51
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Kim HM, Kang B, Park S, Park H, Kim C, Lee H, Yoo M, Kweon MN, Im SH, Kim T, Roh TY. Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions. Nucleic Acids Res 2023; 51:6143-6155. [PMID: 37158258 PMCID: PMC10325893 DOI: 10.1093/nar/gkad361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023] Open
Abstract
Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.
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Affiliation(s)
- Hyo-Min Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Sohyun Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyorim Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Chan Johng Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyeonji Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mijoung Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mi-Na Kweon
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
- ImmunoBiome, Inc., Pohang 37666, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
- Sysgenlab Inc., Pohang 37673, Republic of Korea
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52
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Ansari I, Solé-Boldo L, Ridnik M, Gutekunst J, Gilliam O, Korshko M, Liwinski T, Jickeli B, Weinberg-Corem N, Shoshkes-Carmel M, Pikarsky E, Elinav E, Lyko F, Bergman Y. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. Nat Commun 2023; 14:4005. [PMID: 37414790 PMCID: PMC10326054 DOI: 10.1038/s41467-023-39512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
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Affiliation(s)
- Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Meshi Ridnik
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Maria Korshko
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Timur Liwinski
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, Basel, Switzerland
| | - Birgit Jickeli
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noa Weinberg-Corem
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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53
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Sierra-Pagan JE, Dsouza N, Das S, Larson TA, Sorensen JR, Ma X, Stan P, Wanberg EJ, Shi X, Garry MG, Gong W, Garry DJ. FOXK1 regulates Wnt signalling to promote cardiogenesis. Cardiovasc Res 2023; 119:1728-1739. [PMID: 37036809 PMCID: PMC10325700 DOI: 10.1093/cvr/cvad054] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 04/11/2023] Open
Abstract
AIMS Congenital heart disease (CHD) is the most common genetic birth defect, which has considerable morbidity and mortality. We focused on deciphering key regulators that govern cardiac progenitors and cardiogenesis. FOXK1 is a forkhead/winged helix transcription factor known to regulate cell cycle kinetics and is restricted to mesodermal progenitors, somites, and heart. In the present study, we define an essential role for FOXK1 during cardiovascular development. METHODS AND RESULTS We used the mouse embryoid body system to differentiate control and Foxk1 KO embryonic stem cells into mesodermal, cardiac progenitor cells and mature cardiac cells. Using flow cytometry, immunohistochemistry, cardiac beating, transcriptional and chromatin immunoprecipitation quantitative polymerase chain reaction assays, bulk RNA sequencing (RNAseq) and assay for transposase-accessible chromatin using sequencing (ATACseq) analyses, FOXK1 was observed to be an important regulator of cardiogenesis. Flow cytometry analyses revealed perturbed cardiogenesis in Foxk1 KO embryoid bodies (EBs). Bulk RNAseq analysis at two developmental stages showed a significant reduction of the cardiac molecular program in Foxk1 KO EBs compared to the control EBs. ATACseq analysis during EB differentiation demonstrated that the chromatin landscape nearby known important regulators of cardiogenesis was significantly relaxed in control EBs compared to Foxk1 KO EBs. Furthermore, we demonstrated that in the absence of FOXK1, cardiac differentiation was markedly impaired by assaying for cardiac Troponin T expression and cardiac contractility. We demonstrate that FOXK1 is an important regulator of cardiogenesis by repressing the Wnt/β-catenin signalling pathway and thereby promoting differentiation. CONCLUSION These results identify FOXK1 as an essential transcriptional and epigenetic regulator of cardiovascular development. Mechanistically, FOXK1 represses Wnt signalling to promote the development of cardiac progenitor cells.
