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Saibo NV, Maiti S, Boral S, Banerjee P, Kushwaha T, Inampudi KK, Goswami R, De S. The intrinsically disordered transactivation region of HOXA9 regulates its function by auto-inhibition of its DNA-binding activity. Int J Biol Macromol 2024; 273:132704. [PMID: 38825283 DOI: 10.1016/j.ijbiomac.2024.132704] [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: 11/15/2023] [Revised: 02/19/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
HOXA9 transcription factor is expressed in hematopoietic stem cells and is involved in the regulation of their differentiation and maturation to various blood cells. HOXA9 is linked to various leukemia and is a marker for poor prognosis of acute myeloid leukemia (AML). This protein has a conserved DNA-binding homeodomain and a transactivation domain. We show that this N-terminal transactivation domain is intrinsically disordered and inhibits DNA-binding by the homeodomain. Using NMR spectroscopy and molecular dynamics simulation, we show that the hexapeptide 197AANWLH202 in the disordered region transiently occludes the DNA-binding interface. The hexapeptide also forms a rigid segment, as determined by NMR dynamics, in an otherwise flexible disordered region. Interestingly, this hexapeptide is known to mediate the interaction of HOXA9 and its TALE partner proteins, such as PBX1, and help in cooperative DNA binding. Mutation of tryptophan to alanine in the hexapeptide abrogates the DNA-binding auto-inhibition. We propose that the disordered transactivation region plays a dual role in the regulation of HOXA9 function. In the absence of TALE partners, it inhibits DNA binding, and in the presence of TALE partners it interacts with the TALE protein and facilitates the cooperative DNA binding by the HOX-TALE complex.
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Affiliation(s)
- Nikita V Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Snigdha Maiti
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Soumendu Boral
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Puja Banerjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Ritobrata Goswami
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India.
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2
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [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: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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3
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Salomone J, Farrow E, Gebelein B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Semin Cell Dev Biol 2024; 152-153:93-100. [PMID: 36517343 PMCID: PMC10258226 DOI: 10.1016/j.semcdb.2022.11.016] [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: 07/30/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Hox genes are a family of homeodomain transcription factors that regulate specialized morphological structures along the anterior-posterior axis of metazoans. Over the past few decades, researchers have focused on defining how Hox factors with similar in vitro DNA binding activities achieve sufficient target specificity to regulate distinct cell fates in vivo. In this review, we highlight how protein interactions with other transcription factors, many of which are also homeodomain proteins, result in the formation of transcription factor complexes with enhanced DNA binding specificity. These findings suggest that Hox-regulated enhancers utilize distinct combinations of homeodomain binding sites, many of which are low-affinity, to recruit specific Hox complexes. However, low-affinity sites can only yield reproducible responses with high transcription factor concentrations. To overcome this limitation, recent studies revealed how transcription factors, including Hox factors, use intrinsically disordered domains (IDRs) to form biomolecular condensates that increase protein concentrations. Moreover, Hox factors with altered IDRs have been associated with altered transcriptional activity and human disease states, demonstrating the importance of IDRs in mediating essential Hox output. Collectively, these studies highlight how Hox factors use their DNA binding domains, protein-protein interaction domains, and IDRs to form specific transcription factor complexes that yield accurate gene expression.
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Affiliation(s)
- Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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4
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Bertrums EJM, Smith JL, Harmon L, Ries RE, Wang YCJ, Alonzo TA, Menssen AJ, Chisholm KM, Leonti AR, Tarlock K, Ostronoff F, Pogosova-Agadjanyan EL, Kaspers GJL, Hasle H, Dworzak M, Walter C, Muhlegger N, Morerio C, Pardo L, Hirsch B, Raimondi S, Cooper TM, Aplenc R, Gamis AS, Kolb EA, Farrar JE, Stirewalt D, Ma X, Shaw TI, Furlan SN, Brodersen LE, Loken MR, Van den Heuvel-Eibrink MM, Zwaan CM, Triche TJ, Goemans BF, Meshinchi S. Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica 2023; 108:2044-2058. [PMID: 36815378 PMCID: PMC10388277 DOI: 10.3324/haematol.2022.281653] [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: 06/27/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
NUP98 fusions comprise a family of rare recurrent alterations in AML, associated with adverse outcomes. In order to define the underlying biology and clinical implications of this family of fusions, we performed comprehensive transcriptome, epigenome, and immunophenotypic profiling of 2,235 children and young adults with AML and identified 160 NUP98 rearrangements (7.2%), including 108 NUP98-NSD1 (4.8%), 32 NUP98-KDM5A (1.4%) and 20 NUP98-X cases (0.9%) with 13 different fusion partners. Fusion partners defined disease characteristics and biology; patients with NUP98-NSD1 or NUP98-KDM5A had distinct immunophenotypic, transcriptomic, and epigenomic profiles. Unlike the two most prevalent NUP98 fusions, NUP98-X variants are typically not cryptic. Furthermore, NUP98-X cases are associated with WT1 mutations, and have epigenomic profiles that resemble either NUP98-NSD1 or NUP98-KDM5A. Cooperating FLT3-ITD and WT1 mutations define NUP98-NSD1, and chromosome 13 aberrations are highly enriched in NUP98-KDM5A. Importantly, we demonstrate that NUP98 fusions portend dismal overall survival, with the noteworthy exception of patients bearing abnormal chromosome 13 (clinicaltrials gov. Identifiers: NCT00002798, NCT00070174, NCT00372593, NCT01371981).
