3a, and Wnt5a were discovered to be significantly different between mutant embryos and wild embryos by obtaining mouse embryos at various developmental stages and examining the expression relationship between the TBXT and Wnt signaling pathway-related components in all of these embryos. Therefore, as a transcription factor, TBXT regulates the expression of the aforementioned Wnt signaling pathway components by forming a regulatory network for the normal development of mouse embryos. This study enriches the research on the functional role of the TBXT in the development of mouse embryos and the mechanism by which the short-tailed phenotype in sheep develops.
Collapse
Affiliation(s)
- Hong Su
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China.
| | - Dafu Zhi
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China.
| | - Yongli Song
- College of Life Sciences, Inner Mongolia University, China.
| | - Yanyan Yang
- Inner Mongolia Academy of Agriculture and Animal Husbandry, China.
| | - Daqing Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China; Inner Mongolia Academy of Agriculture and Animal Husbandry, China.
| | - Xiunan Li
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China; Inner Mongolia Academy of Agriculture and Animal Husbandry, China.
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China.
| |
Collapse
|
4
|
Chase DH, Bebenek AM, Nie P, Jaime-Figueroa S, Butrin A, Castro DA, Hines J, Linhares BM, Crews CM. Development of a Small Molecule Downmodulator for the Transcription Factor Brachyury. Angew Chem Int Ed Engl 2024; 63:e202316496. [PMID: 38348945 DOI: 10.1002/anie.202316496] [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: 11/02/2023] [Indexed: 02/29/2024]
Abstract
Brachyury is an oncogenic transcription factor whose overexpression drives chordoma growth. The downmodulation of brachyury in chordoma cells has demonstrated therapeutic potential, however, as a transcription factor it is classically deemed "undruggable". Given that direct pharmacological intervention against brachyury has proven difficult, attempts at intervention have instead targeted upstream kinases. Recently, afatinib, an FDA-approved kinase inhibitor, has been shown to modulate brachyury levels in multiple chordoma cell lines. Herein, we use afatinib as a lead to undertake a structure-based drug design approach, aided by mass-spectrometry and X-ray crystallography, to develop DHC-156, a small molecule that more selectively binds brachyury and downmodulates it as potently as afatinib. We eliminated kinase-inhibition from this novel scaffold while demonstrating that DHC-156 induces the post-translational downmodulation of brachyury that results in an irreversible impairment of chordoma tumor cell growth. In doing so, we demonstrate the feasibility of direct brachyury modulation, which may further be developed into more potent tool compounds and therapies.
Collapse
Affiliation(s)
- Davis H Chase
- Department of Chemistry, Yale University, New Haven, CT-06511
| | - Adrian M Bebenek
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - Pengju Nie
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - Saul Jaime-Figueroa
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - Arseniy Butrin
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - Danielle A Castro
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - John Hines
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - Brian M Linhares
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| | - Craig M Crews
- Department of Chemistry, Yale University, New Haven, CT-06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT-06511
| |
Collapse
|
5
|
Matsuya S, Fujino K, Imai H, Kusakabe KT, Fujii W, Kano K. Establishment of African pygmy mouse induced pluripotent stem cells using defined doxycycline inducible transcription factors. Sci Rep 2024; 14:3204. [PMID: 38331995 PMCID: PMC10853177 DOI: 10.1038/s41598-024-53687-9] [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: 10/14/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Mus minutoides is one of the smallest mammals worldwide; however, the regulatory mechanisms underlying its dwarfism have not been examined. Therefore, we aimed to establish M. minutoides induced pluripotent stem cells (iPSCs) using the PiggyBac transposon system for applications in developmental engineering. The established M. minutoides iPSCs were found to express pluripotency markers and could differentiate into neurons. Based on in vitro differentiation analysis, M. minutoides iPSCs formed embryoid bodies expressing marker genes in all three germ layers. Moreover, according to the in vivo analysis, these cells contributed to the formation of teratoma and development of chimeric mice with Mus musculus. Overall, the M. minutoides iPSCs generated in this study possess properties that are comparable to or closely resemble those of naïve pluripotent stem cells (PSCs). These findings suggest these iPSCs have potential utility in various analytical applications, including methods for blastocyst completion.
Collapse
Affiliation(s)
- Sumito Matsuya
- Laboratory of Developmental Biology, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Laboratory of Veterinary Anatomy, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima, Japan
| | - Kaoru Fujino
- Laboratory of Developmental Biology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1, Yoshida, Yamaguchi Prefecture, 7538511, Japan
| | - Hiroyuki Imai
- Laboratory of Veterinary Anatomy, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Ken Takeshi Kusakabe
- Laboratory of Veterinary Anatomy, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Wataru Fujii
- Laboratory of Biomedical Science, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Kiyoshi Kano
- Laboratory of Developmental Biology, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan.
- Laboratory of Developmental Biology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1, Yoshida, Yamaguchi Prefecture, 7538511, Japan.
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan.
| |
Collapse
|
6
|
Asashima M, Satou-Kobayashi Y. Spemann-Mangold organizer and mesoderm induction. Cells Dev 2024:203903. [PMID: 38295873 DOI: 10.1016/j.cdev.2024.203903] [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: 11/13/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
The discovery of the Spemann-Mangold organizer strongly influenced subsequent research on embryonic induction, with research aiming to elucidate the molecular characteristics of organizer activity being currently underway. Herein, we review the history of research on embryonic induction, and describe how the mechanisms of induction phenomena and developmental processes have been investigated. Classical experiments investigating the differentiation capacity and inductive activity of various embryonic regions were conducted by many researchers, and important theories of region-specific induction and the concept for chain of induction were proposed. The transition from experimental embryology to developmental biology has enabled us to understand the mechanisms of embryonic induction at the molecular level. Consequently, many inducing substances and molecules such as transcriptional factors and peptide growth factors involved in the organizer formation were identified. One of peptide growth factors, activin, acts as a mesoderm- and endoderm-inducing substance. Activin induces several tissues and organs from the undifferentiated cell mass of amphibian embryos in a concentration-dependent manner. We review the extent to which we can control in vitro organogenesis from undifferentiated cells, and discuss the application to stem cell-based regenerative medicine based on insights gained from animal experiments, such as in amphibians.
Collapse
Affiliation(s)
- Makoto Asashima
- Advanced Comprehensive Research Organization, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-0003, Japan.
| | - Yumeko Satou-Kobayashi
- Advanced Comprehensive Research Organization, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-0003, Japan
| |
Collapse
|
7
|
Janssen R, Budd GE. New insights into mesoderm and endoderm development, and the nature of the onychophoran blastopore. Front Zool 2024; 21:2. [PMID: 38267986 PMCID: PMC10809584 DOI: 10.1186/s12983-024-00521-7] [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: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Early during onychophoran development and prior to the formation of the germ band, a posterior tissue thickening forms the posterior pit. Anterior to this thickening forms a groove, the embryonic slit, that marks the anterior-posterior orientation of the developing embryo. This slit is by some authors considered the blastopore, and thus the origin of the endoderm, while others argue that the posterior pit represents the blastopore. This controversy is of evolutionary significance because if the slit represents the blastopore, then this would support the amphistomy hypothesis that suggests that a slit-like blastopore in the bilaterian ancestor evolved into protostomy and deuterostomy. RESULTS In this paper, we summarize our current knowledge about endoderm and mesoderm development in onychophorans and provide additional data on early endoderm- and mesoderm-determining marker genes such as Blimp, Mox, and the T-box genes. CONCLUSION We come to the conclusion that the endoderm of onychophorans forms prior to the development of the embryonic slit, and thus that the slit is not the primary origin of the endoderm. It is thus unlikely that the embryonic slit represents the blastopore. We suggest instead that the posterior pit indeed represents the lips of the blastopore, and that the embryonic slit (and surrounding tissue) represents a morphologically superficial archenteron-like structure. We conclude further that both endoderm and mesoderm development are under control of conserved gene regulatory networks, and that many of the features found in arthropods including the model Drosophila melanogaster are likely derived.
Collapse
Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden.
| | - Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| |
Collapse
|
8
|
Şişli HB, Hayal TB, Şenkal S, Bulut E, Kıratlı B, Asutay AB, Şahin F, Bayrak ÖF, Doğan A. Activation of Wnt Pathway Suppresses Growth of MUG-Chor1 Chordoma Cell Line. Cell Biochem Biophys 2023; 81:823-837. [PMID: 37751039 DOI: 10.1007/s12013-023-01178-5] [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] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Chordoma as a malignant bone tumor, occurs along the axial skeleton and does not have an effective therapy. Brachyury, which is a crucial player for the formation of early embryonic notochord, is abundantly found in both sporadic and familial chordoma. During embryonic development, Brachyury expression was reported to be regulated by the Wnt pathway. The objective of the study is to investigate the role of Wnt signaling in a human chordoma cell line in terms of proliferation, survival, and invasiveness. We tried to elucidate the signaling events that regulate Chordoma cancer. In this regard, Wnt pathway was activated or inhibited using various strategies including small molecules, siRNA-based knockdown and overexpression applications. The results indicated the negative regulatory effect of Wnt signaling activity on proliferation and migration capacity of the chordoma cells. It was revealed that when GSK3β was inhibited, the Wnt pathway was activated and negatively regulated T/Bra expression. Activity of the Wnt pathway caused cell cycle arrest, reduced migration potential of the cells, and led to cell death. Therefore, the present study suggests that the Wnt pathway plays a key role in suppressing the proliferation and invasive characteristics of human chordoma cells and has a great potential as a therapeutic target in further clinical studies.