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Affiliation(s)
- Javier E Sierra-Pagan
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Nikita Dsouza
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Satyabrata Das
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Thijs A Larson
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Jacob R Sorensen
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Xiao Ma
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Patricia Stan
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Erik J Wanberg
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Xiaozhong Shi
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Mary G Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, 2001 6th Street SE Minneapolis, MN 55455, USA
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, 516 Delaware ST SE Minneapolis, MN 55455, USA
| | - Wuming Gong
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, 401 East River ParkwayVCRC 1st Floor, Suite 131 Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, 2001 6th Street SE Minneapolis, MN 55455, USA
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, 516 Delaware ST SE Minneapolis, MN 55455, USA
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54
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Tan C, Norden PR, Yu W, Liu T, Ujiie N, Lee SK, Yan X, Dyakiv Y, Aoto K, Ortega S, De Plaen IG, Sampath V, Kume T. Endothelial FOXC1 and FOXC2 promote intestinal regeneration after ischemia-reperfusion injury. EMBO Rep 2023; 24:e56030. [PMID: 37154714 PMCID: PMC10328078 DOI: 10.15252/embr.202256030] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Intestinal ischemia underlies several clinical conditions and can result in the loss of the intestinal mucosal barrier. Ischemia-induced damage to the intestinal epithelium is repaired by stimulation of intestinal stem cells (ISCs), and paracrine signaling from the vascular niche regulates intestinal regeneration. Here, we identify FOXC1 and FOXC2 as essential regulators of paracrine signaling in intestinal regeneration after ischemia-reperfusion (I/R) injury. Vascular endothelial cell (EC)- and lymphatic EC (LEC)-specific deletions of Foxc1, Foxc2, or both in mice worsen I/R-induced intestinal damage by causing defects in vascular regrowth, expression of chemokine CXCL12 and Wnt activator R-spondin 3 (RSPO3) in blood ECs (BECs) and LECs, respectively, and activation of Wnt signaling in ISCs. Both FOXC1 and FOXC2 directly bind to regulatory elements of the CXCL12 and RSPO3 loci in BECs and LECs, respectively. Treatment with CXCL12 and RSPO3 rescues the I/R-induced intestinal damage in EC- and LEC-Foxc mutant mice, respectively. This study provides evidence that FOXC1 and FOXC2 are required for intestinal regeneration by stimulating paracrine CXCL12 and Wnt signaling.
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Affiliation(s)
- Can Tan
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Pieter R Norden
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Wei Yu
- Division of Neonatology, Department of PediatricsChildren's Mercy HospitalKansas CityMOUSA
| | - Ting Liu
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Naoto Ujiie
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Sun Kyong Lee
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Xiaocai Yan
- Department of Pediatrics, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Yaryna Dyakiv
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Kazushi Aoto
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Sagrario Ortega
- Mouse Genome Editing Unit, Biotechnology ProgramSpanish National Cancer Research CentreMadridSpain
| | - Isabelle G De Plaen
- Department of Pediatrics, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Venkatesh Sampath
- Division of Neonatology, Department of PediatricsChildren's Mercy HospitalKansas CityMOUSA
| | - Tsutomu Kume
- Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
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Khan MA, Khan P, Ahmad A, Fatima M, Nasser MW. FOXM1: A small fox that makes more tracks for cancer progression and metastasis. Semin Cancer Biol 2023; 92:1-15. [PMID: 36958703 PMCID: PMC10199453 DOI: 10.1016/j.semcancer.2023.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/21/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
Transcription factors (TFs) are indispensable for the modulation of various signaling pathways associated with normal cell homeostasis and disease conditions. Among cancer-related TFs, FOXM1 is a critical molecule that regulates multiple aspects of cancer cells, including growth, metastasis, recurrence, and stem cell features. FOXM1 also impact the outcomes of targeted therapies, chemotherapies, and immune checkpoint inhibitors (ICIs) in various cancer types. Recent advances in cancer research strengthen the cancer-specific role of FOXM1, providing a rationale to target FOXM1 for developing targeted therapies. This review compiles the recent studies describing the pivotal role of FOXM1 in promoting metastasis of various cancer types. It also implicates the contribution of FOXM1 in the modulation of chemotherapeutic resistance, antitumor immune response/immunotherapies, and the potential of small molecule inhibitors of FOXM1.
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Affiliation(s)
- Md Arafat Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Aatiya Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mahek Fatima
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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56
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Imamura J, Ganguly S, Muskara A, Liao RS, Nguyen JK, Weight C, Wee CE, Gupta S, Mian OY. Lineage plasticity and treatment resistance in prostate cancer: the intersection of genetics, epigenetics, and evolution. Front Endocrinol (Lausanne) 2023; 14:1191311. [PMID: 37455903 PMCID: PMC10349394 DOI: 10.3389/fendo.2023.1191311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Androgen deprivation therapy is a cornerstone of treatment for advanced prostate cancer, and the development of castrate-resistant prostate cancer (CRPC) is the primary cause of prostate cancer-related mortality. While CRPC typically develops through a gain in androgen receptor (AR) signaling, a subset of CRPC will lose reliance on the AR. This process involves genetic, epigenetic, and hormonal changes that promote cellular plasticity, leading to AR-indifferent disease, with neuroendocrine prostate cancer (NEPC) being the quintessential example. NEPC is enriched following treatment with second-generation anti-androgens and exhibits resistance to endocrine therapy. Loss of RB1, TP53, and PTEN expression and MYCN and AURKA amplification appear to be key drivers for NEPC differentiation. Epigenetic modifications also play an important role in the transition to a neuroendocrine phenotype. DNA methylation of specific gene promoters can regulate lineage commitment and differentiation. Histone methylation can suppress AR expression and promote neuroendocrine-specific gene expression. Emerging data suggest that EZH2 is a key regulator of this epigenetic rewiring. Several mechanisms drive AR-dependent castration resistance, notably AR splice variant expression, expression of the adrenal-permissive 3βHSD1 allele, and glucocorticoid receptor expression. Aberrant epigenetic regulation also promotes radioresistance by altering the expression of DNA repair- and cell cycle-related genes. Novel therapies are currently being developed to target these diverse genetic, epigenetic, and hormonal mechanisms promoting lineage plasticity-driven NEPC.