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Affiliation(s)
- Eline J M Bertrums
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands; Oncode Institute, Utrecht.
| | - Jenny L Smith
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
| | - Lauren Harmon
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI
| | - Rhonda E Ries
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
| | - Yi-Cheng J Wang
- Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA; Children's Oncology Group, Monrovia, CA
| | - Todd A Alonzo
- Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA; Children's Oncology Group, Monrovia, CA
| | | | - Karen M Chisholm
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA
| | - Amanda R Leonti
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
| | - Katherine Tarlock
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA; Division of Hematology and Oncology, Seattle Children's Hospital, Seattle, WA
| | - Fabiana Ostronoff
- Intermountain Blood and Marrow Transplant and Acute Leukemia Program, Intermountain Healthcare, Salt Lake City, UT
| | | | - Gertjan J L Kaspers
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands; Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology, The Netherlands; Dutch Childhood Oncology Group
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Dworzak
- Children's Cancer Research Institute, Medical University of Vienna, Vienna, Austria; St. Anna Kinderspital, Department of Pediatrics, Medical University of Vienna, Vienna
| | - Christiane Walter
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen
| | - Nora Muhlegger
- Children's Cancer Research Institute, Medical University of Vienna, Vienna
| | - Cristina Morerio
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa
| | | | - Betsy Hirsch
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Susana Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Todd M Cooper
- Division of Hematology and Oncology, Seattle Children's Hospital, Seattle, WA
| | - Richard Aplenc
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alan S Gamis
- Division of Hematology/Oncology, Children's Mercy Kansas City, Kansas City, MO
| | - Edward A Kolb
- Nemours Alfred I. duPont Hospital for Children, Wilmington, DE
| | - Jason E Farrar
- Arkansas Children's Research Institute and Department of Pediatrics, Hematology/Oncology Section, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Derek Stirewalt
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
| | - Xiaotu Ma
- Computational Biology Department, St. Jude Children's Research Hospital, Memphis, TN
| | - Tim I Shaw
- Computational Biology Department, St. Jude Children's Research Hospital, Memphis, TN
| | - Scott N Furlan
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
| | | | | | | | - C Michel Zwaan
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands; Dutch Childhood Oncology Group
| | - Timothy J Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA; Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA; Department of Pediatrics, Michigan State University College of Human Medicine, Grand Rapids, MI
| | | | - Soheil Meshinchi
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA; Children's Oncology Group, Monrovia, CA, USA; Division of Hematology and Oncology, Seattle Children's Hospital, Seattle, WA.
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5
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Delage L, Lambert M, Bardel É, Kundlacz C, Chartoire D, Conchon A, Peugnet AL, Gorka L, Auberger P, Jacquel A, Soussain C, Destaing O, Delecluse HJ, Delecluse S, Merabet S, Traverse-Glehen A, Salles G, Bachy E, Billaud M, Ghesquières H, Genestier L, Rouault JP, Sujobert P. BTG1 inactivation drives lymphomagenesis and promotes lymphoma dissemination through activation of BCAR1. Blood 2023; 141:1209-1220. [PMID: 36375119 DOI: 10.1182/blood.2022016943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding the functional role of mutated genes in cancer is required to translate the findings of cancer genomics into therapeutic improvement. BTG1 is recurrently mutated in the MCD/C5 subtype of diffuse large B-cell lymphoma (DLBCL), which is associated with extranodal dissemination. Here, we provide evidence that Btg1 knock out accelerates the development of a lethal lymphoproliferative disease driven by Bcl2 overexpression. Furthermore, we show that the scaffolding protein BCAR1 is a BTG1 partner. Moreover, after BTG1 deletion or expression of BTG1 mutations observed in patients with DLBCL, the overactivation of the BCAR1-RAC1 pathway confers increased migration ability in vitro and in vivo. These modifications are targetable with the SRC inhibitor dasatinib, which opens novel therapeutic opportunities in BTG1 mutated DLBCL.
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Affiliation(s)
- Lorric Delage
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Mireille Lambert
- Université de Paris, Institut Cochin, INSERM U1016, Plateforme BioMecan'IC, Biomécanique de la cellule, Paris, France
| | - Émilie Bardel
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Cindy Kundlacz
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Dimitri Chartoire
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Axel Conchon
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Anne-Laure Peugnet
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Lucas Gorka
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Patrick Auberger
- Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM U1065, Nice, France
| | - Arnaud Jacquel
- Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM U1065, Nice, France
| | - Carole Soussain
- Institut Curie, Site de Saint-Cloud, Hematologie, et INSERM U932 Institut Curie, PSL Research University, Paris, France
| | - Olivier Destaing
- Centre de Recherche UGA, INSERM U1209, Institute for Advanced Biosciences, Grenoble, France
| | | | | | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Alexandra Traverse-Glehen
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Gilles Salles
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emmanuel Bachy
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Marc Billaud
- INSERM Unité Mixte de Recherche (UMR)-U1052, Centre National de la Recherche UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Hervé Ghesquières
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Laurent Genestier
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
| | - Jean-Pierre Rouault
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
- INSERM Unité Mixte de Recherche (UMR)-U1052, Centre National de la Recherche UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Pierre Sujobert
- Centre International de Recherche en Infectiologie (Team LIB), Université Lyon, INSERM, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Faculté de Médecine Lyon-Sud, Université de Lyon, Oullins, France
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6
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Du R, Wang C, Liu J, Wang K, Dai L, Shen W. Phosphorylation of TGIF2 represents a therapeutic target that drives EMT and metastasis of lung adenocarcinoma. BMC Cancer 2023; 23:52. [PMID: 36647029 PMCID: PMC9841675 DOI: 10.1186/s12885-023-10535-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/09/2023] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND TGF-β-induced factor homeobox 2 (TGIF2) is a transcription regulator that is phosphorylated by EGFR/ERK signaling. However, the functions of phosphorylated (p)-TGIF2 in cancer are largely unknown. Here, we investigated the roles of p-TGIF2 in promoting epithelial-mesenchymal transition (EMT) and metastasis in lung adenocarcinoma (LUAD). METHODS In vitro and in vivo experiments were conducted to investigate the role of TGIF2 in LUAD EMT and metastasis. Dual-luciferase reporter and ChIP assays were employed to observe the direct transcriptional regulation of E-cadherin by TGIF2 and HDAC1. Co-immunoprecipitation was performed to identify the interaction between TGIF2 and HDAC1. RESULTS Downregulating the expression of TGIF2 inhibited LUAD cell migration, EMT and metastasis in vitro and in vivo. Phosphorylation of TGIF2 by EGFR/ERK signaling was required for TGIF2-promoted LUAD EMT and metastasis since phosphorylation-deficient TGIF2 mutant lost these functions. Phosphorylation of TGIF2 was necessary to recruit HDAC1 to the E-cadherin promoter sequence and subsequently suppress E-cadherin transcription. Meanwhile, inhibition of HDAC1 repressed the TGIF2 phosphorylation-induced migration and EMT of LUAD cells. In xenograft mouse models, both inhibition of ERK and HDAC1 could significantly inhibited TGIF2-enhanced metastasis. Furthermore, TGIF2-positive staining was significantly correlated with E-cadherin-negative staining in human lung cancer specimens. CONCLUSIONS Our study reveals the novel function of p-TGIF2 in promoting EMT and metastasis in LUAD; p-TGIF2 could be a potential therapeutic target to inhibit LUAD metastasis.