Collapse
Affiliation(s)
- Hatice Burcu Şişli
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Taha Bartu Hayal
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Selinay Şenkal
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Ezgi Bulut
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Binnur Kıratlı
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Ayla Burçin Asutay
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Fikrettin Şahin
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey
| | - Ömer Faruk Bayrak
- Department of Medical Genetics, School of Medicine, Yeditepe University, İstanbul, 34755, Turkey
| | - Ayşegül Doğan
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, İstanbul, 34755, Turkey.
| |
Collapse
|
9
|
Schüle KM, Weckerle J, Probst S, Wehmeyer AE, Zissel L, Schröder CM, Tekman M, Kim GJ, Schlägl IM, Sagar, Arnold SJ. Eomes restricts Brachyury functions at the onset of mouse gastrulation. Dev Cell 2023; 58:1627-1642.e7. [PMID: 37633271 DOI: 10.1016/j.devcel.2023.07.023] [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: 01/26/2023] [Revised: 06/12/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
Mammalian specification of mesoderm and definitive endoderm (DE) is instructed by the two related Tbx transcription factors (TFs) Eomesodermin (Eomes) and Brachyury sharing partially redundant functions. Gross differences in mutant embryonic phenotypes suggest specific functions of each TF. To date, the molecular details of separated lineage-specific gene regulation by Eomes and Brachyury remain poorly understood. Here, we combine mouse embryonic and stem-cell-based analyses to delineate the non-overlapping, lineage-specific transcriptional activities. On a genome-wide scale, binding of both TFs overlaps at promoters of target genes but shows specificity for distal enhancer regions that is conferred by differences in Tbx DNA-binding motifs. The unique binding to enhancer sites instructs the specification of anterior mesoderm (AM) and DE by Eomes and caudal mesoderm by Brachyury. Remarkably, EOMES antagonizes BRACHYURY gene regulatory functions in coexpressing cells during early gastrulation to ensure the proper sequence of early AM and DE lineage specification followed by posterior mesoderm derivatives.
Collapse
Affiliation(s)
- Katrin M Schüle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
| | - Jelena Weckerle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Simone Probst
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Alexandra E Wehmeyer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Lea Zissel
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Chiara M Schröder
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany
| | - Mehmet Tekman
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Gwang-Jin Kim
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Inga-Marie Schlägl
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Sagar
- Department of Medicine II, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany.
| |
Collapse
|
10
|
Sharifnia T, Wawer MJ, Goodale A, Lee Y, Kazachkova M, Dempster JM, Muller S, Levy J, Freed DM, Sommer J, Kalfon J, Vazquez F, Hahn WC, Root DE, Clemons PA, Schreiber SL. Mapping the landscape of genetic dependencies in chordoma. Nat Commun 2023; 14:1933. [PMID: 37024492 PMCID: PMC10079670 DOI: 10.1038/s41467-023-37593-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency, TBXT (T; brachyury), and identifies a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.
Collapse
Affiliation(s)
- Tanaz Sharifnia
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Mathias J Wawer
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Kojin Therapeutics, Boston, MA, 02210, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yenarae Lee
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Mariya Kazachkova
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Sandrine Muller
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Joan Levy
- Chordoma Foundation, Durham, NC, 27702, USA
- Melanoma Research Alliance, Washington, D.C., 20005, USA
| | | | | | - Jérémie Kalfon
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
11
|
Rafeeq MM, Murad HAS, Najumuddin, Ullah S, Ahmed Z, Alam Q, Bilal M, Habib AH, Sain ZM, Khan MJ, Umair M. Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia. Front Genet 2023; 13:1117500. [PMID: 36733940 PMCID: PMC9888409 DOI: 10.3389/fgene.2022.1117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Background: T-box family members are transcription factors characterized by highly conserved residues corresponding to the DNA-binding domain known as the T-box. TBX2 has been implicated in several developmental processes, such as coordinating cell fate, patterning, and morphogenesis of a wide range of tissues and organs, including lungs, limbs, heart, kidneys, craniofacial structures, and mammary glands. Methods: In the present study, we have clinically and genetically characterized a proband showing a severe form of chondrodysplasia with developmental delay. Whole-exome sequencing (WES), Sanger sequencing, and 3D protein modeling were performed in the present investigation. Results: Whole-exome sequencing revealed a novel nonsense variant (c.529A>T; p.Lys177*; NM_005994.4) in TBX2. 3D-TBX2 protein modeling revealed a substantial reduction of the mutated protein, which might lead to a loss of function (LOF) or nonsense-mediated decay (NMD). Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families.
Collapse
Affiliation(s)
- Misbahuddin M. Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hussam Aly Sayed Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najumuddin
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan
| | - Samee Ullah
- National Center for Bioinformatics (NCB), Islamabad, Pakistan
| | - Zaheer Ahmed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Bahrain
| | - Muhammad Bilal
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ziaullah M. Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,*Correspondence: Muhammad Umair, ,
| |
Collapse
|
12
|
Pattanayak S, Sarode BR, Deiters A, Chen JK. Bicyclic Caged Morpholino Oligonucleotides for Optical Gene Silencing. Chembiochem 2022; 23:e202200374. [PMID: 36068175 PMCID: PMC9637763 DOI: 10.1002/cbic.202200374] [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: 07/02/2022] [Revised: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Caged morpholino oligonucleotides (cMOs) are synthetic tools that allow light-inducible gene silencing in live organisms. Previously reported cMOs have utilized hairpin, duplex, and cyclic structures, as well as caged nucleobases. While these antisense technologies enable efficient optical control of RNA splicing and translation, they can have limited dynamic range. A new caging strategy was developed where the two MO termini are conjugated to an internal position through a self-immolative trifunctional linker, thereby generating a bicyclic cMO that is conformationally resistant to RNA binding. The efficacy of this alternative cMO design has been demonstrated in zebrafish embryos and compared to linear MOs and monocyclic constructs.
Collapse
Affiliation(s)
- Sankha Pattanayak
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Present Address, Creyon Bio, Inc., San Diego, CA 92121, USA
| | - Bhagyesh R Sarode
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
13
|
The negative regulation of gene expression by microRNAs as key driver of inducers and repressors of cardiomyocyte differentiation. Clin Sci (Lond) 2022; 136:1179-1203. [PMID: 35979890 PMCID: PMC9411751 DOI: 10.1042/cs20220391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Abstract
Cardiac muscle damage-induced loss of cardiomyocytes (CMs) and dysfunction of the remaining ones leads to heart failure, which nowadays is the number one killer worldwide. Therapies fostering effective cardiac regeneration are the holy grail of cardiovascular research to stop the heart failure epidemic. The main goal of most myocardial regeneration protocols is the generation of new functional CMs through the differentiation of endogenous or exogenous cardiomyogenic cells. Understanding the cellular and molecular basis of cardiomyocyte commitment, specification, differentiation and maturation is needed to devise innovative approaches to replace the CMs lost after injury in the adult heart. The transcriptional regulation of CM differentiation is a highly conserved process that require sequential activation and/or repression of different genetic programs. Therefore, CM differentiation and specification have been depicted as a step-wise specific chemical and mechanical stimuli inducing complete myogenic commitment and cell-cycle exit. Yet, the demonstration that some microRNAs are sufficient to direct ESC differentiation into CMs and that four specific miRNAs reprogram fibroblasts into CMs show that CM differentiation must also involve negative regulatory instructions. Here, we review the mechanisms of CM differentiation during development and from regenerative stem cells with a focus on the involvement of microRNAs in the process, putting in perspective their negative gene regulation as a main modifier of effective CM regeneration in the adult heart.
Collapse
|
14
|
Hu Y, Lu Y, Xing F, Hsu W. FGFR1/MAPK-directed brachyury activation drives PD-L1-mediated immune evasion to promote lung cancer progression. Cancer Lett 2022; 547:215867. [PMID: 35985510 DOI: 10.1016/j.canlet.2022.215867] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/02/2022]
Abstract
Immune checkpoint inhibitors provide promising benefits for patients with cancer. However, efficacy has been encumbered by high resistance rates. It is critical to understand the basic mechanisms of tumor-mediated resistance to this treatment modality. Previous studies have found that the transcription factor brachyury is highly expressed in lung cancer. Here, we show that brachyury activation induces the upregulation of PD-L1 leading to inactivation of T cell proliferation in vitro and inhibited infiltration of CD8+ and CD3+ T cells into tumor in an immunocompetent mouse model. We further demonstrate that FGFR1/MAPK activation regulates brachyury and PD-L1 expressions and promotes immunosuppression. Blocking FGFR1/MAPK suppresses brachyury and PD-L1 expressions, revives immune activity, and reverses the resistance to anti-PD-1 treatment to produce a durable therapeutic response. We also find that lung cancer patients with high activation of the FGFR1-MAPK-brachyury-PD-L1 signature and low expression of CD8A, CD3D, or PDCD1 have worse survival outcomes. These findings elucidate a novel mechanism of immune escape from immune checkpoint therapy and provide an opportunity to enhance its therapeutic efficacy in the treatment of a subset of FGFR1/MAPK/brachyury/PD-L1-driven lung cancer.
Collapse
Affiliation(s)
- Yunping Hu
- Department of Neurological Surgery, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA.
| | - Yong Lu
- The Methodist Hospital Research Institute, 6670 Bertner Avenue, Houston, Houston, TX, 77030, USA
| | - Fei Xing
- Department of Cancer Biology, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA
| | - Wesley Hsu
- Department of Neurological Surgery, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA.
| |
Collapse
|
15
|
Li S, Lu Y, Xu Y, Zhang C, Liu B, Qin A, Qiao Z, Shen C, Shen J, Liang Y, Wu J, Jiang X. Brachyury promotes proliferation and migration of hepatocellular carcinoma via facilitating the transcription of NCAPG2. Am J Cancer Res 2022; 12:3625-3643. [PMID: 36119840 PMCID: PMC9442014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has a poor prognosis because of its limited drug responses in clinical trials. Therefore, it is crucial to clarify the molecular mechanisms of HCC progression to identify new diagnostic markers and therapeutic targets. Here, we report that brachyury, which regulates the gene encoding the non-SMC condensin II complex subunit G2 (NCAPG2), promotes tumorigenesis in HCC. Knockdown of brachyury led to inhibition of cancer progression in vitro and in vivo. Chromatin immunoprecipitation-sequencing data indicated that the oncogene NCAPG2 is a direct target of brachyury. Furthermore, NCAPG2 knockdown inhibited the proliferation and migration of HCC cells and attenuated brachyury-induced tumorigenesis. Overexpression and decreased DNA methylation of NCAPG2 were associated with a poor prognosis, and NCAPG2 was positively correlated with various immune cell infiltrates, cancer-associated fibroblasts, and immune checkpoint molecule expression levels in the tumor microenvironment. Moreover, the effectiveness of immune checkpoint blockade was decreased in the high NCAPG2 expression group. Together, these findings demonstrated a coregulatory effect of the brachyury/NCAPG2 axis during HCC progression.