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Affiliation(s)
- Jarrell Imamura
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Shinjini Ganguly
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Andrew Muskara
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Ross S. Liao
- Glickman Urologic Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Jane K. Nguyen
- Glickman Urologic Institute, Cleveland Clinic, Cleveland, OH, United States
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Christopher Weight
- Glickman Urologic Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Christopher E. Wee
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Shilpa Gupta
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Omar Y. Mian
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
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57
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Cooper BH, Dantas Machado AC, Gan Y, Aparicio O, Rohs R. DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors. Nucleic Acids Res 2023; 51:5621-5633. [PMID: 37177995 PMCID: PMC10287902 DOI: 10.1093/nar/gkad372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Quantifying the nucleotide preferences of DNA binding proteins is essential to understanding how transcription factors (TFs) interact with their targets in the genome. High-throughput in vitro binding assays have been used to identify the inherent DNA binding preferences of TFs in a controlled environment isolated from confounding factors such as genome accessibility, DNA methylation, and TF binding cooperativity. Unfortunately, many of the most common approaches for measuring binding preferences are not sensitive enough for the study of moderate-to-low affinity binding sites, and are unable to detect small-scale differences between closely related homologs. The Forkhead box (FOX) family of TFs is known to play a crucial role in regulating a variety of key processes from proliferation and development to tumor suppression and aging. By using the high-sequencing depth SELEX-seq approach to study all four FOX homologs in Saccharomyces cerevisiae, we have been able to precisely quantify the contribution and importance of nucleotide positions all along an extended binding site. Essential to this process was the alignment of our SELEX-seq reads to a set of candidate core sequences determined using a recently developed tool for the alignment of enriched k-mers and a newly developed approach for the reprioritization of candidate cores.
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Affiliation(s)
- Brendon H Cooper
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ana Carolina Dantas Machado
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Yan Gan
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Oscar M Aparicio
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Departments of Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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58
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Ranjitkar S, Shiri M, Sun J, Tian X. Intergenic transcription in in vivo developed bovine oocytes and pre-implantation embryos. RESEARCH SQUARE 2023:rs.3.rs-2934322. [PMID: 37293046 PMCID: PMC10246250 DOI: 10.21203/rs.3.rs-2934322/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Intergenic transcription, either failure to terminate at the transcription end site (TES), or transcription initiation at other intergenic regions, is present in cultured cells and enhanced in the presence of stressors such as viral infection. Transcription termination failure has not been characterized in natural biological samples such as pre-implantation embryos which express more than 10,000 genes and undergo drastic changes in DNA methylation. Results Using Automatic Readthrough Transcription Detection (ARTDeco) and data of in vivo developed bovine oocytes and embryos, we found abundant intergenic transcripts that we termed as read-outs (transcribed from 5 to 15 kb after TES) and read-ins (transcribed 1 kb up-stream of reference genes, extending up to 15 kb up-stream). Read-throughs (continued transcription from TES of expressed reference genes, 4-15 kb in length), however, were much fewer. For example, the numbers of read-outs and read-ins ranged from 3,084 to 6,565 or 33.36-66.67% of expressed reference genes at different stages of embryo development. The less copious read-throughs were at an average of 10% and significantly correlated with reference gene expression (P < 0.05). Interestingly, intergenic transcription did not seem to be random because many intergenic transcripts (1,504 read-outs, 1,045 read-ins, and 1,021 read-throughs) were associated with common reference genes across all stages of pre-implantation development. Their expression also seemed to be regulated by developmental stages because many were differentially expressed (log2 fold change ≥ 2, P < 0.05). Additionally, while gradual but un-patterned decreases in DNA methylation densities 10 kb both up- and down-stream of the intergenic transcribed regions were observed, the correlation between intergenic transcription and DNA methylation was insignificant. Finally, transcription factor binding motifs and polyadenylation signals were found in 27.2% and 12.15% of intergenic transcripts, respectively, suggesting considerable novel transcription initiation and RNA processing. Conclusion In summary, in vivo developed oocytes and pre-implantation embryos express large numbers of intergenic transcripts, which are not related to the overall DNA methylation profiles either up- or down-stream.
