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Pîrlog LM, Pătrășcanu AA, Ona MD, Cătană A, Rotar IC. HOXA10 and HOXA11 in Human Endometrial Benign Disorders: Unraveling Molecular Pathways and Their Impact on Reproduction. Biomolecules 2025; 15:563. [PMID: 40305321 PMCID: PMC12024888 DOI: 10.3390/biom15040563] [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] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/03/2025] [Accepted: 04/07/2025] [Indexed: 05/02/2025] Open
Abstract
HOX genes, a family of conserved transcription factors, are critical for reproductive tract development and endometrial functionality. This review highlights the molecular underpinnings of HOXA10/HOXA11 in reproductive health and their dysregulation in benign pathologies associated with infertility, such as endometriosis, adenomyosis, and endometrial polyps. These genes are dynamically regulated by estrogen and progesterone, with peak expression during the secretory phase of the menstrual cycle when implantation takes place. The molecular mechanisms underlying their action include the modulation of extracellular matrix (ECM) remodeling via metalloproteinases, cytokines like leukemia inhibitory factor, and cell adhesion molecules such as β3-integrin, all of which are essential for the differentiation of epithelial and stromal cells, as well as for trophoblast invasion. Aberrant HOX gene expression, driven by DNA hypermethylation or altered histone acetylation, compromises endometrial receptivity and implantation. For instance, reduced HOXA10 expression in endometriosis stems from hypermethylation and chronic inflammation, disrupting immune modulation and cytokine signaling. Similarly, adenomyosis alters HOXA11-regulated ECM remodeling and β3-integrin expression, impairing embryo attachment. Furthermore, regulatory pathways involving vitamin D and retinoic acid offer promising therapeutic avenues pathways, as they enhance HOXA10/HOXA11 expression and endometrial receptivity. This review underscores the critical molecular roles of HOXA10/HOXA11 genes as biomarkers and therapeutic targets to optimize fertility outcomes and address reproductive pathologies.
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Affiliation(s)
- Lorin-Manuel Pîrlog
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400012 Cluj-Napoca, Romania; (L.-M.P.); (M.-D.O.)
| | - Andrada-Adelaida Pătrășcanu
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400012 Cluj-Napoca, Romania; (L.-M.P.); (M.-D.O.)
| | - Mara-Diana Ona
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400012 Cluj-Napoca, Romania; (L.-M.P.); (M.-D.O.)
| | - Andreea Cătană
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400012 Cluj-Napoca, Romania; (L.-M.P.); (M.-D.O.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
- Department of Oncogenetics, “Prof. Dr. I. Chiricuță” Institute of Oncology, 400015 Cluj-Napoca, Romania
| | - Ioana Cristina Rotar
- 1st Department of Obstetrics and Gynecology, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400006 Cluj-Napoca, Romania;
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Yang T, Wang Y, Li H, Shi F, Xu S, Wu Y, Xin J, Liu Y, Jiang M. Homeobox C4 Transcription Factor Promotes Adipose Tissue Thermogenesis. Diabetes 2025; 74:472-485. [PMID: 39854216 PMCID: PMC11926272 DOI: 10.2337/db24-0675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Accepted: 01/21/2025] [Indexed: 01/26/2025]
Abstract
ARTICLE HIGHLIGHTS Homeobox C4 (HOXC4) links metabolic pathways and correlates inversely with mouse body weight and positively with Ucp1 expression in mouse adipose tissue. Gain- and loss-of-function experiments in mice demonstrated HOXC4's essential role in promoting adipose thermogenesis and providing metabolic benefits. HOXC4 interacts with the nuclear receptor coactivator 1 cofactor via its hexapeptide motif to activate Ucp1 transcription, revealing a novel mechanism of thermogenic gene regulation.
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Affiliation(s)
- Ting Yang
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
- Department of Anesthesiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuxuan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hang Li
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Fengshou Shi
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Siqi Xu
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yingting Wu
- School of Pharmacy, Capital Medical University, Beijing, China
| | - Jiaqi Xin
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yi Liu
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Mengxi Jiang
- Department of Pharmacology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Zhong D, Li X, Yin Z, Chen P, Li Y, Tian J, Wang L, Liu H, Yin K, Zhu L, Kong L, Chen K, Li Y, Hong C, Wang C. Circ-ITCH promotes the ubiquitination degradation of HOXC10 to facilitate osteogenic differentiation in disuse osteoporosis through stabilizing BRCA1 mRNA via IGF2BP2-mediated m 6A modification. J Transl Med 2025; 23:376. [PMID: 40148953 PMCID: PMC11951756 DOI: 10.1186/s12967-024-06050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 12/25/2024] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND Osteogenic differentiation of bone marrow mesenchymal stem cells (BM-MSCs) facilitated by mechanical loading is a promising therapy for disuse osteoporosis (DOP), however, it is difficult to implement mechanical loading for a majority of patients. Our study aims to identify circ-ITCH-mediated novel approach to facilitate osteogenic differentiation in DOP. METHODS A rat DOP model and human BM-MSCs under microgravity condition were generated as in vivo and in vitro models of DOP, respectively. The bone mineral density (BMD) and bone parameters were examined in rats. The histological changes of bones and mineralization were monitored by H&E, Alcian blue and Alizarin red S staining. Co-IP was employed to examine the ubiquitination of HOXC10 and the interaction between HOXC10 and BRCA1. The direct associations among circ-ITCH, IGFBP2 and BRCA1 mRNA were assessed by RIP, FISH and RNA pull-down assays. RESULTS Circ-ITCH was downregulated in rat model of DOP and BM-MSCs under microgravity stimulation. Circ-ITCH overexpression promoted osteogenic differentiation in BM-MSCs under microgravity condition. The altered bone parameters, such as BMD, trabecular number (Tb.N), trabecular separation (Tb.Sp), trabecular thickness (Tb.Th), and bone microstructure in DOP rats were rescued by circ-ITCH overexpression. Mechanistically, circ-ITCH enhanced the ubiquitination degradation of HOXC10 through enhancing BRCA1 mRNA stability. Circ-ITCH directly bound to IGF2BP2 protein to stabilize BRCA1 mRNA via m6A modification, thus facilitating osteogenic differentiation in BM-MSCs under microgravity condition. CONCLUSION Circ-ITCH stabilized BRCA1 mRNA via IGF2BP2-mediated m6A modification, thereby facilitating the ubiquitination degradation of HOXC10 to promote osteogenic differentiation in DOP.
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Affiliation(s)
- Da Zhong
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Li
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhen Yin
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Peng Chen
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Yusheng Li
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Tian
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Long Wang
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
- The School of Medicine, Nankai University, Tianjin, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China
| | - Ke Yin
- The First Affiliated Hospital, Department of Orthopedics, Hengyang Medical School, University of South China, Hengyang, China
| | - Lemei Zhu
- School of Public Health, Changsha Medical University, Changsha, China
| | - Lingyu Kong
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Kunli Chen
- Department of Rehabilitation Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yaochun Li
- Department of Rehabilitation Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Chungu Hong
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, China
| | - Chenggong Wang
- Department of Orthopaedics, Xiangya Hospital of Central South University, Changsha, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- Department of Orthopaedics, Xiangya Hospital of Central South University, No. 87 Xiangya Road, Changsha, Hunan Province, 410008, China.
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Szabó E, Pálinkás M, Bohár B, Literáti-Nagy B, Korányi L, Poór G, Várady G, Sarkadi B. Genetic Variants of the Human Thiamine Transporter ( SLC19A3, THTR2)-Potential Relevance in Metabolic Diseases. Int J Mol Sci 2025; 26:2972. [PMID: 40243602 PMCID: PMC11988879 DOI: 10.3390/ijms26072972] [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: 01/23/2025] [Revised: 03/20/2025] [Accepted: 03/22/2025] [Indexed: 04/18/2025] Open
Abstract
Thiamine, crucial for energy metabolism, is associated with various human diseases when deficient. We studied how variations in the SLC19A3 gene, encoding THTR2, a thiamine transporter, may influence type 2 diabetes (T2DM) and gout (arthritis urica, AU). We characterized the SLC19A3 gene variants using bioinformatics and analyzed DNA samples from controls, T2DM, and gout patients to explore associations with physical/laboratory parameters. In human cells, we used a luciferase reporter assay to assess how these variants affect gene expression. We examined four large haplotypes (H1-4) in this gene, identified lead SNPs for the minor variants (MV), and explored potential transcription factor binding sites. We found that in T2DM patients, H3-MV correlated significantly with impaired glucose metabolism (pHOMA = 0.0189, pHbA1c% = 0.0102), while H4-MV correlated with altered uric acid (p = 0.0008) and white blood cell levels (p = 0.0272). In AU patients, H3-MV correlated with increased basophil granulocyte levels (p = 0.0273). In model cell lines, H3-MV presence increased gene expression (p = 0.0351), influencing responses to thiamine depletion and metformin (p = 0.0016). Although H4-MV did not directly affect luciferase expression, thiamine and fedratinib co-treatment significantly enhanced gene expression in thiamine-depleted cells (p = 0.04854). Our results suggest a connection between selected SLC19A3 variants and the severity of metabolic diseases or their response to treatment.