Collapse
Affiliation(s)
- Song Li
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Yijie Lu
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Yaopeng Xu
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Cong Zhang
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Biren Liu
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Ancheng Qin
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Zhiming Qiao
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical UniversityNanjing 211166, China
| | - Jun Shen
- Department of Orthopeadic Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow UniversitySuzhou 215006, China
| | - Jianwu Wu
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| | - Xinwei Jiang
- Department of Hepatobiliary Surgery, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhou 215002, China
| |
Collapse
|
16
|
Mellert K, Seeling C, Möller P, Barth TFE. [Chordoma-An update]. PATHOLOGIE (HEIDELBERG, GERMANY) 2022; 43:50-55. [PMID: 36175666 DOI: 10.1007/s00292-022-01118-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Chordomas are rare malignant tumors of the axial skeleton with notochordal differentiation. From a morphological point of view, chordomas display a broad spectrum ranging from the classical, conventional form not otherwise specified (NOS) to forms with hepatoid or renal carcinoma-like differentiation or even poorly or dedifferentiated variants. The detection of brachyury is highly characteristic, though not exclusive. The morphological differential diagnosis from a benign notochordal tumor (BNCT) requires integration of imaging since BNCT is limited to the vertebral bodies and is not osteolytic. Targeted therapy is a current research focus and cell lines as in vitro models are a precondition for the establishment and validation of this approach.
Collapse
Affiliation(s)
- K Mellert
- Institut für Pathologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Deutschland
| | - C Seeling
- Institut für Pathologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Deutschland
- Klinik für Innere Medizin III, Universitätsklinikum Ulm, Ulm, Deutschland
| | - P Möller
- Institut für Pathologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Deutschland
| | - T F E Barth
- Institut für Pathologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Deutschland.
| |
Collapse
|
17
|
Swimming exercise with L-arginine coated nanoparticles supplementation upregulated HAND2 and TBX5 expression in the cardiomyocytes of aging male rats. Biogerontology 2022; 23:473-484. [PMID: 35809117 DOI: 10.1007/s10522-022-09977-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/22/2022] [Indexed: 11/02/2022]
Abstract
We investigated possible cardioprotective mechanisms of L-arginine coated nanoparticles (L-ACN) combined with swimming exercise (SE) in aging male rats considering heart and neural crest derivatives-expressed protein 2 (HAND2) and t-box transcription factor 5 (TBX5). Thirty-five male Wistar rats were randomly assigned into five groups: young, old, old + L-ACN, old + SE, and old + L-ACN + SE (n = 7 in each). L-arginine coated with chitosan nanoparticles was given to L-ACN groups via gavage at 500 mg/kg/day. SE groups performed a swimming exercise program 5 days per week for 6 weeks. The exercise program started with 20 min, gradually increasing to 60 min after four sessions, which was then constant until the completion of the training period. After the protocol completion, the rats were sacrificed, and the heart was fixed and frozen to carry out histological, immunohistochemistry (IHC), and gene expression analyses. The expression of HAND2 protein, HAND2 mRNA, and TBX5 mRNA of the heart tissue was significantly higher in the young group than in all older groups (P < 0.05). The old + L-ACN, old + SE, and old + L-ACN + SE groups showed a significant increase in these factors compared to the old group (P < 0.05). Nano-L-arginine supplement, along with swimming exercises, seems to have cardioprotective potential and improve cardiac function in old age by strengthening cardiomyocyte signaling, especially HAND2 and TBX5. However, more research is required, particularly on human samples.
Collapse
|
18
|
Mashinchian O, De Franceschi F, Nassiri S, Michaud J, Migliavacca E, Aouad P, Metairon S, Pruvost S, Karaz S, Fabre P, Molina T, Stuelsatz P, Hegde N, Le Moal E, Dammone G, Dumont NA, Lutolf MP, Feige JN, Bentzinger CF. An engineered multicellular stem cell niche for the 3D derivation of human myogenic progenitors from iPSCs. EMBO J 2022; 41:e110655. [PMID: 35703167 DOI: 10.15252/embj.2022110655] [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: 01/13/2022] [Revised: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
Fate decisions in the embryo are controlled by a plethora of microenvironmental interactions in a three-dimensional niche. To investigate whether aspects of this microenvironmental complexity can be engineered to direct myogenic human-induced pluripotent stem cell (hiPSC) differentiation, we here screened murine cell types present in the developmental or adult stem cell niche in heterotypic suspension embryoids. We identified embryonic endothelial cells and fibroblasts as highly permissive for myogenic specification of hiPSCs. After two weeks of sequential Wnt and FGF pathway induction, these three-component embryoids are enriched in Pax7-positive embryonic-like myogenic progenitors that can be isolated by flow cytometry. Myogenic differentiation of hiPSCs in heterotypic embryoids relies on a specialized structural microenvironment and depends on MAPK, PI3K/AKT, and Notch signaling. After transplantation in a mouse model of Duchenne muscular dystrophy, embryonic-like myogenic progenitors repopulate the stem cell niche, reactivate after repeated injury, and, compared to adult human myoblasts, display enhanced fusion and lead to increased muscle function. Altogether, we provide a two-week protocol for efficient and scalable suspension-based 3D derivation of Pax7-positive myogenic progenitors from hiPSCs.
Collapse
Affiliation(s)
- Omid Mashinchian
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Sina Nassiri
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joris Michaud
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Patrick Aouad
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylviane Metairon
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Sonia Karaz
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Paul Fabre
- Faculty of Medicine, CHU Sainte-Justine Research Center, School of Rehabilitation, Université de Montréal, Montreal, QC, Canada
| | - Thomas Molina
- Faculty of Medicine, CHU Sainte-Justine Research Center, School of Rehabilitation, Université de Montréal, Montreal, QC, Canada
| | - Pascal Stuelsatz
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Nagabhooshan Hegde
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Emmeran Le Moal
- Département de pharmacologie-physiologie, Faculté de médecine et des sciences de la santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Gabriele Dammone
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Nicolas A Dumont
- Faculty of Medicine, CHU Sainte-Justine Research Center, School of Rehabilitation, Université de Montréal, Montreal, QC, Canada
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Institute of Chemical Sciences and Engineering, School of Basic Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jerome N Feige
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - C Florian Bentzinger
- Nestlé Research, Nestlé Institute of Health Sciences, Lausanne, Switzerland.,Département de pharmacologie-physiologie, Faculté de médecine et des sciences de la santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| |
Collapse
|
19
|
Lopatka A, Moon AM. Complex functional redundancy of Tbx2 and Tbx3 in mouse limb development. Dev Dyn 2022; 251:1613-1627. [PMID: 35506352 DOI: 10.1002/dvdy.484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/07/2022] Open
Abstract
The limb phenotypes of Tbx2 and Tbx3 mutants are distinct: loss of Tbx2 results in isolated duplication of digit 4 in the hindlimb while loss of Tbx3 results in anterior polydactyly and posterior oligodactly in the forelimb. In the face of such disparate phenotypes, we sought to determine whether Tbx2 and Tbx3 have functional redundancy during development of the mouse limb. We found that sequential loss of alleles generates defects that are not simply additive of those observed in single mutants and that multiple structures in both the forelimb and hindlimb display compound sensitivity to decreased gene dosage. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Alika Lopatka
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
| | - Anne M Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, USA
| |
Collapse
|
20
|
Campbell GP, Farkas DR, Chapman DL. Ectopic expression of T in the paraxial mesoderm disrupts somite maturation in the mouse. Dev Biol 2022; 485:37-49. [PMID: 35276131 DOI: 10.1016/j.ydbio.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/03/2022]
Abstract
T is the founding member of the T-box family of transcription factors; family members are critical for cell fate decisions and tissue morphogenesis throughout the animal kingdom. T is expressed in the primitive streak and notochord with mouse mutant studies revealing its critical role in mesoderm formation in the primitive streak and notochord integrity. We previously demonstrated that misexpression of Tbx6 in the paraxial and lateral plate mesoderm results in embryos resembling Tbx15 and Tbx18 nulls. This, together with results from in vitro transcriptional assays, suggested that ectopically expressed Tbx6 can compete with endogenously expressed Tbx15 and Tbx18 at the binding sites of target genes. Since T-box proteins share a similar DNA binding domain, we hypothesized that misexpressing T in the paraxial and lateral plate mesoderm would also interfere with the endogenous Tbx15 and Tbx18, causing embryonic phenotypes resembling those seen upon Tbx6 expression in the somites and limbs. Interestingly, ectopic T expression led to distinct embryonic phenotypes, specifically, reduced-sized somites in embryos expressing the highest levels of T, which ultimately affects axis length and neural tube morphogenesis. We further demonstrate that ectopic T leads to ectopic expression of Tbx6 and Mesogenin 1, known targets of T. These results suggests that ectopic T expression contributes to the phenotype by activating its own targets rather than via a straight competition with endogenous T-box factors.