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Zhang Z, Li M, Sun T, Zhang Z, Liu C. FOXM1: Functional Roles of FOXM1 in Non-Malignant Diseases. Biomolecules 2023; 13:biom13050857. [PMID: 37238726 DOI: 10.3390/biom13050857] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Forkhead box (FOX) proteins are a wing-like helix family of transcription factors in the DNA-binding region. By mediating the activation and inhibition of transcription and interactions with all kinds of transcriptional co-regulators (MuvB complexes, STAT3, β-catenin, etc.), they play significant roles in carbohydrate and fat metabolism, biological aging and immune regulation, development, and diseases in mammals. Recent studies have focused on translating these essential findings into clinical applications in order to improve quality of life, investigating areas such as diabetes, inflammation, and pulmonary fibrosis, and increase human lifespan. Early studies have shown that forkhead box M1 (FOXM1) functions as a key gene in pathological processes in multiple diseases by regulating genes related to proliferation, the cell cycle, migration, and apoptosis and genes related to diagnosis, therapy, and injury repair. Although FOXM1 has long been studied in relation to human diseases, its role needs to be elaborated on. FOXM1 expression is involved in the development or repair of multiple diseases, including pulmonary fibrosis, pneumonia, diabetes, liver injury repair, adrenal lesions, vascular diseases, brain diseases, arthritis, myasthenia gravis, and psoriasis. The complex mechanisms involve multiple signaling pathways, such as WNT/β-catenin, STAT3/FOXM1/GLUT1, c-Myc/FOXM1, FOXM1/SIRT4/NF-κB, and FOXM1/SEMA3C/NRP2/Hedgehog. This paper reviews the key roles and functions of FOXM1 in kidney, vascular, lung, brain, bone, heart, skin, and blood vessel diseases to elucidate the role of FOXM1 in the development and progression of human non-malignant diseases and makes suggestions for further research.
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Affiliation(s)
- Zhenwang Zhang
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Mengxi Li
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, China
| | - Tian Sun
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
- Medical Research Institute, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Zhengrong Zhang
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
- Medical Research Institute, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
- Medical Research Institute, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
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Dec K, Alsaqati M, Morgan J, Deshpande S, Wood J, Hall J, Harwood AJ. A high ratio of linoleic acid (n-6 PUFA) to alpha-linolenic acid (n-3 PUFA) adversely affects early stage of human neuronal differentiation and electrophysiological activity of glutamatergic neurons in vitro. Front Cell Dev Biol 2023; 11:1166808. [PMID: 37255597 PMCID: PMC10225581 DOI: 10.3389/fcell.2023.1166808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/27/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction: There is a growing interest in the possibility of dietary supplementation with polyunsaturated fatty acids (PUFAs) for treatment and prevention of neurodevelopmental and neuropsychiatric disorders. Studies have suggested that of the two important classes of polyunsaturated fatty acids, omega-6 (n-6) and omega-3 (n-3), n-3 polyunsaturated fatty acids support brain development and function, and when used as a dietary supplement may have beneficial effects for maintenance of a healthy brain. However, to date epidemiological studies and clinical trials on children and adults have been inconclusive regarding treatment length, dosage and use of specific n-3 polyunsaturated fatty acids. The aim of this study is to generate a simplified in vitro cell-based model system to test how different n-6 to n-3 polyunsaturated fatty acids ratios affect human-derived neurons activity as a cellular correlate for brain function and to probe the mechanism of their action. Methods: All experiments were performed by use of human induced pluripotent stem cells (iPSCs). In this study, we examined the effect of different ratios of linoleic acid (n-6) to alpha-linolenic acid in cell growth medium on induced pluripotent stem cell proliferation, generation of neuronal precursors and electrophysiology of cortical glutamatergic neurons by multielectrode array (MEA) analysis. Results: This study shows that at a n-6:n-3 ratio of 5:1 polyunsaturated fatty acids induce stem cell proliferation, generating a large increase in number of cells after 72 h treatment; suppress generation of neuronal progenitor cells, as measured by decreased expression of FOXG1 and Nestin in neuronal precursor cells (NPC) after 20 days of development; and disrupt neuronal activity in vitro, increasing spontaneous neuronal firing, reducing synchronized bursting receptor subunits. We observed no significant differences for neuronal precursor cells treated with ratios 1:3 and 3:1, in comparison to 1:1 control ratio, but higher ratios of n-6 to n-3 polyunsaturated fatty acids adversely affect early stages of neuronal differentiation. Moreover, a 5:1 ratio in cortical glutamatergic neurons induce expression of GABA receptors which may explain the observed abnormal electrophysiological activity.