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Affiliation(s)
- Edit Szabó
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary;
| | - Márton Pálinkás
- Department of Rheumatology and Immunology, Semmelweis University, 1023 Budapest, Hungary; (M.P.); (G.P.)
- Department of Internal Medicine and Haematology, Semmelweis University, 1088 Budapest, Hungary
| | - Balázs Bohár
- Doctoral School of Biology, Eötvös Loránd University, 1117 Budapest, Hungary;
| | | | - László Korányi
- Drug Research Center, 8230 Balatonfüred, Hungary; (B.L.-N.); (L.K.)
| | - Gyula Poór
- Department of Rheumatology and Immunology, Semmelweis University, 1023 Budapest, Hungary; (M.P.); (G.P.)
- Department of Internal Medicine and Haematology, Semmelweis University, 1088 Budapest, Hungary
| | - György Várady
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary;
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
| | - Balázs Sarkadi
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary;
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
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Kawanishi T, Takeda H. Dorsoventral patterning beyond the gastrulation stage: Interpretation of early dorsoventral cues and modular development mediated by zic1/zic4. Cells Dev 2025:204012. [PMID: 40010691 DOI: 10.1016/j.cdev.2025.204012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 02/08/2025] [Accepted: 02/20/2025] [Indexed: 02/28/2025]
Abstract
Dorsoventral (DV) patterning is fundamental to vertebrate development, organizing the entire body across different germ layers. Although early DV axis formation, centered on the Spemann-Mangold organizer through the BMP activity gradient, has been extensively studied, the mechanisms shaping DV traits during later development remain largely unexplored. In this review, we highlight recent findings, especially from studies involving the Double anal fin (Da) spontaneous mutant of the small teleost medaka (Oryzias latipes), focusing on the roles of zic1 and zic4 (zic1/zic4) in regulating late DV patterning. These genes establish the dorsal domain of the trunk by converting the initial BMP gradient into distinct on/off spatial compartments within somites and their derivatives, acting as selector genes that define dorsal-specific traits, including myotome structure, body shape, and dorsal fin development. We also discuss how the zic-mediated dorsal domain is established and maintained from embryogenesis through adulthood. Furthermore, we provide evidence that zic-dependent action on the dorsal characteristics is dosage-dependent. We propose that the zic1/zic4-mediated DV patterning mechanism may represent a conserved regulatory framework that has been adapted to support the diverse body plans observed across vertebrate species.
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Affiliation(s)
- Toru Kawanishi
- School of Life Science and Technology, Institute of Science Tokyo, Yokohama 226-8501, Japan.
| | - Hiroyuki Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.
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Zhang X, Lei C, Lu H, Kang B, Liu M, Jiang H, Zan L. Circ_0070934 Regulates the Proliferation, Metastasis, and Epithelial-Mesenchymal Transition of Colorectal Cancer Cells by Targeting miR-203a-3p/HOXA13 Axis. J Biochem Mol Toxicol 2025; 39:e70173. [PMID: 39967473 DOI: 10.1002/jbt.70173] [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: 10/28/2024] [Revised: 01/09/2025] [Accepted: 02/06/2025] [Indexed: 02/20/2025]
Abstract
The present work explored the functions of circ_0070934 in regulating malignant phenotype of colorectal cancer (CRC) cells and its underlying mechanisms. Gene expression data set was acquired based on Gene Expression Omnibus (GEO) database for examining circ_0070934 levels within CRC cells and tissues through quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Kaplan-Meier curve and log-rank test were adopted for assessing CRC patient prognosis based on circ_0070934 level. Functional assays including Cell Counting Kit (CCK)-8, EdU incorporation, Transwell invasion, and scratch assays were conducted to determine CRC cell malignancy. Molecular interactions were predicted using circInteractome and StarBase databases, and validated through luciferase reporter assay. Circ_0070934 was upregulated within CRC cells and tissues, which was related to a dismal prognostic outcome in CRC patients. Knocking down circ_0070934 inhibited CRC cell proliferation, epithelial-mesenchymal transition (EMT), and migration. Further, we identified miR-203a-3p as a target miRNA of circ_0070934, and miR-203a-3p negatively regulated Homeobox A13 (HOXA13) expression. miR-203a-3p/HOXA13 axis mediates the function of circ_0070934 in modulating CRC cell malignancy. These data revealed that circ_0070934 was important for maintaining the malignant phenotype of CRC cells, and circ_0070934 knockdown undermined CRC cell malignancy. Targeting circ_0070934/miR-203a-3p/HOXA13 axis is the promising intervention approach for managing CRC.
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Affiliation(s)
- Xin Zhang
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Changjiang Lei
- Department of Oncology, The Fifth Hospital of Wuhan, Wuhan, Hubei, China
| | - Hongxia Lu
- Department of Gastroenterology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Biao Kang
- Department of Oncology, Dazhou Huakang Hospital, Dazhou, Sichuan Province, China
| | - Maoxi Liu
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Huiyuan Jiang
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Likun Zan
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
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Lewin TD, Liao IJY, Chen ME, Bishop JDD, Holland PWH, Luo YJ. Fusion, fission, and scrambling of the bilaterian genome in Bryozoa. Genome Res 2025; 35:78-92. [PMID: 39762050 PMCID: PMC11789643 DOI: 10.1101/gr.279636.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 10/31/2024] [Indexed: 01/24/2025]
Abstract
Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern of genome evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five bryozoans. Multiple ancient chromosome fusions followed by gene mixing led to the near-complete loss of bilaterian linkage groups in the ancestor of extant bryozoans. A second wave of rearrangements, including chromosome fission, then occurred independently in two bryozoan classes, further scrambling bryozoan genomes. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional but highly debated Lophophorata hypothesis and suggesting macrosynteny to be a potentially powerful source of phylogenetic information. Finally, we show that genome rearrangements led to the dispersion of genes from bryozoan Hox clusters onto multiple chromosomes. Our findings demonstrate that the canonical bilaterian genome structure has been lost across all studied representatives of an entire phylum, and reveal that linkage group fission can occur very frequently in specific lineages.
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Affiliation(s)
- Thomas D Lewin
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Mu-En Chen
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - John D D Bishop
- Marine Biological Association, Plymouth PL1 2PB, United Kingdom
| | - Peter W H Holland
- Department of Biology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Yi-Jyun Luo
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan;
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Kopec K, Quaranto D, DeSouza NR, Jarboe T, Islam HK, Moscatello A, Li XM, Geliebter J, Tiwari RK. The HOX Gene Family's Role as Prognostic and Diagnostic Biomarkers in Hematological and Solid Tumors. Cancers (Basel) 2025; 17:262. [PMID: 39858044 PMCID: PMC11763641 DOI: 10.3390/cancers17020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 01/07/2025] [Accepted: 01/13/2025] [Indexed: 01/27/2025] Open
Abstract
The HOX gene family encodes for regulatory transcription factors that play a crucial role in embryogenesis and differentiation of adult cells. This highly conserved family of genes consists of thirty-nine genes in humans that are located in four clusters, A-D, on different chromosomes. While early studies on the HOX gene family have been focused on embryonic development and its related disorders, research has shifted to examine aberrant expression of HOX genes and the subsequent implication in cancer prediction and progression. Due to their role of encoding master regulatory transcription factors, the abnormal expression of HOX genes has been shown to affect all stages of tumorigenesis and metastasis. This review highlights the novel role of the HOX family's clinical relevance as both prognostic and diagnostic biomarkers in hematological and solid tumors.