Collapse
Affiliation(s)
- Gregory P Campbell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Deborah R Farkas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Deborah L Chapman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| |
Collapse
|
21
|
DNA Methylation Levels of the TBX5 Gene Promoter Are Associated with Congenital Septal Defects in Mexican Paediatric Patients. BIOLOGY 2022; 11:biology11010096. [PMID: 35053095 PMCID: PMC8773106 DOI: 10.3390/biology11010096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 11/17/2022]
Abstract
The TBX5 gene regulates morphological changes during heart development, and it has been associated with epigenetic abnormalities observed in congenital heart defects (CHD). The aim of this research was to evaluate the association between DNA methylation levels of the TBX5 gene promoter and congenital septal defects. DNA methylation levels of six CpG sites in the TBX5 gene promoter were evaluated using pyrosequencing analysis in 35 patients with congenital septal defects and 48 controls. Average methylation levels were higher in individuals with congenital septal defects than in the controls (p < 0.004). In five CpG sites, we also found higher methylation levels in patients than in the controls (p < 0.05). High methylation levels were associated with congenital septal defects (OR = 3.91; 95% CI = 1.02–14.8; p = 0.045). The analysis of Receiver Operating Characteristic (ROC) showed that the methylation levels of the TBX5 gene could be used as a risk marker for congenital septal defects (AUC = 0.68, 95% CI = 0.56–0.80; p = 0.004). Finally, an analysis of environmental factors indicated that maternal infections increased the risk (OR = 2.90; 95% CI = 1.01–8.33; p = 0.048) of congenital septal defects. Our data suggest that a high DNA methylation of the TBX5 gene could be associated with congenital septal defects.
Collapse
|
22
|
Mäkitie RE, Toiviainen-Salo S, Kaitila I, Mäkitie O. A Novel Osteochondrodysplasia With Empty Sella Associates With a TBX2 Variant. Front Endocrinol (Lausanne) 2022; 13:845889. [PMID: 35311234 PMCID: PMC8927981 DOI: 10.3389/fendo.2022.845889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Skeletal dysplasias comprise a heterogenous group of developmental disorders of skeletal and cartilaginous tissues. Several different forms have been described and the full spectrum of their clinical manifestations and underlying genetic causes are still incompletely understood. We report a three-generation Finnish family with an unusual, autosomal dominant form of osteochondrodysplasia and an empty sella. Affected individuals (age range 24-44 years) exhibit unusual codfish-shaped vertebrae, severe early-onset and debilitating osteoarthritis and an empty sella without endocrine abnormalities. Clinical characteristics also include mild dysmorphic features, reduced sitting height ratio, and obesity. Whole-exome sequencing excluded known skeletal dysplasias and identified a novel heterozygous missense mutation c.899C>T (p.Thr300Met) in TBX2, confirmed by Sanger sequencing. TBX2 is important for development of the skeleton and the brain and three prior reports have described variations in TBX2 in patients portraying a complex phenotype with vertebral anomalies, craniofacial dysmorphism and endocrine dysfunctions. Our mutation lies near a previously reported disease-causing variant and is predicted pathogenic with deleterious effects on protein function. Our findings expand the current spectrum of skeletal dysplasias, support the association of TBX2 mutations with skeletal dysplasia and suggest a role for TBX2 in development of the spinal and craniofacial structures and the pituitary gland.
Collapse
Affiliation(s)
- Riikka E. Mäkitie
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Otorhinolaryngology–Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- *Correspondence: Riikka E. Mäkitie,
| | - Sanna Toiviainen-Salo
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Medical Imaging Center, Pediatric Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ilkka Kaitila
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
23
|
Zhang M, Niibe K, Kondo T, Limraksasin P, Okawa H, Miao X, Kamano Y, Yamada M, Jiang X, Egusa H. Rapid and efficient generation of cartilage pellets from mouse induced pluripotent stem cells by transcriptional activation of BMP-4 with shaking culture. J Tissue Eng 2022; 13:20417314221114616. [PMID: 35923173 PMCID: PMC9340412 DOI: 10.1177/20417314221114616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) offer an unlimited source for cartilage
regeneration as they can generate a wide spectrum of cell types. Here, we
established a tetracycline (tet) controlled bone morphogenetic
protein-4 (BMP-4) expressing iPSC
(iPSC-Tet/BMP-4) line in which transcriptional activation
of BMP-4 was associated with enhanced chondrogenesis. Moreover,
we developed an efficient and simple approach for directly guiding
iPSC-Tet/BMP-4 differentiation into chondrocytes in
scaffold-free cartilaginous pellets using a combination of transcriptional
activation of BMP-4 and a 3D shaking suspension culture system.
In chondrogenic induction medium, shaking culture alone significantly
upregulated the chondrogenic markers Sox9, Col2a1, and
Aggrecan in iPSCs-Tet/BMP-4 by day 21. Of
note, transcriptional activation of BMP-4 by addition of tet
(doxycycline) greatly enhanced the expression of these genes. The cartilaginous
pellets derived from iPSCs-Tet/BMP-4 showed an oval morphology
and white smooth appearance by day 21. After day 21, the cells presented a
typical round morphology and the extracellular matrix was stained intensively
with Safranin O, alcian blue, and type II collagen. In addition, the homogenous
cartilaginous pellets derived from iPSCs-Tet/BMP-4 with 28 days
of induction repaired joint osteochondral defects in immunosuppressed rats and
integrated well with the adjacent host cartilage. The regenerated cartilage
expressed the neomycin resistance gene, indicating that the newly formed
cartilage was generated by the transplanted iPSCs-Tet/BMP-4.
Thus, our culture system could be a useful tool for further investigation of the
mechanism of BMP-4 in regulating iPSC differentiation toward the chondrogenic
lineage, and should facilitate research in cartilage development, repair, and
osteoarthritis.
Collapse
Affiliation(s)
- Maolin Zhang
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
- Department of Prosthodontics, Ninth People’s Hospital affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kunimichi Niibe
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Takeru Kondo
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Phoonsuk Limraksasin
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Hiroko Okawa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Xinchao Miao
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Yuya Kamano
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Masahiro Yamada
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Xinquan Jiang
- Department of Prosthodontics, Ninth People’s Hospital affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| |
Collapse
|
24
|
Samarasinghe KTG, An E, Genuth MA, Chu L, Holley SA, Crews CM. OligoTRAFTACs: A generalizable method for transcription factor degradation. RSC Chem Biol 2022; 3:1144-1153. [PMID: 36128504 PMCID: PMC9428672 DOI: 10.1039/d2cb00138a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/24/2022] [Indexed: 11/21/2022] Open
Abstract
Targeted transcription factor degradation using oligonucleotide-based transcription factor targeting chimeras (TRAFTACs).
Collapse
Affiliation(s)
- Kusal T. G. Samarasinghe
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Elvira An
- Department of Pharmacology, Yale University, New Haven, CT, 06511, USA
| | - Miriam A. Genuth
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Ling Chu
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Scott A. Holley
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Craig M. Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
- Department of Pharmacology, Yale University, New Haven, CT, 06511, USA
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| |
Collapse
|
25
|
Niu G, Hao J, Sheng S, Wen F. Role of T-box genes in cancer, epithelial-mesenchymal transition, and cancer stem cells. J Cell Biochem 2021; 123:215-230. [PMID: 34897787 DOI: 10.1002/jcb.30188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Sharing a common DNA binding motif called T-box, transcription factor T-box gene family controls embryonic development and is also involved in cancer progression and metastasis. Cancer metastasis shows therapy resistance and involves complex processes. Among them, epithelial-mesenchymal transition (EMT) triggers cancer cell invasiveness and the acquisition of stemness of cancer cells, called cancer stem cells (CSCs). CSCs are a small fraction of tumor bulk and are capable of self-renewal and tumorsphere formation. Recent progress has highlighted the critical roles of T-box genes in cancer progression, EMT, and CSC function, and such regulatory functions of T-box genes have emerged as potential therapeutic candidates for cancer. Herein we summarize the current understanding of the regulatory mechanisms of T-box genes in cancer, EMT, and CSCs, and discuss the implications of targeting T-box genes as anticancer therapeutics.
Collapse
Affiliation(s)
- Gengle Niu
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Jin Hao
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Surui Sheng
- Department of Oral and Maxillofacial-Head Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangyuan Wen
- Department of Outpatient, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| |
Collapse
|
26
|
Jalessi M, Gholami MS, Razmara E, Hassanzadeh S, Sadeghipour A, Jahanbakhshi A, Tabibkhooei A, Bahrami E, Falah M. Association between TBXT rs2305089 polymorphism and chordoma in Iranian patients identified by a developed T-ARMS-PCR assay. J Clin Lab Anal 2021; 36:e24150. [PMID: 34837714 PMCID: PMC8761424 DOI: 10.1002/jcla.24150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 11/18/2021] [Indexed: 11/20/2022] Open
Abstract
Background Chordoma is a locally aggressive bone tumor with a high capability of recurrence. Because chordoma often occurs at critical locations next to neurovascular structures, there is an urgent need to introduce validated biomarkers. T‐box transcription factor T (TBXT; OMIM: 601397) plays an important role in the pathogenesis and survival of chordoma cells. Methods Herein, we aimed to show whether rs2305089 polymorphism is correlated with chordoma in the Iranian population. In order to detect rs2305089, tetra‐primer amplification refractory mutation system‐polymerase chain reaction (T‐ARMS‐PCR) was used. In total, 19 chordoma patients and 108 normal healthy individuals were recruited and screened using T‐ARMS‐PCR. The results were subsequently validated by Sanger sequencing. Results The genotype distributions and allele frequencies were significantly different among the patient and healthy groups (p‐value <0.05). The A allele of rs2305089 showed a significant positive association with chordoma risk (p‐value <0.05). DNA sequencing verified the T‐ARMS‐PCR results as well. This study demonstrated the association between TBXT rs2305089 and chordoma in an Iranian population using a simple, accurate, and cost‐effective T‐ARMS‐PCR assay. Conclusions Our results were in line with those of previous studies showing that TBXT rs2305089 is associated with chordoma development. We also developed an efficient T‐ARMS‐PCR assay to determine the genotype of rs2305089.