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Affiliation(s)
- Karolina Dec
- Neuroscience and Mental Health Innovation Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Mouhamed Alsaqati
- Neuroscience and Mental Health Innovation Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
- School of Pharmacy, Newcastle University, Newcastle Upon Tyne, England, United Kingdom
| | - Joanne Morgan
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Sumukh Deshpande
- School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Jamie Wood
- Neuroscience and Mental Health Innovation Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Jeremy Hall
- Neuroscience and Mental Health Innovation Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Adrian J. Harwood
- Neuroscience and Mental Health Innovation Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
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Moore XTR, Gheghiani L, Fu Z. The Role of Polo-Like Kinase 1 in Regulating the Forkhead Box Family Transcription Factors. Cells 2023; 12:cells12091344. [PMID: 37174744 PMCID: PMC10177174 DOI: 10.3390/cells12091344] [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: 03/28/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Polo-like kinase 1 (PLK1) is a serine/threonine kinase with more than 600 phosphorylation substrates through which it regulates many biological processes, including mitosis, apoptosis, metabolism, RNA processing, vesicle transport, and G2 DNA-damage checkpoint recovery, among others. Among the many PLK1 targets are members of the FOX family of transcription factors (FOX TFs), including FOXM1, FOXO1, FOXO3, and FOXK1. FOXM1 and FOXK1 have critical oncogenic roles in cancer through their antagonism of apoptotic signals and their promotion of cell proliferation, metastasis, angiogenesis, and therapeutic resistance. In contrast, FOXO1 and FOXO3 have been identified to have broad functions in maintaining cellular homeostasis. In this review, we discuss PLK1-mediated regulation of FOX TFs, highlighting the effects of PLK1 on the activity and stability of these proteins. In addition, we review the prognostic and clinical significance of these proteins in human cancers and, more importantly, the different approaches that have been used to disrupt PLK1 and FOX TF-mediated signaling networks. Furthermore, we discuss the therapeutic potential of targeting PLK1-regulated FOX TFs in human cancers.
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Affiliation(s)
- Xavier T R Moore
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Lilia Gheghiani
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Zheng Fu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
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Tomoshige K, Stuart WD, Fink-Baldauf IM, Ito M, Tsuchiya T, Nagayasu T, Yamatsuji T, Okada M, Fukazawa T, Guo M, Maeda Y. FOXA2 Cooperates with Mutant KRAS to Drive Invasive Mucinous Adenocarcinoma of the Lung. Cancer Res 2023; 83:1443-1458. [PMID: 37067057 PMCID: PMC10160002 DOI: 10.1158/0008-5472.can-22-2805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 04/18/2023]
Abstract
The endoderm-lineage transcription factor FOXA2 has been shown to inhibit lung tumorigenesis in in vitro and xenograft studies using lung cancer cell lines. However, FOXA2 expression in primary lung tumors does not correlate with an improved patient survival rate, and the functional role of FOXA2 in primary lung tumors remains elusive. To understand the role of FOXA2 in primary lung tumors in vivo, here, we conditionally induced the expression of FOXA2 along with either of the two major lung cancer oncogenes, EGFRL858R or KRASG12D, in the lung epithelium of transgenic mice. Notably, FOXA2 suppressed autochthonous lung tumor development driven by EGFRL858R, whereas FOXA2 promoted tumor growth driven by KRASG12D. Importantly, FOXA2 expression along with KRASG12D produced invasive mucinous adenocarcinoma (IMA) of the lung, a fatal mucus-producing lung cancer comprising approximately 5% of human lung cancer cases. In the mouse model in vivo and human lung cancer cells in vitro, FOXA2 activated a gene regulatory network involved in the key mucous transcription factor SPDEF and upregulated MUC5AC, whose expression is critical for inducing IMA. Coexpression of FOXA2 with mutant KRAS synergistically induced MUC5AC expression compared with that induced by FOXA2 alone. ChIP-seq combined with CRISPR interference indicated that FOXA2 bound directly to the enhancer region of MUC5AC and induced the H3K27ac enhancer mark. Furthermore, FOXA2 was found to be highly expressed in primary tumors of human IMA. Collectively, this study reveals that FOXA2 is not only a biomarker but also a driver for IMA in the presence of a KRAS mutation. SIGNIFICANCE FOXA2 expression combined with mutant KRAS drives invasive mucinous adenocarcinoma of the lung by synergistically promoting a mucous transcriptional program, suggesting strategies for targeting this lung cancer type that lacks effective therapies.