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Affiliation(s)
- Renle Du
- grid.207374.50000 0001 2189 3846Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846College of Public Health, Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.207374.50000 0001 2189 3846State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.207374.50000 0001 2189 3846Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Chen Wang
- grid.207374.50000 0001 2189 3846School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052 China
| | - Jingjing Liu
- grid.207374.50000 0001 2189 3846Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Keyan Wang
- grid.207374.50000 0001 2189 3846Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Liping Dai
- grid.207374.50000 0001 2189 3846Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052 China ,grid.207374.50000 0001 2189 3846Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Wenzhi Shen
- grid.449428.70000 0004 1797 7280Department of Pathology and Institute of Precision Medicine, Jining Medical University, Jining, 272067 China
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7
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Jia Y, Reboulet J, Gillet B, Hughes S, Forcet C, Tribollet V, Hajj Sleiman N, Kundlacz C, Vanacker JM, Bleicher F, Merabet S. A Live Cell Protein Complementation Assay for ORFeome-Wide Probing of Human HOX Interactomes. Cells 2023; 12:cells12010200. [PMID: 36611993 PMCID: PMC9818449 DOI: 10.3390/cells12010200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
Biological pathways rely on the formation of intricate protein interaction networks called interactomes. Getting a comprehensive map of interactomes implies the development of tools that allow one to capture transient and low-affinity protein-protein interactions (PPIs) in live conditions. Here we presented an experimental strategy: the Cell-PCA (cell-based protein complementation assay), which was based on bimolecular fluorescence complementation (BiFC) for ORFeome-wide screening of proteins that interact with different bait proteins in the same live cell context, by combining high-throughput sequencing method. The specificity and sensitivity of the Cell-PCA was established by using a wild-type and a single-amino-acid-mutated HOXA9 protein, and the approach was subsequently applied to seven additional human HOX proteins. These proof-of-concept experiments revealed novel molecular properties of HOX interactomes and led to the identification of a novel cofactor of HOXB13 that promoted its proliferative activity in a cancer cell context. Taken together, our work demonstrated that the Cell-PCA was pertinent for revealing and, importantly, comparing the interactomes of different or highly related bait proteins in the same cell context.
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Affiliation(s)
- Yunlong Jia
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Jonathan Reboulet
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
- LiPiCs, 46 Allée d’Italie, 69007 Lyon, France
| | - Benjamin Gillet
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Sandrine Hughes
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Christelle Forcet
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Violaine Tribollet
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Nawal Hajj Sleiman
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Cindy Kundlacz
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Jean-Marc Vanacker
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
| | - Françoise Bleicher
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
- Correspondence: franç (F.B.); (S.M.)
| | - Samir Merabet
- IGFL, CNRS UMR5242, ENS-Lyon, UCBL-1, INRA USC1370, 32 Av. Tony Garnier, 69007 Lyon, France
- Correspondence: franç (F.B.); (S.M.)
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8
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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9
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Kalis AK, Sterrett MC, Armstrong C, Ballmer A, Burkstrand K, Chilson E, Emlen E, Ferrer E, Loeb S, Olin T, Tran K, Wheeler A, Ross Wolff J. Hox proteins interact to pattern neuronal subtypes in Caenorhabditis elegans males. Genetics 2022; 220:iyac010. [PMID: 35137058 PMCID: PMC8982040 DOI: 10.1093/genetics/iyac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/10/2022] [Indexed: 11/14/2022] Open
Abstract
Hox transcription factors are conserved regulators of neuronal subtype specification on the anteroposterior axis in animals, with disruption of Hox gene expression leading to homeotic transformations of neuronal identities. We have taken advantage of an unusual mutation in the Caenorhabditis elegans Hox gene lin-39, lin-39(ccc16), which transforms neuronal fates in the C. elegans male ventral nerve cord in a manner that depends on a second Hox gene, mab-5. We have performed a genetic analysis centered around this homeotic allele of lin-39 in conjunction with reporters for neuronal target genes and protein interaction assays to explore how LIN-39 and MAB-5 exert both flexibility and specificity in target regulation. We identify cis-regulatory modules in neuronal reporters that are both region-specific and Hox-responsive. Using these reporters of neuronal subtype, we also find that the lin-39(ccc16) mutation disrupts neuronal fates specifically in the region where lin-39 and mab-5 are coexpressed, and that the protein encoded by lin-39(ccc16) is active only in the absence of mab-5. Moreover, the fates of neurons typical to the region of lin-39-mab-5 coexpression depend on both Hox genes. Our genetic analysis, along with evidence from Bimolecular Fluorescence Complementation protein interaction assays, supports a model in which LIN-39 and MAB-5 act at an array of cis-regulatory modules to cooperatively activate and to individually activate or repress neuronal gene expression, resulting in regionally specific neuronal fates.