Collapse
Affiliation(s)
- Maryam Jalessi
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeed Gholami
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,Department of Hematology and Blood Transfusion, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Razmara
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Sajad Hassanzadeh
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Sadeghipour
- Pathology Department, Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Amin Jahanbakhshi
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabibkhooei
- Department of Neurosurgery, Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Eshagh Bahrami
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,Department of Neurosurgery, Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Falah
- Skull Base Research Center, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, Hazrat Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
27
|
Darrah K, Wesalo J, Lukasak B, Tsang M, Chen JK, Deiters A. Small Molecule Control of Morpholino Antisense Oligonucleotide Function through Staudinger Reduction. J Am Chem Soc 2021; 143:18665-18671. [PMID: 34705461 DOI: 10.1021/jacs.1c08723] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conditionally activated, caged morpholino antisense agents (cMOs) are tools that enable the temporal and spatial investigation of gene expression, regulation, and function during embryonic development. Cyclic MOs are conformationally gated oligonucleotide analogs that do not block gene expression until they are linearized through the application of an external trigger, such as light or enzyme activity. Here, we describe the first examples of small molecule-responsive cMOs, which undergo rapid and efficient decaging via a Staudinger reduction. This is enabled by a highly flexible linker design that offers opportunities for the installation of chemically activated, self-immolative motifs. We synthesized cyclic cMOs against two distinct, developmentally relevant genes and demonstrated phosphine-triggered knockdown of gene expression in zebrafish embryos. This represents the first report of a small molecule-triggered antisense agent for gene knockdown, adding another bioorthogonal entry to the growing arsenal of gene knockdown tools.
Collapse
Affiliation(s)
- Kristie Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Bradley Lukasak
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
28
|
miR-219-5p targets TBXT and inhibits breast cancer cell EMT and cell migration and invasion. Biosci Rep 2021; 41:229438. [PMID: 34339487 PMCID: PMC8360836 DOI: 10.1042/bsr20210318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
miR-219-5p has been reported to act as either a tumor suppressor or a tumor promoter in different cancers by targeting different genes. In the present study, we demonstrated that miR-219-5p negatively regulated the expression of TBXT, a known epithelial–mesenchymal transition (EMT) inducer, by directly binding to TBXT 3′-untranslated region. As a result of its inhibition on TBXT expression, miR-219-5p suppressed EMT and cell migration and invasion in breast cancer cells. The re-introduction of TBXT in miR-219-5p overexpressing cells decreased the inhibitory effects of miR-219 on EMT and cell migration and invasion. Moreover, miR-219-5p decreased breast cancer stem cell (CSC) marker genes expression and reduced the mammosphere forming capability of cells. Overall, our study highlighted that TBXT is a novel target of miR-219-5p. By suppressing TBXT, miR-219-5p plays an important role in EMT and cell migration and invasion of breast cancer cells.
Collapse
|
29
|
The evolutionary acquisition and mode of functions of promoter-associated non-coding RNAs (pancRNAs) for mammalian development. Essays Biochem 2021; 65:697-708. [PMID: 34328174 DOI: 10.1042/ebc20200143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence has shown that many long non-coding RNAs (lncRNAs) are involved in gene regulation in a variety of ways such as transcriptional, post-transcriptional and epigenetic regulation. Promoter-associated non-coding RNAs (pancRNAs), which are categorized into the most abundant single-copy lncRNA biotype, play vital regulatory roles in finely tuning cellular specification at the epigenomic level. In short, pancRNAs can directly or indirectly regulate downstream genes to participate in the development of organisms in a cell-specific manner. In this review, we will introduce the evolutionarily acquired characteristics of pancRNAs as determined by comparative epigenomics and elaborate on the research progress on pancRNA-involving processes in mammalian embryonic development, including neural differentiation.
Collapse
|
30
|
Induced Cardiomyocyte Proliferation: A Promising Approach to Cure Heart Failure. Int J Mol Sci 2021; 22:ijms22147720. [PMID: 34299340 PMCID: PMC8303201 DOI: 10.3390/ijms22147720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/31/2022] Open
Abstract
Unlike some lower vertebrates which can completely regenerate their heart, the human heart is a terminally differentiated organ. Cardiomyocytes lost during cardiac injury and heart failure cannot be replaced due to their limited proliferative capacity. Therefore, cardiac injury generally leads to progressive failure. Here, we summarize the latest progress in research on methods to induce cardiomyocyte cell cycle entry and heart repair through the alteration of cardiomyocyte plasticity, which is emerging as an effective strategy to compensate for the loss of functional cardiomyocytes and improve the impaired heart functions.
Collapse
|
31
|
Aramaki S, Kagiwada S, Wu G, Obridge D, Adachi K, Kutejova E, Lickert H, Hübner K, Schöler HR. Residual pluripotency is required for inductive germ cell segregation. EMBO Rep 2021; 22:e52553. [PMID: 34156139 PMCID: PMC8344911 DOI: 10.15252/embr.202152553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022] Open
Abstract
Fine‐tuned dissolution of pluripotency is critical for proper cell differentiation. Here we show that the mesodermal transcription factor, T, globally affects the properties of pluripotency through binding to Oct4 and to the loci of other pluripotency regulators. Strikingly, lower T levels coordinately affect naïve pluripotency, thereby directly activating the germ cell differentiation program, in contrast to the induction of germ cell fate of primed models. Contrary to the effect of lower T levels, higher T levels more severely affect the pluripotency state, concomitantly enhancing the somatic differentiation program and repressing the germ cell differentiation program. Consistent with such in vitro findings, nascent germ cells in vivo are detected in the region of lower T levels at the posterior primitive streak. Furthermore, T and core pluripotency regulators co‐localize at the loci of multiple germ cell determinants responsible for germ cell development. In conclusion, our findings indicate that residual pluripotency establishes the earliest and fundamental regulatory mechanism for inductive germline segregation from somatic lineages.
Collapse
Affiliation(s)
- Shinya Aramaki
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Saya Kagiwada
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - David Obridge
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Eva Kutejova
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Heiko Lickert
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Karin Hübner
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Medical Faculty, University of Münster, Münster, Germany
| |
Collapse
|
32
|
Traylor JI, Pernik MN, Plitt AR, Lim M, Garzon-Muvdi T. Immunotherapy for Chordoma and Chondrosarcoma: Current Evidence. Cancers (Basel) 2021; 13:2408. [PMID: 34067530 PMCID: PMC8156915 DOI: 10.3390/cancers13102408] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
Chordomas and chondrosarcomas are rare but devastating neoplasms that are characterized by chemoradiation resistance. For both tumors, surgical resection is the cornerstone of management. Immunotherapy agents are increasingly improving outcomes in multiple cancer subtypes and are being explored in chordoma and chondrosarcoma alike. In chordoma, brachyury has been identified as a prominent biomarker and potential molecular immunotherapy target as well as PD-1 inhibition. While studies on immunotherapy in chondrosarcoma are sparse, there is emerging evidence and ongoing clinical trials for PD-1 as well as IDH inhibitors. This review highlights potential biomarkers and targets for immunotherapy in chordoma and chondrosarcoma, as well as current clinical evidence and ongoing trials.
Collapse
Affiliation(s)
- Jeffrey I. Traylor
- Department of Neurological Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (J.I.T.); (M.N.P.); (A.R.P.)
| | - Mark N. Pernik
- Department of Neurological Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (J.I.T.); (M.N.P.); (A.R.P.)
| | - Aaron R. Plitt
- Department of Neurological Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (J.I.T.); (M.N.P.); (A.R.P.)
| | - Michael Lim
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA;
| | - Tomas Garzon-Muvdi
- Department of Neurological Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; (J.I.T.); (M.N.P.); (A.R.P.)
| |
Collapse
|
33
|
Hayashi K, Galli C, Diecke S, Hildebrandt TB. Artificially produced gametes in mice, humans and other species. Reprod Fertil Dev 2021; 33:91-101. [PMID: 38769675 DOI: 10.1071/rd20265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
The production of gametes from pluripotent stem cells in culture, also known as invitro gametogenesis, will make an important contribution to reproductive biology and regenerative medicine, both as a unique tool for understanding germ cell development and as an alternative source of gametes for reproduction. Invitro gametogenesis was developed using mouse pluripotent stem cells but is increasingly being applied in other mammalian species, including humans. In principle, the entire process of germ cell development is nearly reconstitutable in culture using mouse pluripotent stem cells, although the fidelity of differentiation processes and the quality of resultant gametes remain to be refined. The methodology in the mouse system is only partially applicable to other species, and thus it must be optimised for each species. In this review, we update the current status of invitro gametogenesis in mice, humans and other animals, and discuss challenges for further development of this technology.
Collapse
Affiliation(s)
- Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-0054, Japan; and Corresponding author
| | - Cesare Galli
- Avantea, Laboratory of Reproductive Technologies, 26100 Cremona, Italy; and Fondazione Avantea, 26100 Cremona, Italy
| | - Sebastian Diecke
- Max-Delbrueck-Center for Molecular Medicine, 13092 Berlin, Germany
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, D-10315 Berlin, Germany; and Freie Universität Berlin, D-14195 Berlin, Germany
| |
Collapse
|
34
|
Morine Y, Utsunomiya T, Saito Y, Yamada S, Imura S, Ikemoto T, Kitagawa A, Kobayashi Y, Takao S, Kosai K, Mimori K, Tanaka Y, Shimada M. Reduction of T-Box 15 gene expression in tumor tissue is a prognostic biomarker for patients with hepatocellular carcinoma. Oncotarget 2020; 11:4803-4812. [PMID: 33447348 PMCID: PMC7779253 DOI: 10.18632/oncotarget.27852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/08/2020] [Indexed: 01/19/2023] Open
Abstract
Genome-wide analysis is widely applied to detect molecular alterations during oncogenesis and tumor progression. We analyzed DNA methylation profiles of hepatocellular carcinoma (HCC), and investigated the clinical role of most heypermethylated of tumor, encodes T-box 15 (TBX15), which was originally involved in mesodermal differentiation. We conducted a genome-wide analysis of DNA methylation of tumor and non-tumor tissue of 15 patients with HCC, and revealed TBX15 was the most hypermethylated gene of tumor (Beta-value in tumor tissue = 0.52 compared with non-tumor tissue). Another validation set, which comprised 58 HCC with radical resection, was analyzed to investigate the relationships between tumor phenotype and TBX15 mRNA expression. TBX15 mRNA levels in tumor tissues were significantly lower compared with those of nontumor tissues (p < 0.0001). When we assigned a cutoff value = 0.5-fold, the overall survival 5-year survival rates of the low-expression group (n = 17) were significantly shorter compared with those of the high-expression group (n = 41) (43.3% vs. 86.2%, p = 0.001). Multivariate analysis identified low TBX15 expression as an independent prognostic factor for overall and disease-free survival. Therefore, genome-wide DNA methylation profiling indicates that hypermethylation and reduced expression of TBX15 in tumor tissue represents a potential biomarker for predicting poor survival of patients with HCC.