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Affiliation(s)
- Koichi Tomoshige
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - William D. Stuart
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Iris M. Fink-Baldauf
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Masaoki Ito
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tomoshi Tsuchiya
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Nagayasu
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoki Yamatsuji
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takuya Fukazawa
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yutaka Maeda
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Niu XJ, Sun YH, Wang LJ, Huang YY, Wang Y, Guo XQ, Xu BH, Wang C. Fox transcription factor AccGRF1 in response to glyphosate stress in Apis cerana cerana. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 192:105419. [PMID: 37105625 DOI: 10.1016/j.pestbp.2023.105419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/23/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Glyphosate is an herbicide commonly used in agriculture, and its widespread use has adversely affected the survival of nontarget organisms. Among these organisms, bees in particular are important pollinators, and declining bee populations have severely affected crop yields around the world. However, the molecular mechanism by which glyphosate harms bees remains unclear. In our experiment, we screened and cloned a glyphosate-induced gene in Apis cerana cerana (A. c. cerana) and named glyphosate response factor 1 (AccGRF1). Sequence analysis showed that AccGRF1 contains a winged-helix DNA binding domain, which suggests that it belongs to the Forkhead box (Fox) protein family. qRT-PCR and heterologous expression in Escherichia coli and yeast showed that AccGRF1 can respond to glyphosate and oxidative stress. After AccGRF1 knockdown by means of RNA interference (RNAi), the resistance of A. c. cerana to glyphosate stress improved. The results suggested that AccGRF1 is involved in A. c. cerana glyphosate stress tolerance. This study reveals the functions of Fox transcription factors in response to glyphosate stress and provides molecular insights into the regulation of glyphosate responses in honeybees.
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Affiliation(s)
- Xiao-Jing Niu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yun-Hao Sun
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Li-Jun Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yuan-Yuan Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Xing-Qi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Bao-Hua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian 271018, Shandong, China.
| | - Chen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China.
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Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SA, Shah SF, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MC, Novelli A, Magliozzi M, Fadda MT, Streff H, Machol K, Lewis RA, Zoete V, Squeo GM, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang YB, Antonarakis SE. FOXI3 pathogenic variants cause one form of craniofacial microsomia. Nat Commun 2023; 14:2026. [PMID: 37041148 PMCID: PMC10090152 DOI: 10.1038/s41467-023-37703-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.
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Affiliation(s)
- Ke Mao
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Jules-Gonin Eye Hospital, Department of Ophthalmology, University of Lausanne, 1004, Lausanne, Switzerland
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Bingqing Wang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Xiaopeng Xu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Qiang Li
- Department of Plastic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Hao Zhu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Qi Chen
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Fujun Jin
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Harinarayana Ankamreddy
- Department of Biotechnology, School of Bioengineering, SRMIST, Kattankulathur, Tamilnadu, 603203, India
| | - Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongyuan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaogang Wang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Peiwei Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Sohail Aziz Paracha
- Anatomy Department, Khyber Medical University Institute of Medical Sciences (KIMS), Kohat, Pakistan
| | - Syed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences (KIMS), DHQ Hospital KDA, Kohat, Pakistan
| | - Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Daniela Melis
- Department of Medicine, Surgery, and Dentistry, Università University degli of Studi di Salerno, Salerno, Italy
| | - Bruno Dallapiccola
- Medical Genetics and Rare Disease Research Division, Pediatric Cardiology, Medical Genetics Laboratory, Neuropsychiatry, Scientific Rectorate, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Monia Magliozzi
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Maria Teresa Fadda
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges, 1066, Switzerland
| | - Gabriella Maria Squeo
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Giorgia Mancano
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Giulia Gori
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Milena Mariani
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Stavroula Psoni
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Helen Fryssira
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sandrine Marlin
- Centre de Référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Shouqin Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Timothy C Cox
- Departments of Oral & Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Andrew K Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qingguo Zhang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China.
| | - Yong-Biao Zhang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland.