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Affiliation(s)
- Andrea K Kalis
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Maria C Sterrett
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Cecily Armstrong
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | | | - Kylie Burkstrand
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Elizabeth Chilson
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Estee Emlen
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Emma Ferrer
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Seanna Loeb
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Taylor Olin
- Department of Biology, St. Catherine University, St. Paul, MN 55105, USA
| | - Kevin Tran
- Department of Biology, Carleton College, Northfield, MN 55057, USA
| | - Andrew Wheeler
- Department of Biology, Carleton College, Northfield, MN 55057, USA
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10
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The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia. Int J Mol Sci 2022; 23:ijms23063192. [PMID: 35328612 PMCID: PMC8952210 DOI: 10.3390/ijms23063192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/10/2022] Open
Abstract
Homeobox genes encode transcription factors that control basic developmental decisions. Knowledge of their hematopoietic activities casts light on normal and malignant immune cell development. Recently, we constructed the so-called lymphoid TALE-code that codifies expression patterns of all active TALE class homeobox genes in early hematopoiesis and lymphopoiesis. Here, we present the corresponding myeloid TALE-code to extend this gene signature, covering the entire hematopoietic system. The collective data showed expression patterns for eleven TALE homeobox genes and highlighted the exclusive expression of IRX1 in megakaryocyte-erythroid progenitors (MEPs), implicating this TALE class member in a specific myeloid differentiation process. Analysis of public profiling data from acute myeloid leukemia (AML) patients revealed aberrant activity of IRX1 in addition to IRX3 and IRX5, indicating an oncogenic role for these TALE homeobox genes when deregulated. Screening of RNA-seq data from 100 leukemia/lymphoma cell lines showed overexpression of IRX1, IRX3, and IRX5 in megakaryoblastic and myelomonocytic AML cell lines, chosen as suitable models for studying the regulation and function of these homeo-oncogenes. Genomic copy number analysis of IRX-positive cell lines demonstrated chromosomal amplification of the neighboring IRX3 and IRX5 genes at position 16q12 in MEGAL, underlying their overexpression in this cell line model. Comparative gene expression analysis of these cell lines revealed candidate upstream factors and target genes, namely the co-expression of GATA1 and GATA2 together with IRX1, and of BMP2 and HOXA10 with IRX3/IRX5. Subsequent knockdown and stimulation experiments in AML cell lines confirmed their activating impact in the corresponding IRX gene expression. Furthermore, we demonstrated that IRX1 activated KLF1 and TAL1, while IRX3 inhibited GATA1, GATA2, and FST. Accordingly, we propose that these regulatory relationships may represent major physiological and oncogenic activities of IRX factors in normal and malignant myeloid differentiation, respectively. Finally, the established myeloid TALE-code is a useful tool for evaluating TALE homeobox gene activities in AML.
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11
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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12
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Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Dev Biol 2021; 479:61-76. [PMID: 34310923 DOI: 10.1016/j.ydbio.2021.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022]
Abstract
Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.
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13
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Weldon SA, Münsterberg AE. Somite development and regionalisation of the vertebral axial skeleton. Semin Cell Dev Biol 2021; 127:10-16. [PMID: 34690064 DOI: 10.1016/j.semcdb.2021.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022]
Abstract
A critical stage in the development of all vertebrate embryos is the generation of the body plan and its subsequent patterning and regionalisation along the main anterior-posterior axis. This includes the formation of the vertebral axial skeleton. Its organisation begins during early embryonic development with the periodic formation of paired blocks of mesoderm tissue called somites. Here, we review axial patterning of somites, with a focus on studies using amniote model systems - avian and mouse. We summarise the molecular and cellular mechanisms that generate paraxial mesoderm and review how the different anatomical regions of the vertebral column acquire their specific identity and thus shape the body plan. We also discuss the generation of organoids and embryo-like structures from embryonic stem cells, which provide insights regarding axis formation and promise to be useful for disease modelling.
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Affiliation(s)
- Shannon A Weldon
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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14
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Blasi F, Bruckmann C. MEIS1 in Hematopoiesis and Cancer. How MEIS1-PBX Interaction Can Be Used in Therapy. J Dev Biol 2021; 9:jdb9040044. [PMID: 34698191 PMCID: PMC8544432 DOI: 10.3390/jdb9040044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Recently MEIS1 emerged as a major determinant of the MLL-r leukemic phenotype. The latest and most efficient drugs effectively decrease the levels of MEIS1 in cancer cells. Together with an overview of the latest drugs developed to target MEIS1 in MLL-r leukemia, we review, in detail, the role of MEIS1 in embryonic and adult hematopoiesis and suggest how a more profound knowledge of MEIS1 biochemistry can be used to design potent and effective drugs against MLL-r leukemia. In addition, we present data showing that the interaction between MEIS1 and PBX1 can be blocked efficiently and might represent a new avenue in anti-MLL-r and anti-leukemic therapy.
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15
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Hombría JCG, García-Ferrés M, Sánchez-Higueras C. Anterior Hox Genes and the Process of Cephalization. Front Cell Dev Biol 2021; 9:718175. [PMID: 34422836 PMCID: PMC8374599 DOI: 10.3389/fcell.2021.718175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
During evolution, bilateral animals have experienced a progressive process of cephalization with the anterior concentration of nervous tissue, sensory organs and the appearance of dedicated feeding structures surrounding the mouth. Cephalization has been achieved by the specialization of the unsegmented anterior end of the body (the acron) and the sequential recruitment to the head of adjacent anterior segments. Here we review the key developmental contribution of Hox1-5 genes to the formation of cephalic structures in vertebrates and arthropods and discuss how this evolved. The appearance of Hox cephalic genes preceded the evolution of a highly specialized head in both groups, indicating that Hox gene involvement in the control of cephalic structures was acquired independently during the evolution of vertebrates and invertebrates to regulate the genes required for head innovation.
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Affiliation(s)
- James C-G Hombría
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
| | - Mar García-Ferrés
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
| | - Carlos Sánchez-Higueras
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
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16
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Feng W, Yang X, Wang L, Wang R, Yang F, Wang H, Liu X, Ren Q, Zhang Y, Zhu X, Zheng G. P2X7 promotes the progression of MLL-AF9 induced acute myeloid leukemia by upregulation of Pbx3. Haematologica 2021; 106:1278-1289. [PMID: 32165482 PMCID: PMC8094107 DOI: 10.3324/haematol.2019.243360] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Indexed: 12/21/2022] Open
Abstract
Nucleotides mediate intercellular communication by activating purinergic receptors and take part in various physiological and pathological processes. Abnormal purinergic signaling plays important roles in malignant progression. P2X7, which belongs to the P2X family of purinergic receptors, is abnormally expressed in various types of malignancies including leukemia. However, its role and molecular mechanism in leukemia have not been elucidated. Here, we analyzed the correlation between P2X7 expression and AML clinical outcome; explored the role and mechanism of P2X7 in AML progression by using mouse acute myeloid leukemia (AML), nude mouse xenograft and patient-derived xenograft models. High levels of P2X7 expression were correlated with worse survival in AML. P2X7 was highly expressed in MLL-rearranged AML. Furthermore, P2X7 accelerated the progression of MLL-rearranged AML by both promoting cell proliferation and increasing leukemia stem cell (LSC) levels. Moreover, P2X7 caused upregulation of Pbx3 accounts for its pro-leukemic effects. The P2X7-Pbx3 pathway might also contribute to the progression of other types of leukemia as well as solid tumors with high levels of P2X7 expression. Our study provides new insights into the malignant progression caused by abnormal purinergic signaling.