Collapse
Affiliation(s)
- Yuji Morine
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tohru Utsunomiya
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yu Saito
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shinichiro Yamada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Satoru Imura
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tetsuya Ikemoto
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Akihiro Kitagawa
- Department of Surgery, Kyushu University Beppu Hospital, Beppu 874-0838, Japan
| | - Yuta Kobayashi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu 874-0838, Japan
| | - Seiichiro Takao
- Department of Surgery, Kyushu University Beppu Hospital, Beppu 874-0838, Japan
| | - Keisuke Kosai
- Department of Surgery, Kyushu University Beppu Hospital, Beppu 874-0838, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu 874-0838, Japan
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mitsuo Shimada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| |
Collapse
|
35
|
Gill CM, Fowkes M, Shrivastava RK. Emerging Therapeutic Targets in Chordomas: A Review of the Literature in the Genomic Era. Neurosurgery 2020; 86:E118-E123. [PMID: 31504814 DOI: 10.1093/neuros/nyz342] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
Chordomas are rare primary malignant tumors of the bones that occur along the skull base, spine, and sacrum. Long-term survival and neurological outcome continue to be challenging with continued low percentages of long-term survival. Recent studies have used genome, exome, transcriptome, and proteome sequencing to assess the mutational profile of chordomas. Most notably, Brachyury, or T-protein, has been shown to be an early mutational event in chordoma evolution. Clinically actionable mutations, including in the PI3K pathway, were identified. Preliminary evidence suggests that there may be mutational differences associated with primary tumor location. In this study, we review the therapeutic landscape of chordomas and discuss emerging targets in the genomic era.
Collapse
Affiliation(s)
- Corey M Gill
- Department of Neurosurgery, Mount Sinai Medical Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mary Fowkes
- Department of Pathology, Mount Sinai Medical Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Raj K Shrivastava
- Department of Neurosurgery, Mount Sinai Medical Center, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
36
|
Swedlund B, Lescroart F. Cardiopharyngeal Progenitor Specification: Multiple Roads to the Heart and Head Muscles. Cold Spring Harb Perspect Biol 2020; 12:a036731. [PMID: 31818856 PMCID: PMC7397823 DOI: 10.1101/cshperspect.a036731] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During embryonic development, the heart arises from various sources of undifferentiated mesodermal progenitors, with an additional contribution from ectodermal neural crest cells. Mesodermal cardiac progenitors are plastic and multipotent, but are nevertheless specified to a precise heart region and cell type very early during development. Recent findings have defined both this lineage plasticity and early commitment of cardiac progenitors, using a combination of single-cell and population analyses. In this review, we discuss several aspects of cardiac progenitor specification. We discuss their markers, fate potential in vitro and in vivo, early segregation and commitment, and also intrinsic and extrinsic cues regulating lineage restriction from multipotency to a specific cell type of the heart. Finally, we also discuss the subdivisions of the cardiopharyngeal field, and the shared origins of the heart with other mesodermal derivatives, including head and neck muscles.
Collapse
Affiliation(s)
- Benjamin Swedlund
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | | |
Collapse
|
37
|
Chen M, Wu Y, Zhang H, Li S, Zhou J, Shen J. The Roles of Embryonic Transcription Factor BRACHYURY in Tumorigenesis and Progression. Front Oncol 2020; 10:961. [PMID: 32695672 PMCID: PMC7338565 DOI: 10.3389/fonc.2020.00961] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/15/2020] [Indexed: 12/16/2022] Open
Abstract
Transcription factor brachyury, with a DNA-binding T-domain, regulates posterior mesoderm formation and notochord development through binding with highly conserved palindromic consensus sequence in a variety of organisms. The absence of brachyury expression in majority of adult normal tissues and exclusive tumor-specific expression provides the potential to be developed into a novel and promising diagnostic and therapeutic target in cancer. As a sensitive and specific marker in the diagnosis of chordoma, brachyury protein has been verified to involve in the process of carcinogenesis and progression of chordoma and several epithelial carcinomas in various studies, but the mechanism by which brachyury promotes tumor cells migrate, invade and metastasis still remains less clear. To this end, we attempt to summarize the literature on the upstream regulatory pathway of brachyury transcription and downstream controlling network by brachyury activation, all of which involve in both the embryonic development and tumor progression. We present the respective correlation of brachyury expression with tumor progression, distant metastasis, survival rate and prognosis in several types of tumor samples (including chordoma, lung cancer, breast carcinoma, and prostate cancer), and various brachyury gain-of-function and loss-of-function experiments are summarized to explore its specific role in respective tumor cell line in vitro. In addition, we also discuss another two programs relating to brachyury function: epithelial-to-mesenchymal transition (EMT) and cell cycle control, both of which implicate in the regulation of brachyury on biological behavior of tumor cells. This review will provide an overview of the function of master transcriptional factor brachyury, compare the similarities and differences of its role between embryonic development and carcinogenesis, and list the evidence on which brachyury-target therapies have the potential to help control advanced cancer populations.
Collapse
Affiliation(s)
- Ming Chen
- Department of Orthopeadic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Department of Orthopeadic Surgery, Wuxi No. 2 People's Hospital, Nanjing Medical University, Wuxi, China
| | - Yinghui Wu
- Department of Orthopeadic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Suzhou Municipal Hospital, Suzhou, China
| | - Hong Zhang
- Department of Orthopeadic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Suzhou Municipal Hospital, Suzhou, China
| | - Suoyuan Li
- Department of Orthopeadic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Suzhou Municipal Hospital, Suzhou, China
| | - Jundong Zhou
- Suzhou Cancer Center Core Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jun Shen
- Department of Orthopeadic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Suzhou Municipal Hospital, Suzhou, China
| |
Collapse
|
38
|
Reich S, Kayastha P, Teegala S, Weinstein DC. Tbx2 mediates dorsal patterning and germ layer suppression through inhibition of BMP/GDF and Activin/Nodal signaling. BMC Mol Cell Biol 2020; 21:39. [PMID: 32466750 PMCID: PMC7257154 DOI: 10.1186/s12860-020-00282-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/11/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Members of the T-box family of DNA-binding proteins play a prominent role in the differentiation of the three primary germ layers. VegT, Brachyury, and Eomesodermin function as transcriptional activators and, in addition to directly activating the transcription of endoderm- and mesoderm-specific genes, serve as regulators of growth factor signaling during induction of these germ layers. In contrast, the T-box gene, tbx2, is expressed in the embryonic ectoderm, where Tbx2 functions as a transcriptional repressor and inhibits mesendodermal differentiation by the TGFβ ligand Activin. Tbx2 misexpression also promotes dorsal ectodermal fate via inhibition of the BMP branch of the TGFβ signaling network. RESULTS Here, we report a physical association between Tbx2 and both Smad1 and Smad2, mediators of BMP and Activin/Nodal signaling, respectively. We perform structure/function analysis of Tbx2 to elucidate the roles of both Tbx2-Smad interaction and Tbx2 DNA-binding in germ layer suppression. CONCLUSION Our studies demonstrate that Tbx2 associates with intracellular mediators of the Activin/Nodal and BMP/GDF pathways. We identify a novel repressor domain within Tbx2, and have determined that Tbx2 DNA-binding activity is required for repression of TGFβ signaling. Finally, our data also point to overlapping yet distinct mechanisms for Tbx2-mediated repression of Activin/Nodal and BMP/GDF signaling.
Collapse
Affiliation(s)
- Shoshana Reich
- The Graduate Center, The City University of New York, New York, NY, 10016, USA
| | - Peter Kayastha
- Department of Biology, Queens College, The City University of New York, Queens, NY, 11367, USA
| | - Sushma Teegala
- Department of Biology, Queens College, The City University of New York, Queens, NY, 11367, USA
| | - Daniel C Weinstein
- The Graduate Center, The City University of New York, New York, NY, 10016, USA. .,Department of Biology, Queens College, The City University of New York, Queens, NY, 11367, USA.
| |
Collapse
|
39
|
Osborn DPS, Li K, Cutty SJ, Nelson AC, Wardle FC, Hinits Y, Hughes SM. Fgf-driven Tbx protein activities directly induce myf5 and myod to initiate zebrafish myogenesis. Development 2020; 147:147/8/dev184689. [PMID: 32345657 PMCID: PMC7197714 DOI: 10.1242/dev.184689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/14/2020] [Indexed: 01/02/2023]
Abstract
Skeletal muscle derives from dorsal mesoderm formed during vertebrate gastrulation. Fibroblast growth factor (Fgf) signalling cooperates with Tbx transcription factors to promote dorsal mesoderm formation, but their role in myogenesis has been unclear. Using zebrafish, we show that dorsally derived Fgf signals act through Tbx16 and Tbxta to induce slow and fast trunk muscle precursors at distinct dorsoventral positions. Tbx16 binds to and directly activates the myf5 and myod genes, which are required for commitment to myogenesis. Tbx16 activity depends on Fgf signalling from the organiser. In contrast, Tbxta is not required for myf5 expression, but binds a specific site upstream of myod that is not bound by Tbx16 and drives (dependent on Fgf signals) myod expression in adaxial slow precursors, thereby initiating trunk myogenesis. After gastrulation, when similar muscle cell populations in the post-anal tail are generated from tailbud, declining Fgf signalling is less effective at initiating adaxial myogenesis, which is instead initiated by Hedgehog signalling from the notochord. Our findings suggest a hypothesis for ancestral vertebrate trunk myogenic patterning and how it was co-opted during tail evolution to generate similar muscle by new mechanisms. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: Tbx16 and Tbxta activate myf5 and myod directly during the earliest myogenesis in zebrafish, and Fgf signalling acts through Tbx16 to drive myogenesis in trunk but not tail.