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Affiliation(s)
- Kaci Kopec
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
| | - Nicole R. DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
| | - Humayun K. Islam
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
| | - Augustine Moscatello
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
| | - Xiu-Min Li
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
- Department of Dermatology, New York Medical College, Valhalla, NY 10595, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K. Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (K.K.); (D.Q.); (N.R.D.); (T.J.); (H.K.I.); (A.M.); (X.-M.L.); (R.K.T.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
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Nurhidayat L, Benes V, Blom S, Gomes I, Firdausi N, de Bakker MAG, Spaink HP, Richardson MK. Tokay gecko tail regeneration involves temporally collinear expression of HOXC genes and early expression of satellite cell markers. BMC Biol 2025; 23:6. [PMID: 39780185 PMCID: PMC11715542 DOI: 10.1186/s12915-024-02111-9] [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: 08/26/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Regeneration is the replacement of lost or damaged tissue with a functional copy. In axolotls and zebrafish, regeneration involves stem cells produced by de-differentiation. These cells form a growth zone which expresses developmental patterning genes at its apex. This system resembles an embryonic developmental field where cells undergo pattern formation. Some lizards, including geckos, can regenerate their tails, but it is unclear whether they show a "development-like" regeneration pathway. RESULTS Using the tokay gecko (Gekko gecko) model species, we examined seven stages of tail regeneration, and three stages of embryonic tail bud development, using transcriptomics, single-cell sequencing, and in situ hybridization. We find no apical growth zone in the regenerating tail. The transcriptomes of the regenerating vs. embryonic tails are quite different with respect to developmental patterning genes. Posterior HOXC genes were activated in a temporally collinear sequence in the regenerating tail. The major precursor populations were stromal cells (regenerating tail) vs. pluripotent stem cells (embryonic tail). Segmented skeletal muscles were regenerated with no expression of classical segmentation genes, but with the early activation of satellite cell markers. CONCLUSIONS Our study suggests that tail regeneration in the tokay gecko-unlike tail development-might rely on the activation of resident stem cells, guided by pre-existing positional information.
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Affiliation(s)
- Luthfi Nurhidayat
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Faculty of Biology, Universitas Gadjah Mada, Jalan Teknika Selatan Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory Heidelberg, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Sira Blom
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Inês Gomes
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Nisrina Firdausi
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Merijn A G de Bakker
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Herman P Spaink
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Michael K Richardson
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Toolan KP, McGrath BT, Brinkmeier ML, Camper SA, Bielas SL. Ash1l loss-of-function results in structural birth defects and altered cortical development. Brain 2025; 148:55-68. [PMID: 38943682 PMCID: PMC11706301 DOI: 10.1093/brain/awae218] [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: 01/08/2024] [Revised: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 07/01/2024] Open
Abstract
The histone methyltransferase ASH1L plays a crucial role in regulating gene expression across various organ systems during development, yet its role in brain development remains largely unexplored. Over 130 individuals with autism harbour heterozygous loss-of-function ASH1L variants, and population studies confirm it as a high-risk autism gene. Previous studies on Ash1l deficient mice have reported autistic-like behaviours and provided insights into the underlying neuropathophysiology. In this study, we used mice with a cre-inducible deletion of Ash1l exon 4, which results in a frame shift and premature stop codon (p.V1693Afs*2). Our investigation evaluated the impact of Ash1l loss-of-function on survival and craniofacial skeletal development. Using a tamoxifen-inducible cre strain, we targeted Ash1l knockout early in cortical development [Emx1-Cre-ERT2; embryonic Day (e) 10.5]. Immunohistochemistry was utilized to assess cortical lamination, while EdU incorporation aided in birthdating cortical neurons. Additionally, single-cell RNA sequencing was employed to compare cortical cell populations and identify genes with differential expression. At e18.5, the proportion of homozygous Ash1l germline knockout embryos appeared normal; however, no live Ash1l null pups were present at birth (e18.5: n = 77, P = 0.90; p0: n = 41, P = 0.00095). Notably, Ash1l-/- exhibited shortened nasal bones (n = 31, P = 0.017). In the cortical-specific knockout model, SATB2 neurons showed increased numbers (n = 6/genotype, P = 0.0001) and were distributed through the cortical plate. Birthdating revealed generation of ectopically placed deep layer neurons that express SATB2 (e13.5 injection: n = 4/genotype, P = 0.0126). Single cell RNA sequencing revealed significant differences in gene expression between control and mutant upper layer neurons, leading to distinct clustering. Pseudotime analysis indicated that the mutant cluster followed an altered cell differentiation trajectory. This study underscores the essential role of Ash1l in postnatal survival and normal craniofacial development. In the cortex, ASH1L exerts broad effects on gene expression and is indispensable for determining the fate of upper layer cortical neurons. These findings provide valuable insights into the potential mechanisms of ASH1L neuropathology, shedding light on its significance in neurodevelopmental disorders like autism.
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Affiliation(s)
- Kevin P Toolan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI48109, USA
| | - Brian T McGrath
- Cell and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michelle L Brinkmeier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI48109, USA
| | - Sally A Camper
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI48109, USA
- Cell and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI48109, USA
- Cell and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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11
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Marchese D, Evrard L, Bergiers I, Boas L, Duphénieux J, Hermant M, Pringels T, Zeqiri F, Pirson M, Twizere JC, Gofflot F, Rezsohazy R, Bridoux L. Homeodomain Involvement in Nuclear HOX Protein Homo- and Heterodimerization. Int J Mol Sci 2025; 26:423. [PMID: 39796276 PMCID: PMC11721573 DOI: 10.3390/ijms26010423] [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: 12/12/2024] [Revised: 01/03/2025] [Accepted: 01/04/2025] [Indexed: 01/13/2025] Open
Abstract
HOX genes play essential roles in patterning the anteroposterior axis of animal embryos and in the formation of various organs. In mammals, there are 39 HOX genes organized into four clusters (HOXA-D) located on different chromosomes. In relationship with their orderly arrangement along the chromosomes, these genes show nested expression patterns which imply that embryonic territories co-express multiple HOX genes along the main body axis. Interactomic database entries, as well as a handful of publications, support that some HOX proteins can form homodimers or interact with other HOX proteins. However, the consequences of HOX protein interactions have been poorly investigated and remain largely elusive. In this study, we compiled a repository of all HOX-HOX interactions from available databases, and taking HOXA1, HOXA2, and HOXA5 as examples, we investigated the capacity of HOX proteins to form homo- and heterodimers. We revealed that while the DNA-binding domain, the homeodomain, is not necessary for HOXA1 homodimerization, the nuclear localization of the dimerization is dependent on the homeodomain, particularly the integrity of the third helix of HOXA1. Furthermore, we demonstrated that HOXA1 can influence the localization of HOXA1 when it is deprived of the homeodomain, increasing its abundance in the chromatin-containing fraction. Moreover, HOXA1 nuclear homodimerization occurs independently of the integrity of the hexapeptide and, consequently, of its well-known interactor, the homeodomain protein PBX. These results hint at a potential involvement of dimerization in the complex landscape of HOX regulatory mechanisms.