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland.
- iGE3 Institute of Genetics and Genomes in Geneva, Geneva, Switzerland.
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65
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Moparthi L, Koch S. FOX transcription factors are common regulators of Wnt/β-catenin-dependent gene transcription. J Biol Chem 2023; 299:104667. [PMID: 37011861 DOI: 10.1016/j.jbc.2023.104667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/16/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The Wnt/β-catenin pathway is a critical regulator of development and stem cell maintenance. Mounting evidence suggests that the outcome of Wnt signaling is determined by the collaborative action of multiple transcription factors, including members of the highly conserved forkhead box (FOX) protein family. However, the contribution of FOX transcription factors to Wnt signaling has not been investigated in a systematic manner. Here, we performed complementary screens of all 44 human FOX proteins to identify new Wnt pathway regulators. By combining β-catenin reporter assays with Wnt pathway-focused qPCR arrays and proximity proteomics of selected candidates, we determine that most FOX proteins are involved in the regulation of Wnt pathway activity. As proof-of-principle, we additionally characterize class D and I FOX transcription factors as physiologically relevant regulators of Wnt/β-catenin signaling. We conclude that FOX proteins are common regulators of the Wnt/β-catenin-dependent gene transcription that may control Wnt pathway activity in a tissue-specific manner.
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66
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Jiang W, Li Y, Li R, Chen W, Song M, Zhang Q, Chen S. The Prognostic Significance of FOXD1 Expression in Head and Neck Squamous Cell Carcinoma. J Pers Med 2023; 13:jpm13030530. [PMID: 36983712 PMCID: PMC10053205 DOI: 10.3390/jpm13030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
It has been reported that forkhead box D1 (FOXD1) plays an established role in human early embryonic development and is broadly involved in various malignancies. However, there is limited information regarding FOXD1 expression in head and neck squamous cell carcinoma (HNSCC). This present study aimed to explore the clinical significance of FOXD1 in patients with HNSCC. Tissue microarrays of 334 primary HNSCC patients who underwent surgery between 2008 and 2010 at Sun Yat-sen University Cancer Center were investigated by immunohistochemistry regarding FOXD1 expression. χ2 test was used to estimate the relationship of FOXD1 expression with clinicopathologic characteristics. Univariate and multivariate analyses were performed to identify FOXD1 expression as an independent prognostic indicator of overall survival (OS) and disease-free survival (DFS). FOXD1 expression is closely associated with postoperative recurrence. HNSCC patients with high FOXD1 expression have poorer prognoses than the low-expression group (p < 0.05). According to multivariate analysis, FOXD1 was an independent prognostic factor for OS and DFS. The results revealed that FOXD1 could be a prognostic factor for HNSCC and might serve as a potential target for novel therapies.
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67
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Rani M, Kumari R, Singh SP, Devi A, Bansal P, Siddiqi A, Alsahli MA, Almatroodi SA, Rahmani AH, Rizvi MMA. MicroRNAs as master regulators of FOXO transcription factors in cancer management. Life Sci 2023; 321:121535. [PMID: 36906255 DOI: 10.1016/j.lfs.2023.121535] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023]
Abstract
MicroRNAs are critical regulators of the plethora of genes, including FOXO "forkhead" dependent transcription factors, which are bonafide tumour suppressors. The FOXO family members modulate a hub of cellular processes like apoptosis, cell cycle arrest, differentiation, ROS detoxification, and longevity. Aberrant expression of FOXOs in human cancers has been observed due to their down-regulation by diverse microRNAs, which are predominantly involved in tumour initiation, chemo-resistance and tumour progression. Chemo-resistance is a major obstacle in cancer treatment. Over 90% of casualties in cancer patients are reportedly associated with chemo-resistance. Here, we have primarily discussed the structure, functions of FOXO and also their post-translational modifications which influence the activities of these FOXO family members. Further, we have addressed the role of microRNAs in carcinogenesis by regulating the FOXOs at post-transcriptional level. Therefore, microRNAs-FOXO axis can be exploited as a novel cancer therapy. The administration of microRNA-based cancer therapy is likely to be beneficial to curb chemo-resistance in cancers.