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Affiliation(s)
- Wenli Feng
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Xiao Yang
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Lina Wang
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Rong Wang
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Feifei Yang
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Hao Wang
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Xiaoli Liu
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Qian Ren
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Yingchi Zhang
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Xiaofan Zhu
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
| | - Guoguang Zheng
- Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, China
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17
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Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression. J Dev Biol 2021; 9:jdb9010006. [PMID: 33546292 PMCID: PMC7931043 DOI: 10.3390/jdb9010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/23/2022] Open
Abstract
Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif HB1RE (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel HB1RE motif contributes to HOXB1 function in part through a repressive role in gene expression.
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18
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Gİrgİn B, KaradaĞ-Alpaslan M, KocabaŞ F. Oncogenic and tumor suppressor function of MEIS and associated factors. ACTA ACUST UNITED AC 2021; 44:328-355. [PMID: 33402862 PMCID: PMC7759197 DOI: 10.3906/biy-2006-25] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
MEIS proteins are historically associated with tumorigenesis, metastasis, and invasion in cancer. MEIS and associated PBX-HOX proteins may act as tumor suppressors or oncogenes in different cellular settings. Their expressions tend to be misregulated in various cancers. Bioinformatic analyses have suggested their upregulation in leukemia/lymphoma, thymoma, pancreas, glioma, and glioblastoma, and downregulation in cervical, uterine, rectum, and colon cancers. However, every cancer type includes, at least, a subtype with high MEIS expression. In addition, studies have highlighted that MEIS proteins and associated factors may function as diagnostic or therapeutic biomarkers for various diseases. Herein, MEIS proteins and associated factors in tumorigenesis are discussed with recent discoveries in addition to how they could be modulated by noncoding RNAs or newly developed small-molecule MEIS inhibitors.
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Affiliation(s)
- Birkan Gİrgİn
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
| | - Medine KaradaĞ-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun Turkey
| | - Fatih KocabaŞ
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
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19
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Jia Y, Bleicher F, Reboulet J, Merabet S. Bimolecular Fluorescence Complementation (BiFC) and Multiplexed Imaging of Protein-Protein Interactions in Human Living Cells. Methods Mol Biol 2021; 2350:173-190. [PMID: 34331286 DOI: 10.1007/978-1-0716-1593-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Deciphering protein-protein interactions (PPIs) in vivo is crucial to understand protein function. Bimolecular fluorescence complementation (BiFC) makes applicable the analysis of PPIs in many different native contexts, including human live cells. It relies on the property of monomeric fluorescent proteins to be reconstituted from two separate subfragments upon spatial proximity. Candidate partners fused to such complementary subfragments can form a fluorescent protein complex upon interaction, allowing visualization of weak and transient PPIs. It can also be applied for investigation of distinct PPIs at the same time using a multicolor setup. In this chapter, we provide a detailed protocol for analyzing PPIs by doing BiFC in cultured cells. Proof-of-principle experiments rely on the complementation property between the N-terminal fragment of mVenus (designated VN173) and the C-terminal fragment of mCerulean (designated CC155) and the partnership between HOXA7 and PBX1 proteins. This protocol is compatible with any other fluorescent complementation pair fragments and any type of candidate interacting proteins.
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Affiliation(s)
- Yunlong Jia
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Françoise Bleicher
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Jonathan Reboulet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France.
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20
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Bridoux L, Zarrineh P, Mallen J, Phuycharoen M, Latorre V, Ladam F, Losa M, Baker SM, Sagerstrom C, Mace KA, Rattray M, Bobola N. HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation. PLoS Genet 2020; 16:e1009162. [PMID: 33315856 PMCID: PMC7769617 DOI: 10.1371/journal.pgen.1009162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 12/28/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022] Open
Abstract
Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.
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Affiliation(s)
- Laure Bridoux
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Peyman Zarrineh
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Joshua Mallen
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Mike Phuycharoen
- Department of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Victor Latorre
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Frank Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusets, United States of America
| | - Marta Losa
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Syed Murtuza Baker
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Charles Sagerstrom
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusets, United States of America
| | - Kimberly A. Mace
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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21
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Singh NP, De Kumar B, Paulson A, Parrish ME, Zhang Y, Florens L, Conaway JW, Si K, Krumlauf R. A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. Genes Dev 2020; 34:1680-1696. [PMID: 33184220 PMCID: PMC7706710 DOI: 10.1101/gad.342329.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/09/2020] [Indexed: 01/19/2023]
Abstract
Gene duplication and divergence is a major driver in the emergence of evolutionary novelties. How variations in amino acid sequences lead to loss of ancestral activity and functional diversification of proteins is poorly understood. We used cross-species functional analysis of Drosophila Labial and its mouse HOX1 orthologs (HOXA1, HOXB1, and HOXD1) as a paradigm to address this issue. Mouse HOX1 proteins display low (30%) sequence similarity with Drosophila Labial. However, substituting endogenous Labial with the mouse proteins revealed that HOXA1 has retained essential ancestral functions of Labial, while HOXB1 and HOXD1 have diverged. Genome-wide analysis demonstrated similar DNA-binding patterns of HOXA1 and Labial in mouse cells, while HOXB1 binds to distinct targets. Compared with HOXB1, HOXA1 shows an enrichment in co-occupancy with PBX proteins on target sites and exists in the same complex with PBX on chromatin. Functional analysis of HOXA1-HOXB1 chimeric proteins uncovered a novel six-amino-acid C-terminal motif (CTM) flanking the homeodomain that serves as a major determinant of ancestral activity. In vitro DNA-binding experiments and structural prediction show that CTM provides an important domain for interaction of HOXA1 proteins with PBX. Our findings show that small changes outside of highly conserved DNA-binding regions can lead to profound changes in protein function.