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Affiliation(s)
- Damien Marchese
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Laetitia Evrard
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Isabelle Bergiers
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Ludovic Boas
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Justine Duphénieux
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Maryse Hermant
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Fisnik Zeqiri
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Marc Pirson
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Jean-Claude Twizere
- Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté de Gembloux, 5030 Gembloux, Belgium
| | - Françoise Gofflot
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Louvain Institute of Molecular Science and Technology, Université catholique de Louvain, 5 (L7.07.10) Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
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12
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Frenette B, Guéno J, Houde N, Landry-Truchon K, Giguère A, Ashok T, Ryckman A, Morton BR, Mansfield JH, Jeannotte L. Loss of Hoxa5 function affects Hox gene expression in different biological contexts. Sci Rep 2024; 14:30903. [PMID: 39730789 DOI: 10.1038/s41598-024-81867-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 11/29/2024] [Indexed: 12/29/2024] Open
Abstract
Hoxa5 plays numerous roles in development, but its downstream molecular effects are mostly unknown. We applied bulk RNA-seq assays to characterize the transcriptional impact of the loss of Hoxa5 gene function in seven different biological contexts, including developing respiratory and musculoskeletal tissues that present phenotypes in Hoxa5 mouse mutants. This global analysis revealed few common transcriptional changes, suggesting that HOXA5 acts mainly via the regulation of context-specific effectors. However, Hox genes themselves appeared as potentially conserved targets of HOXA5 across tissues. Notably, a trend toward reduced expression of HoxA genes was observed in Hoxa5 null mutants in several tissue contexts. Comparative analysis of epigenetic marks along the HoxA cluster in lung tissue from two different Hoxa5 mutant mouse lines revealed limited effect of either mutation indicating that Hoxa5 gene targeting did not significantly perturb the chromatin landscape of the surrounding HoxA cluster. Combined with the shared impact of the two Hoxa5 mutant alleles on phenotype and Hox expression, these data argue against the contribution of local cis effects to Hoxa5 mutant phenotypes and support the notion that the HOXA5 protein acts in trans in the control of Hox gene expression.
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Affiliation(s)
- Béatrice Frenette
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
| | - Josselin Guéno
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
| | - Nicolas Houde
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
| | - Kim Landry-Truchon
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
| | - Anthony Giguère
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada
| | - Theyjasvi Ashok
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Abigail Ryckman
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Brian R Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Jennifer H Mansfield
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA.
| | - Lucie Jeannotte
- Centre de Recherche sur le Cancer de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval (Oncology), 1401, 18e Rue, Québec, QC, G1J 1Z4, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada.
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13
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Duboule D, Rekaik H. Comments on the Hox timer and related issues. Cells Dev 2024:203991. [PMID: 39734021 DOI: 10.1016/j.cdev.2024.203991] [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: 11/23/2024] [Revised: 12/26/2024] [Accepted: 12/26/2024] [Indexed: 12/31/2024]
Abstract
2024 not only marked the 100th anniversary of the discovery of the organizer by Hilde Pröscholdt-Mangold and Hans Spemann, but also the 40th anniversary of the discovery of the homeobox, a DNA region encoding a DNA binding peptide present in several transcription factors of critical importance for the gastrulating embryo. In particular, this sequence is found in the 39 members of the amniote Hox gene family, a series of genes activated in mid-gastrulation and involved in organizing morphologies along the extending anterior to posterior (AP) body axis. Over the past 30 years, the study of their coordinated regulation in various contexts has progressively revealed their surprising regulatory strategies, based on mechanisms acting in-cis, which can translate a linear distribution of series of genes along the chromatin fiber into the proper sequences of morphologies observed along our various body axes. The first regulatory layer is controlled by the Hox timer, a mechanism implementing a time-sequenced activation of these genes following their chromosomal order. Here, we discuss various aspects of this mechanism, emphasizing some of its singularities.
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Affiliation(s)
- Denis Duboule
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Hocine Rekaik
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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14
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Chatterjee K, Uyehara CM, Kasliwal K, Madhuranath S, Scourzic L, Polyzos A, Apostolou E, Stadtfeld M. Coordinated repression of totipotency-associated gene loci by histone methyltransferase EHMT2 through binding to LINE-1 regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.18.629181. [PMID: 39763795 PMCID: PMC11702699 DOI: 10.1101/2024.12.18.629181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2025]
Abstract
Mouse embryonic stem cells (mESCs) and other naïve pluripotent stem cells can reverse typical developmental trajectories and, at low frequency, de-differentiate into 2-cell-like cells (2CLCs) that resemble the mammalian embryo during zygotic genome activation (ZGA). This affords the opportunity to reveal molecular principles that govern the pre-implantation stages of mammalian development. We leveraged a multipurpose allele for acute protein depletion and efficient immunoprecipitation to dissect the molecular functions of the chromatin repressor EHMT2, a candidate antagonist of the mESC-to-2CLC transition. This allowed us to define categories of EHMT2 target genes characterized by distinct modes of EHMT2 chromatin engagement and repression. Most notably, EHMT2 directly represses large clusters of co-regulated gene loci that comprise a significant fraction of the 2CLC-specific transcriptome by initiating H3K9me2 spreading from distal LINE-1 elements. EHMT2 counteracts the recruitment of the activator DPPA2/4 to promoter-proximal endogenous retroviral elements (ERVs) at 2CLC genes. EHMT2 depletion elevates the expression of ZGA-associated transcripts in 2CLCs and synergizes with spliceosome inhibition and retinoic acid signaling in facilitating the mESC-to-2CLC transition. In contrast to ZGA-associated genes, repression of germ layer-associated transcripts by EHMT2 occurs outside of gene clusters in collaboration with ZFP462 and entails binding to non-repeat enhancers. Our observations show that EHMT2 attenuates the bidirectional differentiation potential of mouse pluripotent stem cells and define molecular modes for locus-specific transcriptional repression by this essential histone methyltransferase.
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Affiliation(s)
- K Chatterjee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - C M Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - K Kasliwal
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - S Madhuranath
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - L Scourzic
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - A Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - E Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - M Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
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15
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Huang Y, Wang Y, Li R, Liu Y, Yang Y. miR-450b-5p promotes development of endometriosis by inhibiting the GABPA/HOXD10 axis. iScience 2024; 27:111487. [PMID: 39759007 PMCID: PMC11696641 DOI: 10.1016/j.isci.2024.111487] [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: 03/28/2024] [Revised: 10/18/2024] [Accepted: 11/25/2024] [Indexed: 01/07/2025] Open
Abstract
Despite decades of research, the pathogenesis of endometriosis remains unclear. Recent studies have shown that microRNAs play an important role in this condition. In this study, we found that the expression level of miR-450b-5p was increased in ectopic endometrial tissues and that GA-binding protein A (GABPA) and HOXD10 expression levels were decreased. Overexpression of miR-450b-5p or knockdown of GABPA significantly promoted the proliferation and invasion of hEM15A cells and inhibited apoptosis in vivo and in vitro. Furthermore, GABPA was shown to be a direct target of miR-450b-5p and to bind directly to the promoter of the HOXD10 gene, regulating its transcription. Finally, intraperitoneal injection of HOXD10-overexpressing lentivirus in mice significantly attenuated ectopic endometrial lesions. miR-450b-5p directly targets GABPA, regulates expression of HOXD10, and promotes the growth of ectopic endometriotic lesions. Therefore, the miR-450b-5p/GABPA/HOXD10 signaling pathway may be a potential target for treatment of heterotopic endothelial cell disease.
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Affiliation(s)
- Yi Huang
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China
- Reproductive Medicine Center, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Yidan Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China
- Gansu International Scientific and Technological Cooperation, Base of Reproductive Medicine Transformation Application, Key Laboratory for Reproductive Medicine and Embryo, Lanzhou 730000, China
| | - Ruiyun Li
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China
| | - Yongmei Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China
| | - Yuan Yang
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, China
- Reproductive Medicine Center, The First Hospital of Lanzhou University, Lanzhou 730000, China
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16
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Corsaro L, Sacco D, Corbetta C, Gentilini D, Faversani A, Ferrara F, Costantino L. A new approach to study stochastic epigenetic mutations in sperm methylome of Vietnam war veterans directly exposed to Agent Orange. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae020. [PMID: 39664489 PMCID: PMC11631699 DOI: 10.1093/eep/dvae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 09/16/2024] [Accepted: 10/28/2024] [Indexed: 12/13/2024]
Abstract
Among the various environmental pollutants, dioxin, a highly toxic and widely used compound, is associated with numerous adverse health effects, including a potentially toxic multigenerational effect. Understanding the mechanisms by which dioxin exposure can affect sperm epigenetics is critical to comprehending the potential consequences for offspring health and development. This study investigates the possible association between weighted epimutations, hypothesized as markers of epigenetic drift, and dioxin exposure in sperm tissues. We used a public online methylation dataset consisting of 37 participants: 26 Vietnam veterans exposed to Agent Orange, an herbicide contaminated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and 11 individuals not directly exposed to TCDD but whose serum dioxin levels are equivalent to the background. In our study, conducted at the gene level, 437 epimutated genes were identified as significantly associated with each single-digit increase in serum dioxin levels. We found no significant association between the rise in total epimutation load and serum dioxin levels. The pathway analysis performed on the genes reveals biological processes mainly related to changes in embryonic morphology, development, and reproduction. Results from our current study suggest the importance of further investigations on the consequences of dioxin exposure in humans with specific reference to germinal tissue and related heredity.