Collapse
Affiliation(s)
- Daniel P S Osborn
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Kuoyu Li
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Stephen J Cutty
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Andrew C Nelson
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Fiona C Wardle
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Yaniv Hinits
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Simon M Hughes
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| |
Collapse
|
40
|
Inhibition of cardiomyocyte differentiation of human induced pluripotent stem cells by Ribavirin: Implication for its cardiac developmental toxicity. Toxicology 2020; 435:152422. [PMID: 32112805 DOI: 10.1016/j.tox.2020.152422] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/16/2020] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
Ribavirin has been proven to be an antiviral treatment, whereas there are still risks of hemolysis and congenital malformation. Abnormal cardiac development contributes to the occurrence and development of many heart diseases. However, there is so far no evidence that ribavirin induces human cardiac developmental toxicity. Herein, we employed the cardiac differentiation model of human induced pluripotent stem cells (hiPSCs) to determine the impact of ribavirin on heart development. Our data showed that ribavirin at clinically high concentrations (5 and 10 μM) significantly inhibited the proliferation and differentiation of hiPSCs from mesoderm to cardiac progenitor cells and cardiac progenitor cells to cardiomyocytes, but not from pluripotent status to mesoderm. Meanwhile, DCFH-DA staining revealed that ribavirin could increase ROS content in the mid-phase of differentiation. In addition, ribavirin treatment (1, 5 and 10 μM) remarkably caused DNA damage which was shown by the increase of γH2AX-positive cells and upregulation of the p53 during the differentiation of hiPSCs from mesoderm to cardiac progenitor cells. Moreover, exposuring to ribavirin (5 and 10 μM) markedly upregulated the expression of lncRNAs Gas5 in both mid-phase and late phase of differentiation and HBL1 in the mid-phase. In conclusion, our results suggest that ribavirin is detrimental in cardiac differentiation of hiPSCs, which may be associated with DNA damage, upregulated p53 and increased Gas5. It may provide the evidence for the rational clinical application of ribavirin.
Collapse
|
41
|
Ozair MZ, Shah PP, Mathios D, Lim M, Moss NS. New Prospects for Molecular Targets for Chordomas. Neurosurg Clin N Am 2020; 31:289-300. [PMID: 32147018 DOI: 10.1016/j.nec.2019.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chordomas are malignant, highly recurrent tumors of the midline skeleton that arise from the remnants of the notochord. The development of systemic therapy is critically important to ultimately managing this tumor. Several ongoing trials are attempting to use molecular targeted therapies for mutated pathways in recurrent and advanced chordomas and have shown promise. In addition, immunotherapies, including brachyury-directed vaccination and checkpoint inhibition, have also been attempted with encouraging results. This article discusses the major pathways that have been implicated in the pathogenesis of chordoma with an emphasis on molecular vulnerabilities that future therapies are attempting to exploit.
Collapse
Affiliation(s)
- Mohammad Zeeshan Ozair
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Pavan Pinkesh Shah
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21287, USA
| | - Dimitrios Mathios
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21287, USA
| | - Michael Lim
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21287, USA
| | - Nelson S Moss
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
42
|
Yu H, Zhao F, Li J, Zhu K, Lin H, Pan Z, Zhu M, Yao M, Yan M. TBX2 Identified as a Potential Predictor of Bone Metastasis in Lung Adenocarcinoma via Integrated Bioinformatics Analyses and Verification of Functional Assay. J Cancer 2020; 11:388-402. [PMID: 31897234 PMCID: PMC6930436 DOI: 10.7150/jca.31636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
Objective: Bone metastasis from patients with advanced lung adenocarcinoma (LAC) is a very serious complication. To better understand the molecular mechanism, our current study sheds light on identification of hub genes mediating bone metastatic spread by combining bioinformatic analysis with functional verification. Methods: First, we downloaded a lung adenocarcinoma dataset (GSE76194) from Gene Expression Omnibus, analyzed differentially expressed genes (DEGs) through Limma package in R software and constructed a protein-protein interaction network. Based on that preliminary data, we further performed modular and topological analysis using Cystoscope to obtain biological connected genes. Through literature searching and performing mRNA expression analysis on the other independent public dataset (GSE10799), we finally focused on TBX2. Functional effects of TBX2 were performed in tumorigenicity assays including migration and invasion assays, cell proliferation assay, and cell cycle assay. In addition, mechanically, we found enriched pathways related to bone metastasis using Gene Set Enrichment Analysis (GSEA) and validated our results by western blot. Result: A total of 1132 significant genes were sorted initially. We selected common significant genes (log FC>2; p<0.01) from both the biological network data and microarray data. In total, 44 such genes were identified. we found TBX2, along with 10 other genes, to be reported with relevance to bone metastasis in other cancer types. Moreover, TBX2 showed significantly higher expression levels in patients that were found positive for metastasis to bone marrow compared to patients that did not exhibit this type of metastasis in the other separated cohort (GSE10799). Thus, we finally focused on TBX2. We found that TBX2 had detectable expression in LAC cell lines and silencing endogenous TBX2 expression in A549 and H1299 cell lines markedly suppressed migration and invasion, cell proliferation and arrested cell-cycle. Pathway enrichment analyses suggested that TBX2 drove LAC oncogenesis and metastasis through various pathways with epithelial mesenchymal transition (EMT) figuring prominently in the bone metastatic group, which was evidenced by western blot. Conclusion: Collectively, TBX2 plays as a potential predictor of bone metastasis from LAC, yielding a better promise view towards "driver" gene responsible for bone metastasis.
Collapse
Affiliation(s)
- Huajian Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangyu Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kechao Zhu
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hechun Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Pan
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Miaoxin Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingxia Yan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
43
|
Witman N, Zhou C, Grote Beverborg N, Sahara M, Chien KR. Cardiac progenitors and paracrine mediators in cardiogenesis and heart regeneration. Semin Cell Dev Biol 2019; 100:29-51. [PMID: 31862220 DOI: 10.1016/j.semcdb.2019.10.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/13/2019] [Accepted: 10/21/2019] [Indexed: 12/17/2022]
Abstract
The mammalian hearts have the least regenerative capabilities among tissues and organs. As such, heart regeneration has been and continues to be the ultimate goal in the treatment against acquired and congenital heart diseases. Uncovering such a long-awaited therapy is still extremely challenging in the current settings. On the other hand, this desperate need for effective heart regeneration has developed various forms of modern biotechnologies in recent years. These involve the transplantation of pluripotent stem cell-derived cardiac progenitors or cardiomyocytes generated in vitro and novel biochemical molecules along with tissue engineering platforms. Such newly generated technologies and approaches have been shown to effectively proliferate cardiomyocytes and promote heart repair in the diseased settings, albeit mainly preclinically. These novel tools and medicines give somehow credence to breaking down the barriers associated with re-building heart muscle. However, in order to maximize efficacy and achieve better clinical outcomes through these cell-based and/or cell-free therapies, it is crucial to understand more deeply the developmental cellular hierarchies/paths and molecular mechanisms in normal or pathological cardiogenesis. Indeed, the morphogenetic process of mammalian cardiac development is highly complex and spatiotemporally regulated by various types of cardiac progenitors and their paracrine mediators. Here we discuss the most recent knowledge and findings in cardiac progenitor cell biology and the major cardiogenic paracrine mediators in the settings of cardiogenesis, congenital heart disease, and heart regeneration.
Collapse
Affiliation(s)
- Nevin Witman
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Chikai Zhou
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Niels Grote Beverborg
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Surgery, Yale University School of Medicine, CT, USA.
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
| |
Collapse
|
44
|
Chi H, Sørmo KG, Diao J, Dalmo RA. T-box transcription factor eomesodermin/Tbr2 in Atlantic cod (Gadus morhua L.): Molecular characterization, promoter structure and function analysis. FISH & SHELLFISH IMMUNOLOGY 2019; 93:28-38. [PMID: 31302288 DOI: 10.1016/j.fsi.2019.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/01/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Eomesodermin (Eomes) is a member of T-box transcription factor family and plays an important role in the regulation of a wide variety of developmental processes and immune response in animals. Here we report cloning and characterization of the full-length cDNA of Atlantic cod Eomes (GmEomes), which possesses a TBOX_3 domain similar to its counterpart in mammals. The regulated expression was observed in head kidney and spleen in response to live Vibrio anguillarum infection in vivo, and spleen leukocytes in vitro after PMA and poly I:C stimulation. Furthermore, we determined a 694 bp sequence, upstream of the transcriptional start site (TSS), to contain a number of sequence motifs that matched known transcription factor-binding sites. Activities of the presumptive regulatory gene were assessed by transfecting different 5'-deletion constructs in CHSE-214 cells. The results showed that the basal promoters and positive transcriptional regulator activities of GmEomes were dependent by sequences located from -694 to -376 bp upstream of TSS. Furthermore, we found that some Eomes binding sites were present in the 5'-flanking regions of the cod IFNγ gene predicted by bioinformatics. However, Co-transfection of eomesodermin overexpression plasmids with INFγ reporter vector into CHSE-214 cells determined that Atlantic cod eomesodermin played a minor role in activation of the INFγ promoter.