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Affiliation(s)
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Molecular and Integrative Physiology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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22
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Duffraisse M, Paul R, Carnesecchi J, Hudry B, Banreti A, Reboulet J, Ajuria L, Lohmann I, Merabet S. Role of a versatile peptide motif controlling Hox nuclear export and autophagy in the Drosophila fat body. J Cell Sci 2020; 133:jcs241943. [PMID: 32878938 DOI: 10.1242/jcs.241943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Hox proteins are major regulators of embryonic development, acting in the nucleus to regulate the expression of their numerous downstream target genes. By analyzing deletion forms of the Drosophila Hox protein Ultrabithorax (Ubx), we identified the presence of an unconventional nuclear export signal (NES) that overlaps with a highly conserved motif originally described as mediating the interaction with the PBC proteins, a generic and crucial class of Hox transcriptional cofactors that act in development and cancer. We show that this unconventional NES is involved in the interaction with the major exportin protein CRM1 (also known as Embargoed in flies) in vivo and in vitro We find that this interaction is tightly regulated in the Drosophila fat body to control the autophagy-repressive activity of Ubx during larval development. The role of the PBC interaction motif as part of an unconventional NES was also uncovered in other Drosophila and human Hox proteins, highlighting the evolutionary conservation of this novel function. Together, our results reveal the extreme molecular versatility of a unique short peptide motif for controlling the context-dependent activity of Hox proteins both at transcriptional and non-transcriptional levels.
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Affiliation(s)
- Marilyne Duffraisse
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Rachel Paul
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Julie Carnesecchi
- Centre for Organismal Studies, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Bruno Hudry
- Institut de Biologie Valrose, Parc Valrose, 06108 Nice, France
| | - Agnes Banreti
- Institut de Biologie Valrose, Parc Valrose, 06108 Nice, France
| | - Jonathan Reboulet
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Leiore Ajuria
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
| | - Ingrid Lohmann
- Centre for Organismal Studies, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, ENS-Lyon, 32/34 Av. Tony Garnier, 69007 Lyon, France
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23
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Ao X, Ding W, Ge H, Zhang Y, Ding D, Liu Y. PBX1 is a valuable prognostic biomarker for patients with breast cancer. Exp Ther Med 2020; 20:385-394. [PMID: 32565927 PMCID: PMC7286203 DOI: 10.3892/etm.2020.8705] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pre-B-cell leukemia transcription factor (PBX) proteins have important roles in the development of numerous organs. To date, four members of the PBX family have been identified to be involved in human cancer but little is known about their expression patterns and precise functions in breast cancer (BC) progression. The aim of the present study was to determine whether they have the potential to be prognostic biomarkers in patients with BC. The expression patterns of PBXs were evaluated using Oncomine, Cancer Cell Line Encyclopedia and Gene expression-based Outcome for Breast cancer Online algorithm analyses. The prognostic value of PBX1 was determined by Kaplan-Meier plotter analysis. It was observed that, among all PBX family members, only PBX1 was significantly upregulated in BC vs. normal tissues. Meta-analysis in the Oncomine database revealed that PBX1 was significantly upregulated in invasive breast carcinoma stroma, ductal breast carcinoma, invasive lobular breast carcinoma, invasive mixed breast carcinoma and male breast carcinoma compared with normal tissues. In addition, PBX1 was significantly correlated with forkhead box protein A1. Subtype analysis indicated that PBX1 overexpression was associated with luminal-like and hormone receptor-sensitive subtypes. In the survival analysis, a high expression level of PBX1 was associated with poor prognosis of patients with estrogen receptor (ER)-positive, luminal A and luminal B subtypes of BC. The results of the present study indicate that PBX1 may serve as a specific biomarker and essential prognostic factor for ER-positive, luminal A and luminal B subtypes of BC.
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Affiliation(s)
- Xiang Ao
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Wei Ding
- Department of Comprehensive Internal Medicine, Affiliated Hospital, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Hu Ge
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China.,Department of Molecular Informatics, Hengrui Pharmaceutical Co., Ltd., Shanghai 200245, P.R. China
| | - Yuan Zhang
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Dan Ding
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Ying Liu
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
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24
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Du R, Shen W, Liu Y, Gao W, Zhou W, Li J, Zhao S, Chen C, Chen Y, Liu Y, Sun P, Xiang R, Shi Y, Luo Y. TGIF2 promotes the progression of lung adenocarcinoma by bridging EGFR/RAS/ERK signaling to cancer cell stemness. Signal Transduct Target Ther 2019; 4:60. [PMID: 31871777 PMCID: PMC6908606 DOI: 10.1038/s41392-019-0098-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
TGF-β-induced factor homeobox 2 (TGIF2) is a transcription regulator that plays essential roles in the regulation of development and cell fate decisions. Aberrant expression of TGIF family proteins has been observed in several cancers, including ovarian, esophageal, and colorectal cancers. Here, we report that TGIF2 mediates the EGFR-RAS-ERK signaling pathway to enhance the stemness of lung adenocarcinoma (LUAD) cells and, therefore, promote the progression and metastasis of LUAD. We found that high TGIF2 expression was closely correlated with tumor growth, lymph node metastasis, and survival of patients with LUAD. Mice bearing TGIF2-silenced H1299 xenografts developed smaller tumors and fewer lung metastases. Importantly, silencing TGIF2 decreased the cancer stem cell (CSC)-like properties in A549 and H1299 cells. Furthermore, we identified that TGIF2 binding to the OCT4 promoter promotes its expression. In both LUAD cells and in vivo LUAD mouse models, we revealed that EGFR-RAS-ERK signaling phosphorylated TGIF2 and increased its stability, which was important for TGIF2-promoted LUAD stemness since phosphorylation-deficient TGIF2 mutants lost these functions. Thus, our study revealed that an important factor, TGIF2, bridges EGFR signaling to the CSC characteristics of LUAD cells, which can be utilized as an effective target for LUAD therapy.