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Affiliation(s)
- Luigi Corsaro
- Medical Genetics Laboratory, Centro Diagnostico Italiano, Milan, MI 20147, Italy
- Department of Brain and Behavioural Sciences, Università di Pavia, Pavia, PV 27100, Italy
| | - Davide Sacco
- Medical Genetics Laboratory, Centro Diagnostico Italiano, Milan, MI 20147, Italy
- Department of Brain and Behavioural Sciences, Università di Pavia, Pavia, PV 27100, Italy
| | - Carlo Corbetta
- Integrated Laboratory Medicine Services, Centro Diagnostico Italiano, Milan, MI 20147, Italy
| | - Davide Gentilini
- Department of Brain and Behavioural Sciences, Università di Pavia, Pavia, PV 27100, Italy
| | - Alice Faversani
- Medical Genetics Laboratory, Centro Diagnostico Italiano, Milan, MI 20147, Italy
| | - Fulvio Ferrara
- Integrated Laboratory Medicine Services, Centro Diagnostico Italiano, Milan, MI 20147, Italy
| | - Lucy Costantino
- Medical Genetics Laboratory, Centro Diagnostico Italiano, Milan, MI 20147, Italy
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17
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Okino R, Goda Y, Ono Y. The Hox-based positional memory in muscle stem cells. J Biochem 2024; 176:277-283. [PMID: 39194026 DOI: 10.1093/jb/mvae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/09/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024] Open
Abstract
The skeletal muscle is a contractile tissue distributed throughout the body with various anatomical sizes, shapes and functions. In pathological conditions, such as muscular dystrophy, age-related sarcopenia and cancer cachexia, skeletal muscles are not uniformly affected throughout the body. This region-specific vulnerability cannot be fully explained by known physiological classifications, including muscle fiber types. Accumulating evidence indicates that the expression patterns of topographic homeobox (Hox) genes provide a molecular signature of positional memory, reflecting the anatomical locations and embryonic history of muscles and their associated muscle stem cells in adult mice and humans. Hox-based positional memory is not merely a remnant of embryonic development but is expected to be an intrinsic determinant controlling muscle function because recent studies have shown that aberrant Hox genes affect muscle stem cells. In this review, we discuss the concept of Hox-based positional memory, which may offer a new perspective on the region-specific pathophysiology of muscle disorders.
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Affiliation(s)
- Ryosuke Okino
- Muscle Biology Laboratory, Research Team for Aging Science, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Yuki Goda
- Muscle Biology Laboratory, Research Team for Aging Science, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Yusuke Ono
- Muscle Biology Laboratory, Research Team for Aging Science, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, 2-2-1 Honjo, Kumamoto, 860-0811, Japan
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18
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Zhang Y, Li J. Recent advancements in understanding of biological role of homeobox C9 in human cancers. World J Clin Oncol 2024; 15:1168-1176. [PMID: 39351453 PMCID: PMC11438841 DOI: 10.5306/wjco.v15.i9.1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/14/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Homeobox (HOX) C9, a member of the HOX family, is an important transcription factor, and it plays a significant role in various biological processes. This family of genes is highly valued for their essential roles in establishing and maintaining the body axis during embryonic development and adult tissues. Further, HOXC9 plays a central role in neuronal differentiation, angiogenesis, and adipose distribution, which are essential for the development of the nervous system, maturation of tissues and organs, and maintenance of energy balance and metabolic health. Recent research has found that abnormal HOXC9 expression is closely associated with the development and progression of various tumor types. The HOXC9 expression level can be an indicator of tumor prognosis. Therefore, elucidating the association between HOXC9 expression and its regulatory mechanisms and tumorigenesis can provide novel insights on the diagnosis and treatment of patients with cancer.
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Affiliation(s)
- Yong Zhang
- Department of Clinical Laboratory, The Affiliated Lianyungang Oriental Hospital of Kangda College of Nanjing Medical University, Lianyungang 222042, Jiangsu Province, China
| | - Jing Li
- Department of Respiratory and Critical Care Medicine, The Affiliated Lianyungang Oriental Hospital of Kangda College of Nanjing Medical University, Lianyungang 222042, Jiangsu Province, China
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19
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Zhao Q, Pedroza A, Sharma D, Gu W, Dalal A, Weldy C, Jackson W, Li DY, Ryan Y, Nguyen T, Shad R, Palmisano BT, Monteiro JP, Worssam M, Berezwitz A, Iyer M, Shi H, Kundu R, Limbu L, Kim JB, Kundaje A, Fischbein M, Wirka R, Quertermous T, Cheng P. A cell and transcriptome atlas of the human arterial vasculature. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612293. [PMID: 39314359 PMCID: PMC11419041 DOI: 10.1101/2024.09.10.612293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Vascular beds show different propensities for different vascular pathologies, yet mechanisms explaining these fundamental differences remain unknown. We sought to build a transcriptomic, cellular, and spatial atlas of human arterial cells across multiple different arterial segments to understand this phenomenon. We found significant cell type-specific segmental heterogeneity. Determinants of arterial identity are predominantly encoded in fibroblasts and smooth muscle cells, and their differentially expressed genes are particularly enriched for vascular disease-associated loci and genes. Adventitial fibroblast-specific heterogeneity in gene expression coincides with numerous vascular disease risk genes, suggesting a previously unrecognized role for this cell type in disease risk. Adult arterial cells from different segments cluster not by anatomical proximity but by embryonic origin, with differentially regulated genes heavily influenced by developmental master regulators. Non-coding transcriptomes across arterial cells contain extensive variation in lnc-RNAs expressed in cell type- and segment-specific patterns, rivaling heterogeneity in protein coding transcriptomes, and show enrichment for non-coding genetic signals for vascular diseases.
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20
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Garge RK, Lynch V, Fields R, Casadei S, Best S, Stone J, Snyder M, McGann CD, Shendure J, Starita LM, Hamazaki N, Schweppe DK. The proteomic landscape and temporal dynamics of mammalian gastruloid development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.609098. [PMID: 39282277 PMCID: PMC11398484 DOI: 10.1101/2024.09.05.609098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
Abstract
Gastrulation is the highly coordinated process by which the early embryo breaks symmetry, establishes germ layers and a body plan, and sets the stage for organogenesis. As early mammalian development is challenging to study in vivo, stem cell-derived models have emerged as powerful surrogates, e.g. human and mouse gastruloids. However, although single cell RNA-seq (scRNA-seq) and high-resolution imaging have been extensively applied to characterize such in vitro embryo models, a paucity of measurements of protein dynamics and regulation leaves a major gap in our understanding. Here, we sought to address this by applying quantitative proteomics to human and mouse gastruloids at four key stages of their differentiation (naïve ESCs, primed ESCs, early gastruloids, late gastruloids). To the resulting data, we perform network analysis to map the dynamics of expression of macromolecular protein complexes and biochemical pathways, including identifying cooperative proteins that associate with them. With matched RNA-seq and phosphosite data from these same stages, we investigate pathway-, stage- and species-specific aspects of translational and post-translational regulation, e.g. finding peri-gastrulation stages of human and mice to be discordant with respect to the mitochondrial transcriptome vs. proteome, and nominating novel kinase-substrate relationships based on phosphosite dynamics. Finally, we leverage correlated dynamics to identify conserved protein networks centered around congenital disease genes. Altogether, our data (https://gastruloid.brotmanbaty.org/) and analyses showcase the potential of intersecting in vitro embryo models and proteomics to advance our understanding of early mammalian development in ways not possible through transcriptomics alone.