Collapse
Affiliation(s)
- Heng Chi
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway; Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, China; Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Institute of Oceanology, 266071, Qingdao, China.
| | - Kristian Gillebo Sørmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jing Diao
- Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, China
| | - Roy Ambli Dalmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway.
| |
Collapse
|
45
|
Abstract
Despite the continuous discovery of long noncoding RNAs (lncRNAs) with critical developmental roles, our knowledge of lncRNAs that control cardiac lineage commitment is still limited. In this issue, Guo et al. (2018) report a novel lncRNA-mediated multiprotein complex assembly that directly regulates the key transcriptional programs of murine cardiogenesis.
Collapse
Affiliation(s)
- Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Medicine-Cardiology, Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Elif Eroglu
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Medicine-Cardiology, Karolinska Institutet, 141 86 Stockholm, Sweden.
| |
Collapse
|
46
|
Fu H, Wang L, Wang J, Bennett BD, Li JL, Zhao B, Hu G. Dioxin and AHR impairs mesoderm gene expression and cardiac differentiation in human embryonic stem cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1038-1046. [PMID: 30266049 PMCID: PMC6547817 DOI: 10.1016/j.scitotenv.2018.09.247] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 05/21/2023]
Abstract
Dioxin and dioxin-related polychlorinated biphenyls are potent toxicants with association with developmental heart defects and congenital heart diseases. However, the underlying mechanism of their developmental toxicity is not fully understood. Further, different animals show distinct susceptibility and phenotypes after exposure, suggesting possible species-specific effects. Using a human embryonic stem cell (ESC) cardiomyocyte differentiation model, we examined the impact, susceptible window, and dosage of 2,3,7,8‑tetrachlorodibenzo‑p‑dioxin (TCDD) on human cardiac development. We showed that treatment of human ESCs with TCDD at the ESC stage inhibits cardiomyocyte differentiation, and the effect is largely mediated by the aryl hydrocarbon receptor (AHR). We further identified genes that are differentially expressed after TCDD treatment by RNA-sequencing, and genomic regions that are occupied by AHR by chromatin immunoprecipitation and high-throughput sequencing. Our results support the model that TCDD impairs human ESC cardiac differentiation by promoting AHR binding and repression of key mesoderm genes. More importantly, our study demonstrates the toxicity of dioxin in human embryonic development and uncovered a novel mechanism by which dioxin and AHR regulates lineage commitment. It also illustrates the power of ESC-based models in the systematic study of developmental toxicology.
Collapse
Affiliation(s)
- Hualing Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiajia Wang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brian D Bennett
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
47
|
Sharifnia T, Wawer MJ, Chen T, Huang QY, Weir BA, Sizemore A, Lawlor MA, Goodale A, Cowley GS, Vazquez F, Ott CJ, Francis JM, Sassi S, Cogswell P, Sheppard HE, Zhang T, Gray NS, Clarke PA, Blagg J, Workman P, Sommer J, Hornicek F, Root DE, Hahn WC, Bradner JE, Wong KK, Clemons PA, Lin CY, Kotz JD, Schreiber SL. Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nat Med 2019; 25:292-300. [PMID: 30664779 PMCID: PMC6633917 DOI: 10.1038/s41591-018-0312-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Chordoma is a primary bone cancer with no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors2,3. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed, enhancer-associated oncogenic transcription factors4,5. In chordoma, we find that T is associated with a 1.5-Mb region containing 'super-enhancers' and is the most highly expressed super-enhancer-associated transcription factor. Notably, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all models tested. In vivo, CDK7/12/13-inhibitor treatment substantially reduces tumor growth. Together, these data demonstrate small-molecule targeting of brachyury transcription factor addiction in chordoma, identify a mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to discover vulnerabilities in genomically quiet cancers.
Collapse
Affiliation(s)
| | | | - Ting Chen
- New York University Langone Medical Center, New York, NY, USA
| | - Qing-Yuan Huang
- New York University Langone Medical Center, New York, NY, USA
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Cambridge, MA, USA
| | - Ann Sizemore
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Lawlor
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Glenn S Cowley
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Janssen R&D, Spring House, PA, USA
| | | | - Christopher J Ott
- Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
| | - Joshua M Francis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Gritstone Oncology, Cambridge, MA, USA
| | - Slim Sassi
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | | | - Francis Hornicek
- Massachusetts General Hospital, Boston, MA, USA
- UCLA Medical Center, Santa Monica, CA, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kwok K Wong
- New York University Langone Medical Center, New York, NY, USA
| | | | | | - Joanne D Kotz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Jnana Therapeutics, Boston, MA, USA.
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
48
|
Shah SR, David JM, Tippens ND, Mohyeldin A, Martinez-Gutierrez JC, Ganaha S, Schiapparelli P, Hamilton DH, Palena C, Levchenko A, Quiñones-Hinojosa A. Brachyury-YAP Regulatory Axis Drives Stemness and Growth in Cancer. Cell Rep 2018; 21:495-507. [PMID: 29020634 DOI: 10.1016/j.celrep.2017.09.057] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 07/19/2017] [Accepted: 09/15/2017] [Indexed: 12/16/2022] Open
Abstract
Molecular factors that define stem cell identity have recently emerged as oncogenic drivers. For instance, brachyury, a key developmental transcriptional factor, is also implicated in carcinogenesis, most notably of chordoma, through mechanisms that remain elusive. Here, we show that brachyury is a crucial regulator of stemness in chordoma and in more common aggressive cancers. Furthermore, this effect of brachyury is mediated by control of synthesis and stability of Yes-associated protein (YAP), a key regulator of tissue growth and homeostasis, providing an unexpected mechanism of control of YAP expression. We further demonstrate that the brachyury-YAP regulatory pathway is associated with tumor aggressiveness. These results elucidate a mechanism of controlling both tumor stemness and aggressiveness through regulatory coupling of two developmental factors.
Collapse
Affiliation(s)
- Sagar R Shah
- Department of Neurologic Surgery, The Mayo Clinic, Jacksonville, FL, USA; Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Justin M David
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel D Tippens
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ahmed Mohyeldin
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Sara Ganaha
- Department of Neurologic Surgery, The Mayo Clinic, Jacksonville, FL, USA
| | | | - Duane H Hamilton
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Claudia Palena
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Andre Levchenko
- Department of Biomedical Engineering and Systems Biology Institute, Yale University, New Haven, CT, USA.
| | | |
Collapse
|
49
|
Zhou J, Plagge A, Murray P. Functional comparison of distinct Brachyury+ states in a renal differentiation assay. Biol Open 2018; 7:bio.031799. [PMID: 29666052 PMCID: PMC5992531 DOI: 10.1242/bio.031799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mesodermal populations can be generated in vitro from mouse embryonic stem cells (mESCs) using three-dimensional (3-D) aggregates called embryoid bodies or two-dimensional (2-D) monolayer culture systems. Here, we investigated whether Brachyury-expressing mesodermal cells generated using 3-D or 2-D culture systems are equivalent or, instead, have different properties. Using a Brachyury-GFP/E2-Crimson reporter mESC line, we isolated Brachyury-GFP + mesoderm cells using flow-activated cell sorting and compared their gene expression profiles and ex vivo differentiation patterns. Quantitative real-time polymerase chain reaction analysis showed significant up-regulation of Cdx2, Foxf1 and Hoxb1 in the Brachyury-GFP+ cells isolated from the 3-D system compared with those isolated from the 2-D system. Furthermore, using an ex vivo mouse kidney rudiment assay, we found that, irrespective of their source, Brachyury-GFP+ cells failed to integrate into developing nephrons, which are derived from the intermediate mesoderm. However, Brachyury-GFP+ cells isolated under 3-D conditions appeared to differentiate into endothelial-like cells within the kidney rudiments, whereas the Brachyury-GFP+ isolated from the 2-D conditions only did so to a limited degree. The high expression of Foxf1 in the 3-D Brachyury-GFP+ cells combined with their tendency to differentiate into endothelial-like cells suggests that these mesodermal cells may represent lateral plate mesoderm.
Collapse
Affiliation(s)
- Jing Zhou
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Antonius Plagge
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Patricia Murray
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| |
Collapse
|
50
|
Guo X, Xu Y, Wang Z, Wu Y, Chen J, Wang G, Lu C, Jia W, Xi J, Zhu S, Jiapaer Z, Wan X, Liu Z, Gao S, Kang J. A Linc1405/Eomes Complex Promotes Cardiac Mesoderm Specification and Cardiogenesis. Cell Stem Cell 2018; 22:893-908.e6. [PMID: 29754779 DOI: 10.1016/j.stem.2018.04.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/07/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
Abstract
Large intergenic non-coding RNAs (lincRNAs) play widespread roles in epigenetic regulation during multiple differentiation processes, but little is known about their mode of action in cardiac differentiation. Here, we identified the key roles of a lincRNA, termed linc1405, in modulating the core network of cardiac differentiation by functionally interacting with Eomes. Chromatin- and RNA-immunoprecipitation assays showed that exon 2 of linc1405 physically mediates a complex consisting of Eomes, trithorax group (TrxG) subunit WDR5, and histone acetyltransferase GCN5 binding at the enhancer region of Mesp1 gene and activates its expression during cardiac mesoderm specification of embryonic stem cells. Importantly, linc1405 co-localizes with Eomes, WDR5, and GCN5 at the primitive streak, and linc1405 depletion impairs heart development and function in vivo. In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.
Collapse
Affiliation(s)
- Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Institute of Regenerative Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zikang Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guiying Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chenqi Lu
- Department of Biostatistics and Computational Biology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wenwen Jia
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Songcheng Zhu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zeyidan Jiapaer
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China
| | - Zhongmin Liu
- Institute of Regenerative Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| |
Collapse
|