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Affiliation(s)
- Renle Du
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Wenzhi Shen
- Department of Pathology and Institute of Precision Medicine, Jining Medical University, Jining, 272067 China
| | - Yi Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Wenjuan Gao
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Wei Zhou
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Jun Li
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Shuangtao Zhao
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Chong Chen
- Department of Immunology, Institute of Basic Medical Science, Chinese Academy of Medical Science, School of Basic Medicine, Peking Union Medical College, Beijing, 100005 China
| | - Yanan Chen
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
- 2011 Project Collaborative Innovation Center for Biotherapy of Ministry of Education, Tianjin, 300071 China
- Tianjin Key Laboratory of Tumour Microenvironment and Neurovascular Regulation, Tianjin, 300071 China
| | - Yanhua Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
- 2011 Project Collaborative Innovation Center for Biotherapy of Ministry of Education, Tianjin, 300071 China
- Tianjin Key Laboratory of Tumour Microenvironment and Neurovascular Regulation, Tianjin, 300071 China
| | - Peiqing Sun
- Department of Cancer Biology, School of Medicine, Wake Forest University, Winston-Salem, NC 27157 USA
| | - Rong Xiang
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
- 2011 Project Collaborative Innovation Center for Biotherapy of Ministry of Education, Tianjin, 300071 China
- Tianjin Key Laboratory of Tumour Microenvironment and Neurovascular Regulation, Tianjin, 300071 China
| | - Yi Shi
- Department of Immunology, School of Medicine, Nankai University, Tianjin, 300071 China
- 2011 Project Collaborative Innovation Center for Biotherapy of Ministry of Education, Tianjin, 300071 China
- Tianjin Key Laboratory of Tumour Microenvironment and Neurovascular Regulation, Tianjin, 300071 China
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Science, Chinese Academy of Medical Science, School of Basic Medicine, Peking Union Medical College, Beijing, 100005 China
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25
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Schulte D, Geerts D. MEIS transcription factors in development and disease. Development 2019; 146:146/16/dev174706. [PMID: 31416930 DOI: 10.1242/dev.174706] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
MEIS transcription factors are key regulators of embryonic development and cancer. Research on MEIS genes in the embryo and in stem cell systems has revealed novel and surprising mechanisms by which these proteins control gene expression. This Primer summarizes recent findings about MEIS protein activity and regulation in development, and discusses new insights into the role of MEIS genes in disease, focusing on the pathogenesis of solid cancers.
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Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, 60528 Frankfurt, Germany
| | - Dirk Geerts
- Department of Medical Biology L2-109, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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26
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Porcelli D, Fischer B, Russell S, White R. Chromatin accessibility plays a key role in selective targeting of Hox proteins. Genome Biol 2019; 20:115. [PMID: 31159833 PMCID: PMC6547607 DOI: 10.1186/s13059-019-1721-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/21/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hox transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. While the different Hox family members show clear functional specificity in vivo, they all show similar binding specificity in vitro and a satisfactory understanding of in vivo Hox target selectivity is still lacking. RESULTS Using transient transfection in Kc167 cells, we systematically analyze the binding of all eight Drosophila Hox proteins. We find that Hox proteins show considerable binding selectivity in vivo even in the absence of canonical Hox cofactors Extradenticle and Homothorax. Hox binding selectivity is strongly associated with chromatin accessibility, being highest in less accessible chromatin. Individual Hox proteins exhibit different propensities to bind less accessible chromatin, and high binding selectivity is associated with high-affinity binding regions, leading to a model where Hox proteins derive binding selectivity through affinity-based competition with nucleosomes. Extradenticle/Homothorax cofactors generally facilitate Hox binding, promoting binding to regions in less accessible chromatin but with little effect on the overall selectivity of Hox targeting. These cofactors collaborate with Hox proteins in opening chromatin, in contrast to the pioneer factor, Glial cells missing, which facilitates Hox binding by independently generating accessible chromatin regions. CONCLUSIONS These studies indicate that chromatin accessibility plays a key role in Hox selectivity. We propose that relative chromatin accessibility provides a basis for subtle differences in binding specificity and affinity to generate significantly different sets of in vivo genomic targets for different Hox proteins.
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Affiliation(s)
- Damiano Porcelli
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QR UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QR UK
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
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27
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A Case of Identity: HOX Genes in Normal and Cancer Stem Cells. Cancers (Basel) 2019; 11:cancers11040512. [PMID: 30974862 PMCID: PMC6521190 DOI: 10.3390/cancers11040512] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/14/2022] Open
Abstract
Stem cells are undifferentiated cells that have the unique ability to self-renew and differentiate into many different cell types. Their function is controlled by core gene networks whose misregulation can result in aberrant stem cell function and defects of regeneration or neoplasia. HOX genes are master regulators of cell identity and cell fate during embryonic development. They play a crucial role in embryonic stem cell differentiation into specific lineages and their expression is maintained in adult stem cells along differentiation hierarchies. Aberrant HOX gene expression is found in several cancers where they can function as either oncogenes by sustaining cell proliferation or tumor-suppressor genes by controlling cell differentiation. Emerging evidence shows that abnormal expression of HOX genes is involved in the transformation of adult stem cells into cancer stem cells. Cancer stem cells have been identified in most malignancies and proved to be responsible for cancer initiation, recurrence, and metastasis. In this review, we consider the role of HOX genes in normal and cancer stem cells and discuss how the modulation of HOX gene function could lead to the development of novel therapeutic strategies that target cancer stem cells to halt tumor initiation, progression, and resistance to treatment.
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28
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The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors. Sci Rep 2019; 9:5664. [PMID: 30952900 PMCID: PMC6450960 DOI: 10.1038/s41598-019-42096-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/22/2019] [Indexed: 12/15/2022] Open
Abstract
HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, leading to a global dispensability of the HX motif for trimeric complex formation in the large majority of HOX proteins. In addition, it was shown that the anterior HOXB3 and central HOXA7 and HOXC8 proteins could use different alternative TALE interaction motifs, with or without the HX motif, depending on the DNA-binding site and cell context. Here we dissected the molecular interaction properties of the human posterior HOXA9 protein with its TALE cofactors, PBX1 and MEIS1. Analysis was performed on different DNA-binding sites in vitro and by doing Bimolecular Fluorescence Complementation (BiFC) in different cell lines. Notably, we observed that the HOXA9-TALE interaction relies consistently on the redundant activity of the HX motif and two paralog-specific residues of the HOXA9 HD. Together with previous work, our results show that HOX proteins interact with their generic TALE cofactors through various modalities, ranging from unique and context-independent to versatile and context-dependent TALE binding interfaces.