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Affiliation(s)
- Riddhiman K. Garge
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Valerie Lynch
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Silvia Casadei
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Sabrina Best
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jeremy Stone
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Matthew Snyder
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Chris D. McGann
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
- Seattle Hub for Synthetic Biology, Seattle, Washington, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
- Seattle Hub for Synthetic Biology, Seattle, Washington, USA
| | - Devin K. Schweppe
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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21
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Jasim SA, Farhan SH, Ahmad I, Hjazi A, Kumar A, Jawad MA, Pramanik A, Altalbawy FMA, Alsaadi SB, Abosaoda MK. Role of homeobox genes in cancer: immune system interactions, long non-coding RNAs, and tumor progression. Mol Biol Rep 2024; 51:964. [PMID: 39240390 DOI: 10.1007/s11033-024-09857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 08/09/2024] [Indexed: 09/07/2024]
Abstract
The intricate interplay between Homeobox genes, long non-coding RNAs (lncRNAs), and the development of malignancies represents a rapidly expanding area of research. Specific discernible lncRNAs have been discovered to adeptly regulate HOX gene expression in the context of cancer, providing fresh insights into the molecular mechanisms that govern cancer development and progression. An in-depth comprehension of these intricate associations may pave the way for innovative therapeutic strategies in cancer treatment. The HOX gene family is garnering increasing attention due to its involvement in immune system regulation, interaction with long non-coding RNAs, and tumor progression. Although initially recognized for its crucial role in embryonic development, this comprehensive exploration of the world of HOX genes contributes to our understanding of their diverse functions, potentially leading to immunology, developmental biology, and cancer research discoveries. Thus, the primary objective of this review is to delve into these aspects of HOX gene biology in greater detail, shedding light on their complex functions and potential therapeutic applications.
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Affiliation(s)
| | - Shireen Hamid Farhan
- Biotechnology Department, College of Applied Science, Fallujah University, Al-Fallujah, Iraq
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Ashwani Kumar
- Department of Life Sciences, School of Sciences, Jain (Deemed-to-Be) University, Bengaluru, Karnataka, 560069, India
- Department of Pharmacy, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | | | - Atreyi Pramanik
- School of Applied and Life Sciences, Division of Research and Innovation, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Farag M A Altalbawy
- Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | - Salim B Alsaadi
- Department of Pharmaceutics, Al-Hadi University College, Baghdad, 10011, Iraq
| | - Munther Kadhim Abosaoda
- College of Pharmacy, the Islamic University, Najaf, Iraq
- College of Pharmacy, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Pharmacy, the Islamic University of Babylon, Al Diwaniyah, Iraq
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22
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Hjazi A, Jasim SA, Al-Dhalimy AMB, Bansal P, Kaur H, Qasim MT, Mohammed IH, Deorari M, Jawad MA, Zwamel AH. HOXA9 versus HOXB9; particular focus on their controversial role in tumor pathogenesis. J Appl Genet 2024; 65:473-492. [PMID: 38753266 DOI: 10.1007/s13353-024-00868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 08/09/2024]
Abstract
The Homeobox (HOX) gene family is essential to regulating cellular processes because it maintains the exact coordination required for tissue homeostasis, cellular differentiation, and embryonic development. The most distinctive feature of this class of genes is the presence of the highly conserved DNA region known as the homeobox, which is essential for controlling their regulatory activities. Important players in the intricate process of genetic regulation are the HOX genes. Many diseases, especially in the area of cancer, are linked to their aberrant functioning. Due to their distinctive functions in biomedical research-particularly in the complex process of tumor advancement-HOXA9 and HOXB9 have drawn particular attention. HOXA9 and HOXB9 are more significant than what is usually connected with HOX genes since they have roles in the intricate field of cancer and beyond embryonic processes. The framework for a focused study of the different effects of HOXA9 and HOXB9 in the context of tumor biology is established in this study.
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Affiliation(s)
- Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | | | | | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-Be) University, Bengaluru, Karnataka, 560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh, 247341, India
- Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand, 831001, India
| | - Maytham T Qasim
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Nasiriyah, 64001, Iraq
| | - Israa Hussein Mohammed
- College of Nursing, National University of Science and Technology, Dhi Qar, Nasiriyah, Iraq
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Mohammed Abed Jawad
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq
| | - Ahmed Hussein Zwamel
- Medical Laboratory Technique College, The Islamic University, Najaf, Iraq
- Medical Laboratory Technique College, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- Medical Laboratory Technique College, The Islamic University of Babylon, Babylon, Iraq
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23
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Cuevas D, Amigo R, Agurto A, Heredia AA, Guzmán C, Recabal-Beyer A, González-Pecchi V, Caprile T, Haigh JJ, Farkas C. The Role of Epithelial-to-Mesenchymal Transition Transcription Factors (EMT-TFs) in Acute Myeloid Leukemia Progression. Biomedicines 2024; 12:1915. [PMID: 39200378 PMCID: PMC11351244 DOI: 10.3390/biomedicines12081915] [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: 07/12/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
Acute myeloid leukemia (AML) is a diverse malignancy originating from myeloid progenitor cells, with significant genetic and clinical variability. Modern classification systems like those from the World Health Organization (WHO) and European LeukemiaNet use immunophenotyping, molecular genetics, and clinical features to categorize AML subtypes. This classification highlights crucial genetic markers such as FLT3, NPM1 mutations, and MLL-AF9 fusion, which are essential for prognosis and directing targeted therapies. The MLL-AF9 fusion protein is often linked with therapy-resistant AML, highlighting the risk of relapse due to standard chemotherapeutic regimes. In this sense, factors like the ZEB, SNAI, and TWIST gene families, known for their roles in epithelial-mesenchymal transition (EMT) and cancer metastasis, also regulate hematopoiesis and may serve as effective therapeutic targets in AML. These genes contribute to cell proliferation, differentiation, and extramedullary hematopoiesis, suggesting new possibilities for treatment. Advancing our understanding of the molecular mechanisms that promote AML, especially how the bone marrow microenvironment affects invasion and drug resistance, is crucial. This comprehensive insight into the molecular and environmental interactions in AML emphasizes the need for ongoing research and more effective treatments.
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Affiliation(s)
- Diego Cuevas
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción 4030000, Chile; (D.C.); (A.A.); (A.A.H.); (C.G.); (V.G.-P.)
| | - Roberto Amigo
- Laboratorio de Regulación Transcripcional, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Adolfo Agurto
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción 4030000, Chile; (D.C.); (A.A.); (A.A.H.); (C.G.); (V.G.-P.)
| | - Adan Andreu Heredia
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción 4030000, Chile; (D.C.); (A.A.); (A.A.H.); (C.G.); (V.G.-P.)
| | - Catherine Guzmán
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción 4030000, Chile; (D.C.); (A.A.); (A.A.H.); (C.G.); (V.G.-P.)
| | - Antonia Recabal-Beyer
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Valentina González-Pecchi
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción 4030000, Chile; (D.C.); (A.A.); (A.A.H.); (C.G.); (V.G.-P.)
| | - Teresa Caprile
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Jody J. Haigh
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Carlos Farkas
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción 4030000, Chile; (D.C.); (A.A.); (A.A.H.); (C.G.); (V.G.-P.)
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24
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Yadav C, Yadav R, Nanda S, Ranga S, Ahuja P, Tanwar M. Role of HOX genes in cancer progression and their therapeutical aspects. Gene 2024; 919:148501. [PMID: 38670395 DOI: 10.1016/j.gene.2024.148501] [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: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
HOX genes constitute a family of evolutionarily conserved transcription factors that play pivotal roles in embryonic development, tissue patterning, and cell differentiation. These genes are essential for the precise spatial and temporal control of body axis formation in vertebrates. In addition to their developmental functions, HOX genes have garnered significant attention for their involvement in various diseases, including cancer. Deregulation of HOX gene expression has been observed in numerous malignancies, where they can influence tumorigenesis, progression, and therapeutic responses. This review provides an overview of the diverse roles of HOX genes in development, disease, and potential therapeutic targets, highlighting their significance in understanding biological processes and their potential clinical implications.
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Affiliation(s)
- Chetna Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Ritu Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India.
| | - Smiti Nanda
- Retd. Senior Professor and Head, Department of Gynaecology and Obstetrics, Pt. B.D. Sharma University of Health Sciences, Rohtak 124001, India
| | - Shalu Ranga
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Parul Ahuja
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Mukesh Tanwar
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana 124001, India
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25
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Loubet-Senear K, Srivastava M. Brittle star genome provides information on the evolution of regeneration. Nat Ecol Evol 2024; 8:1385-1386. [PMID: 39030275 DOI: 10.1038/s41559-024-02459-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Affiliation(s)
- Kaitlyn Loubet-Senear
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.
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26
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Shikina S, Yoshioka Y, Chiu YL, Uchida T, Chen E, Cheng YC, Lin TC, Chu YL, Kanda M, Kawamitsu M, Fujie M, Takeuchi T, Zayasu Y, Satoh N, Shinzato C. Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp. Commun Biol 2024; 7:899. [PMID: 39048698 PMCID: PMC11269664 DOI: 10.1038/s42003-024-06544-4] [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: 12/21/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Coral polyps are composed of four tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of tentacles (Te), mesenterial filaments (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. This dataset and new insights into tissue functions will facilitate a deeper understanding of symbiotic biology, immunology, biomineralization, digestive biology, and neurobiology in corals.
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Affiliation(s)
- Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yi-Ling Chiu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Emma Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yin-Chu Cheng
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tzu-Chieh Lin
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yu-Ling Chu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Miyuki Kanda
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.
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27
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May-Davis S, Eckelbarger PB, Dzingle D, Saber E. Characterization and Association of the Missing Ventral Tubercle(s) from the Sixth Cervical Vertebra and Transpositions on the Ventral Surface of the Seventh Cervical Vertebra in Modern Equus ferus caballus. Animals (Basel) 2024; 14:1830. [PMID: 38929448 PMCID: PMC11200614 DOI: 10.3390/ani14121830] [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: 05/09/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
In recent years, equine complex vertebral malformation (ECVM) has been of concern in the equine community, with studies identifying numerous associative morphological variations. Here, we examine the morphological association between C6 and C7 for dependency in ECVM cases, where the partially absent ventral process of C6 transposes on the ventral surface of C7. A C6 ventral process presents two tubercles, one cranial (CrVT) and one caudal (CVT). In this study, the C6 osseous specimens (n = 85) demonstrated a partial or completely absent CVT (aCVT) graded 1-4 that often extended cranially creating a partially absent cranial ventral tubercle (aCrVT) graded 1-3. In the 85 C6 osseous specimens examined, the corresponding C7s demonstrated either a complete or incomplete transposition of the ventral process from C6 in 44/85, with 30/44 replicating a transverse foramen. A strong statistical dependency existed between C6 grade 4 aCVTs and grades 1-3 aCrVTs and C7 transpositions with replicated transverse foramen. Sidedness was also demonstrated, where a left sided absent C6 associated with transposition on the left ventral surface of C7. This likewise applied to right sidedness and most bilateral cases. These findings might benefit practitioners when radiographing the extent of the ECVM configuration in patients presenting caudal cervical pain.
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Affiliation(s)
- Sharon May-Davis
- Canine and Equine Research Group, University of New England, Armidale, NSW 2351, Australia
| | | | - Diane Dzingle
- Equus Soma—Equine Osteology and Anatomy Learning Center, Aiken, SC 29805, USA; (P.B.E.); (D.D.)
| | - Elle Saber
- Biological Data Science Institute, Australian National University, Canberra, ACT 2601, Australia;
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28
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Zhang Z, Westover D, Tang Z, Liu Y, Sun J, Sun Y, Zhang R, Wang X, Zhou S, Hesilaiti N, Xia Q, Du Z. Wnt/β-catenin signaling in the development and therapeutic resistance of non-small cell lung cancer. J Transl Med 2024; 22:565. [PMID: 38872189 PMCID: PMC11170811 DOI: 10.1186/s12967-024-05380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Wnt/β-catenin signaling is a critical pathway that influences development and therapeutic response of non-small cell lung cancer (NSCLC). In recent years, many Wnt regulators, including proteins, miRNAs, lncRNAs, and circRNAs, have been found to promote or inhibit signaling by acting on Wnt proteins, receptors, signal transducers and transcriptional effectors. The identification of these regulators and their underlying molecular mechanisms provides important implications for how to target this pathway therapeutically. In this review, we summarize recent studies of Wnt regulators in the development and therapeutic response of NSCLC.
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Affiliation(s)
- Zixu Zhang
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - David Westover
- High-Throughput Analytics, Analytical Research and Development, Merck & Co. Inc., Rahway, NJ, USA
| | - Zhantong Tang
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Yue Liu
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Jinghan Sun
- School of Life Science and Technology, Southeast University, Nanjing, 210018, China
| | - Yunxi Sun
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Runqing Zhang
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Xingyue Wang
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Shihui Zhou
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Nigaerayi Hesilaiti
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Qi Xia
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China
| | - Zhenfang Du
- Department of Genetic and Developmental Biology, School of Medicine, Southeast University, Nanjing, 210003, China.
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29
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Kulakova MA, Maslakov GP, Poliushkevich LO. Irreducible Complexity of Hox Gene: Path to the Canonical Function of the Hox Cluster. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:987-1001. [PMID: 38981695 DOI: 10.1134/s0006297924060014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 07/11/2024]
Abstract
The evolution of major taxa is often associated with the emergence of new gene families. In all multicellular animals except sponges and comb jellies, the genomes contain Hox genes, which are crucial regulators of development. The canonical function of Hox genes involves colinear patterning of body parts in bilateral animals. This general function is implemented through complex, precisely coordinated mechanisms, not all of which are evolutionarily conserved and fully understood. We suggest that the emergence of this regulatory complexity was preceded by a stage of cooperation between more ancient morphogenetic programs or their individual elements. Footprints of these programs may be present in modern animals to execute non-canonical Hox functions. Non-canonical functions of Hox genes are involved in maintaining terminal nerve cell specificity, autophagy, oogenesis, pre-gastrulation embryogenesis, vertical signaling, and a number of general biological processes. These functions are realized by the basic properties of homeodomain protein and could have triggered the evolution of ParaHoxozoa and Nephrozoa subsequently. Some of these non-canonical Hox functions are discussed in our review.
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Affiliation(s)
- Milana A Kulakova
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.
| | - Georgy P Maslakov
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Liudmila O Poliushkevich
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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30
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De Sousa PA, Perfect L, Ye J, Samuels K, Piotrowska E, Gordon M, Mate R, Abranches E, Wishart TM, Dockrell DH, Courtney A. Hyaluronan in mesenchymal stromal cell lineage differentiation from human pluripotent stem cells: application in serum free culture. Stem Cell Res Ther 2024; 15:130. [PMID: 38702837 PMCID: PMC11069290 DOI: 10.1186/s13287-024-03719-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/05/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Hyaluronan (HA) is an extracellular glycosaminoglycan polysaccharide with widespread roles throughout development and in healthy and neoplastic tissues. In pluripotent stem cell culture it can support both stem cell renewal and differentiation. However, responses to HA in culture are influenced by interaction with a range of cognate factors and receptors including components of blood serum supplements, which alter results. These may contribute to variation in cell batch production yield and phenotype as well as heighten the risks of adventitious pathogen transmission in the course of cell processing for therapeutic applications. MAIN: Here we characterise differentiation of a human embryo/pluripotent stem cell derived Mesenchymal Stromal Cell (hESC/PSC-MSC)-like cell population by culture on a planar surface coated with HA in serum-free media qualified for cell production for therapy. Resulting cells met minimum criteria of the International Society for Cellular Therapy for identification as MSC by expression of. CD90, CD73, CD105, and lack of expression for CD34, CD45, CD14 and HLA-II. They were positive for other MSC associated markers (i.e.CD166, CD56, CD44, HLA 1-A) whilst negative for others (e.g. CD271, CD71, CD146). In vitro co-culture assessment of MSC associated functionality confirmed support of growth of hematopoietic progenitors and inhibition of mitogen activated proliferation of lymphocytes from umbilical cord and adult peripheral blood mononuclear cells, respectively. Co-culture with immortalized THP-1 monocyte derived macrophages (Mɸ) concurrently stimulated with lipopolysaccharide as a pro-inflammatory stimulus, resulted in a dose dependent increase in pro-inflammatory IL6 but negligible effect on TNFα. To further investigate these functionalities, a bulk cell RNA sequence comparison with adult human bone marrow derived MSC and hESC substantiated a distinctive genetic signature more proximate to the former. CONCLUSION Cultivation of human pluripotent stem cells on a planar substrate of HA in serum-free culture media systems is sufficient to yield a distinctive developmental mesenchymal stromal cell lineage with potential to modify the function of haematopoietic lineages in therapeutic applications.