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29
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Selleri L, Zappavigna V, Ferretti E. 'Building a perfect body': control of vertebrate organogenesis by PBX-dependent regulatory networks. Genes Dev 2019; 33:258-275. [PMID: 30824532 PMCID: PMC6411007 DOI: 10.1101/gad.318774.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pbx genes encode transcription factors that belong to the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. We have witnessed a surge in information about the roles of this gene family as leading actors in the transcriptional control of development. PBX proteins represent a clear example of how transcription factors can regulate developmental processes by combinatorial properties, acting within multimeric complexes to implement activation or repression of transcription depending on their interaction partners. Here, we revisit long-emphasized functions of PBX transcription factors as cofactors for HOX proteins, major architects of the body plan. We further discuss new knowledge on roles of PBX proteins in different developmental contexts as upstream regulators of Hox genes-as factors that interact with non-HOX proteins and can work independently of HOX-as well as potential pioneer factors. Committed to building a perfect body, PBX proteins govern regulatory networks that direct essential morphogenetic processes and organogenesis in vertebrate development. Perturbations of PBX-dependent networks can cause human congenital disease and cancer.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, University of California at San Francisco, San Francisco, California 94143, USA.,Institute of Human Genetics, University of California at San Francisco, San Francisco, California 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Orofacial Sciences, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Anatomy, University of California at San Francisco, San Francisco, California 94143, USA
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elisabetta Ferretti
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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30
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Luo Z, Rhie SK, Farnham PJ. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel) 2019; 11:cancers11030323. [PMID: 30866492 PMCID: PMC6468460 DOI: 10.3390/cancers11030323] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
Homeobox genes (HOX) are a large family of transcription factors that direct the formation of many body structures during early embryonic development. There are 39 genes in the subgroup of homeobox genes that constitute the human HOX gene family. Correct embryonic development of flies and vertebrates is, in part, mediated by the unique and highly regulated expression pattern of the HOX genes. Disruptions in these fine-tuned regulatory mechanisms can lead to developmental problems and to human diseases such as cancer. Unfortunately, the molecular mechanisms of action of the HOX family of transcription factors are severely under-studied, likely due to idiosyncratic details of their structure, expression, and function. We suggest that a concerted and collaborative effort to identify interacting protein partners, produce genome-wide binding profiles, and develop HOX network inhibitors in a variety of human cell types will lead to a deeper understanding of human development and disease. Within, we review the technological challenges and possible approaches needed to achieve this goal.
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Affiliation(s)
- Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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31
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Dai BW, Yang ZM, Deng P, Chen YR, He ZJ, Yang X, Zhang S, Wu HJ, Ren ZH. HOXC10 promotes migration and invasion via the WNT-EMT signaling pathway in oral squamous cell carcinoma. J Cancer 2019; 10:4540-4551. [PMID: 31528218 PMCID: PMC6746115 DOI: 10.7150/jca.30645] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 06/11/2019] [Indexed: 12/25/2022] Open
Abstract
As a master regulator of embryonic morphogenesis, homeodomain-containing gene 10 (HOXC10) has been found to promote progression of human cancers and indicate poor survival outcome. Therefore, we concentrate on elucidating the role of HOXC10 in progression of oral squamous cell carcinoma (OSCC). In our study, the expression of HOXC10 was significantly increased in human OSCC samples and was significantly correlated with TNM stage and lymph node metastasis. Upregulation of HOXC10 indicated a poor overall survival of OSCC patients according to the Kaplan-Meier survival curves. Furthermore, HOXC10-knockdown dramatically suppressed migration, invasion, and expression of N-Cadherin, Vimentin and Snail, as well as increased E-cadherin level both in vivo and in vitro. Bioinformatics and cellular study further confirmed that HOXC10 may promote invasion and migration of OSCC cells by regulating the WNT/epithelial-mesenchymal transition (EMT) signaling pathway. These findings suggest that HOXC10 plays a pivotal role in the metastasis of OSCC and highlight its usefulness as a potential prognostic marker or therapeutic target in human OSCC.
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Affiliation(s)
- Bo-Wen Dai
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhi-Min Yang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ping Deng
- Department of Occupational Health, Third Military Medical University, Chongqing, China
| | - Yan-Rong Chen
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhi-Jing He
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xi Yang
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng Zhang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- ✉ Corresponding authors: Zhen-Hu Ren, Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. E-mail: Han-Jiang Wu, Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China. E-mail: Sheng Zhang, Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China. E-mail:
| | - Han-Jiang Wu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- ✉ Corresponding authors: Zhen-Hu Ren, Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. E-mail: Han-Jiang Wu, Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China. E-mail: Sheng Zhang, Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China. E-mail:
| | - Zhen-Hu Ren
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- ✉ Corresponding authors: Zhen-Hu Ren, Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. E-mail: Han-Jiang Wu, Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China. E-mail: Sheng Zhang, Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China. E-mail:
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32
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Phenotypic Nonspecificity as the Result of Limited Specificity of Transcription Factor Function. GENETICS RESEARCH INTERNATIONAL 2018; 2018:7089109. [PMID: 30510805 PMCID: PMC6230420 DOI: 10.1155/2018/7089109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/09/2018] [Indexed: 11/18/2022]
Abstract
Drosophila transcription factor (TF) function is phenotypically nonspecific. Phenotypic nonspecificity is defined as one phenotype being induced or rescued by multiple TFs. To explain this unexpected result, a hypothetical world of limited specificity is explored where all TFs have unique random distributions along the genome due to low information content of DNA sequence recognition and somewhat promiscuous cooperative interactions with other TFs. Transcription is an emergent property of these two conditions. From this model, explicit predictions are made. First, many more cases of TF nonspecificity are expected when examined. Second, the genetic analysis of regulatory sequences should uncover cis-element bypass and, third, genetic analysis of TF function should generally uncover differential pleiotropy. In addition, limited specificity provides evolutionary opportunity and explains the inefficiency of expression analysis in identifying genes required for biological processes.
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Saurin AJ, Delfini MC, Maurel-Zaffran C, Graba Y. The Generic Facet of Hox Protein Function. Trends Genet 2018; 34:941-953. [PMID: 30241969 DOI: 10.1016/j.tig.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/07/2018] [Accepted: 08/21/2018] [Indexed: 11/16/2022]
Abstract
Hox transcription factors are essential to promote morphological diversification of the animal body. A substantial number of studies have focused on how Hox proteins reach functional specificity, an issue that arises from the fact that these transcription factors control distinct developmental functions despite sharing similar molecular properties. In this review, we highlight that, besides specific functions, for which these transcription factors are renowned, Hox proteins also often have nonspecific functions. We next discuss some emerging principles of these generic functions and how they relate to specific functions and explore our current grasp of the underlying molecular mechanisms.
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Affiliation(s)
- Andrew J Saurin
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/.
| | - Marie Claire Delfini
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/
| | - Corinne Maurel-Zaffran
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/
| | - Yacine Graba
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/.
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