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Affiliation(s)
- Paul A De Sousa
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Stroma Therapeutics Ltd, Glasgow, UK.
| | - Leo Perfect
- Biotherapeutics and Advanced Therapies, Science Research and Innovation Group, UK Stem Cell Bank, MHRA, South Mimms, UK
| | - Jinpei Ye
- Institute of Biomedical Science, Shanxi University, Taiyuan, Shanxi, China
| | - Kay Samuels
- Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Ewa Piotrowska
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Department of Molecular Biology, University of Gdansk, Gdańsk, Poland
| | - Martin Gordon
- Biotherapeutics and Advanced Therapies, Science Research and Innovation Group, UK Stem Cell Bank, MHRA, South Mimms, UK
| | - Ryan Mate
- Biotherapeutics and Advanced Therapies, Science Research and Innovation Group, UK Stem Cell Bank, MHRA, South Mimms, UK
| | - Elsa Abranches
- Biotherapeutics and Advanced Therapies, Science Research and Innovation Group, UK Stem Cell Bank, MHRA, South Mimms, UK
| | | | - David H Dockrell
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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32
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. SCIENCE ADVANCES 2024; 10:eadl4239. [PMID: 38507484 PMCID: PMC10954218 DOI: 10.1126/sciadv.adl4239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In animal models, Nipbl deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange syndrome, the most common cause of which is Nipbl haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA sequencing on wild-type and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than wild-type and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and Cornelia de Lange syndrome.
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Affiliation(s)
- Stephenson Chea
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Jesse Kreger
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martha E. Lopez-Burks
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Anne L. Calof
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
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33
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Li J, Mascarinas P, McGlinn E. The expanding roles of Nr6a1 in development and evolution. Front Cell Dev Biol 2024; 12:1357968. [PMID: 38440075 PMCID: PMC10909835 DOI: 10.3389/fcell.2024.1357968] [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: 12/19/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
The Nuclear Receptor (NR) family of transcriptional regulators possess the ability to sense signalling molecules and directly couple that to a transcriptional response. While this large class of proteins are united by sequence and structural homology, individual NR functional output varies greatly depending on their expression, ligand selectivity and DNA binding sequence specificity. Many NRs have remained somewhat enigmatic, with the absence of a defined ligand categorising them as orphan nuclear receptors. One example is Nuclear Receptor subfamily 6 group A member 1 (Nr6a1), an orphan nuclear receptor that has no close evolutionary homologs and thus is alone in subfamily 6. Nonetheless, Nr6a1 has emerged as an important player in the regulation of key pluripotency and developmental genes, as functionally critical for mid-gestational developmental progression and as a possible molecular target for driving evolutionary change in animal body plan. Here, we review the current knowledge on this enigmatic nuclear receptor and how it impacts development and evolution.
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34
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl +/- mouse embryos foreshadows the development of syndromic birth defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.558465. [PMID: 37905011 PMCID: PMC10614802 DOI: 10.1101/2023.10.16.558465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl-deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and CdLS. Teaser Gene expression changes during gastrulation of Nipbl-deficient mice shed light on early origins of structural birth defects.
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35
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Frith TJR, Briscoe J, Boezio GLM. From signalling to form: the coordination of neural tube patterning. Curr Top Dev Biol 2023; 159:168-231. [PMID: 38729676 DOI: 10.1016/bs.ctdb.2023.11.004] [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] [Indexed: 05/12/2024]
Abstract
The development of the vertebrate spinal cord involves the formation of the neural tube and the generation of multiple distinct cell types. The process starts during gastrulation, combining axial elongation with specification of neural cells and the formation of the neuroepithelium. Tissue movements produce the neural tube which is then exposed to signals that provide patterning information to neural progenitors. The intracellular response to these signals, via a gene regulatory network, governs the spatial and temporal differentiation of progenitors into specific cell types, facilitating the assembly of functional neuronal circuits. The interplay between the gene regulatory network, cell movement, and tissue mechanics generates the conserved neural tube pattern observed across species. In this review we offer an overview of the molecular and cellular processes governing the formation and patterning of the neural tube, highlighting how the remarkable complexity and precision of vertebrate nervous system arises. We argue that a multidisciplinary and multiscale understanding of the neural tube development, paired with the study of species-specific strategies, will be crucial to tackle the open questions.
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Affiliation(s)
| | - James Briscoe
- The Francis Crick Institute, London, United Kingdom.
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36
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Singh M, Spendlove SJ, Wei A, Bondhus LM, Nava AA, de L Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. Hum Genet 2023; 142:1705-1720. [PMID: 37861717 PMCID: PMC10676314 DOI: 10.1007/s00439-023-02608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features, including intellectual disability, developmental and speech delay, and hypotonia, and affects multiple organ systems. KAT6A is the enzymatic core of a histone-acetylation protein complex; however, the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n = 8) and control (n = 14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23% (14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, and HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah J Spendlove
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Angela Wei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Leroy M Bondhus
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen A Nava
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Francisca N de L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Seth Amano
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA.
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37
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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38
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Dai Q. Blocking the blocker. eLife 2023; 12:e92076. [PMID: 37698172 PMCID: PMC10497280 DOI: 10.7554/elife.92076] [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] [Indexed: 09/13/2023] Open
Abstract
An unexpected interaction between a long non-coding RNA locus and a genetic insulator called Fub-1 has an important role in gene regulation during development in Drosophila.
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Affiliation(s)
- Qi Dai
- Department of Molecular Bioscience, The Wenner-Gren Institute, Stockholm UniversityStockholmSweden
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39
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Singh M, Spendlove S, Wei A, Bondhus L, Nava A, de L. Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.550595. [PMID: 37577627 PMCID: PMC10418288 DOI: 10.1101/2023.08.03.550595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features including intellectual disability, developmental and speech delay, hypotonia and affects multiple organ systems. KAT6A is highly expressed in early development and plays a key role in cell-type specific differentiation. KAT6A is the enzymatic core of a histone-acetylation protein complex, however the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n=8) and control (n=14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23%(14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah Spendlove
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
| | - Angela Wei
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
| | - Leroy Bondhus
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen Nava
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Seth Amano
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
| | - Valerie A. Arboleda
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
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May-Davis S, Dzingle D, Saber E, Blades Eckelbarger P. Characterization of the Caudal Ventral Tubercle in the Sixth Cervical Vertebra in Modern Equus ferus caballus. Animals (Basel) 2023; 13:2384. [PMID: 37508161 PMCID: PMC10376820 DOI: 10.3390/ani13142384] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
This study examined the anomalous variations of the ventral process of C6 in modern E. ferus caballus. The aim was to provide an incremental grading protocol measuring the absence of the caudal ventral tubercle (CVT) in this ventral process. The findings revealed the most prevalent absent CVT (aCVT) was left unilateral (n = 35), with bilateral (n = 29) and right unilateral (n = 12). Grading was determined in equal increments of absence 1/4, 2/4, 3/4, with 4/4 representing a complete aCVT in 56/76, with a significance of p = 0.0013. This also applied to bilateral specimens. In those C6 osseous specimens displaying a 4/4 grade aCVT, 41/56 had a partial absence of the caudal aspect of the cranial ventral tubercle (CrVT). Here, grading absent CrVTs (aCrVT) followed similarly to aCVTs, though 4/4 was not observed. The significance between 4/4 grade aCVTs and the presentation of an aCrVT was left p = 0.00001 and right p = 0.00018. In bilateral specimens, C6 morphologically resembled C5, implying a homeotic transformation that limited the attachment sites for the cranial and thoracal longus colli muscle. This potentially diminishes function and caudal cervical stability. Therefore, it is recommended that further studies examine the morphological extent of this equine complex vertebral malformation (ECVM) as well as its interrelationships and genetic code/blueprint.
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Affiliation(s)
- Sharon May-Davis
- Canine and Equine Research Group, University of New England, Armidale, NSW 2351, Australia
| | - Diane Dzingle
- Equus Soma-Equine Osteology and Anatomy Learning Center, Aiken, SC 29805, USA
| | - Elle Saber
- Biological Data Science Institute, Australian National University, Canberra, ACT 2601, Australia
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