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Affiliation(s)
- Madhu Rani
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rashmi Kumari
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shashi Prakash Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; Centre for Pharmacology and Therapeutics, Rosewell Park Comprehensive Care Centre, 665 Elm Street, Buffalo, NY, USA 14203
| | - Annu Devi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Preeti Bansal
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Aisha Siddiqi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Buraydah 51452, Saudi Arabia
| | - Saleh A Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Buraydah 51452, Saudi Arabia
| | - M Moshahid Alam Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Baker P, Barkan E, Bertagnolli D, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, Dolbeare T, Ellingwood L, Gee J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Jin K, Kroll M, Lathia K, Leon A, Long B, Maltzer Z, Martin N, McCue R, Meyerdierks E, Nguyen TN, Pham T, Rimorin C, Ruiz A, Shapovalova N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Cuevas NV, Wadhwani K, Ward K, Levi B, Farrell C, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith KA, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531121. [PMID: 37034735 PMCID: PMC10081189 DOI: 10.1101/2023.03.06.531121] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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69
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Rehman S, Hadj-Moussa H, Hawkins L, Storey KB. Role of FOXO transcription factors in the tolerance of whole-body freezing in the wood frog, Rana sylvatica. Cryobiology 2023; 110:44-48. [PMID: 36539050 DOI: 10.1016/j.cryobiol.2022.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The wood frog (Rana Sylvatica) can endure the sub-zero temperatures of winter by freezing up to 65% of total body water as extracellular ice and retreating into a prolonged hypometabolic state. Freeze survival requires the coordination of various adaptations, including a global suppression of metabolic functions and select activation of pro-survival genes. Transcription factors playing roles in metabolism, stress tolerance, and cell proliferation may assist in making survival in a frozen state possible. In this study, the role of Forkhead box 'other' (FOXO) transcription factors in freeze tolerance, and related changes to the insulin pathway, are investigated. Immunoblotting was used to assess total and phosphorylated amounts of FOXO proteins in wood frogs subjected to freezing for 24 h and thawed recovery for 8 h. Levels of active FOXO3 increased in brain, kidney, and liver during freezing and thawing, suggesting a need to maintain or enhance antioxidant defenses under these stresses. Results implicate FOXO involvement in the metabolic regulation of natural freeze tolerance.
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Affiliation(s)
- Saif Rehman
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Hanane Hadj-Moussa
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Liam Hawkins
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada.
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70
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Wong YF, Kumar Y, Proks M, Herrera JAR, Rothová MM, Monteiro RS, Pozzi S, Jennings RE, Hanley NA, Bickmore WA, Brickman JM. Expansion of ventral foregut is linked to changes in the enhancer landscape for organ-specific differentiation. Nat Cell Biol 2023; 25:481-492. [PMID: 36690849 PMCID: PMC10014581 DOI: 10.1038/s41556-022-01075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Cell proliferation is fundamental for almost all stages of development and differentiation that require an increase in cell number. Although cell cycle phase has been associated with differentiation, the actual process of proliferation has not been considered as having a specific role. Here we exploit human embryonic stem cell-derived endodermal progenitors that we find are an in vitro model for the ventral foregut. These cells exhibit expansion-dependent increases in differentiation efficiency to pancreatic progenitors that are linked to organ-specific enhancer priming at the level of chromatin accessibility and the decommissioning of lineage-inappropriate enhancers. Our findings suggest that cell proliferation in embryonic development is about more than tissue expansion; it is required to ensure equilibration of gene regulatory networks allowing cells to become primed for future differentiation. Expansion of lineage-specific intermediates may therefore be an important step in achieving high-fidelity in vitro differentiation.
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Affiliation(s)
- Yan Fung Wong
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Yatendra Kumar
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Jose Alejandro Romero Herrera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Michaela Mrugala Rothová
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rita S Monteiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rachel E Jennings
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil A Hanley
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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71
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Li J, Gao L, Wang A, Qian H, Zhu J, Ji S, Chen J, Liu Z, Ji C. Forkhead box L2 is a target of miR-133b and plays an important role in the pathogenesis of non-small cell lung cancer. Cancer Med 2023; 12:9826-9842. [PMID: 36846934 PMCID: PMC10166978 DOI: 10.1002/cam4.5746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/21/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Forkhead box L2 (FOXL2) has been recognized as a transcription factor in the progression of many malignancies, but its role in non-small cell lung cancer (NSCLC) remains unclear. This research clarified on the role of FOXL2 and the specific molecular mechanism in NSCLC. METHODS RNA and protein levels were detected by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting assays. Cell proliferation was examined by cell counting kit-8 (CCK-8) and clonogenic assays. Transwell and wound healing assays were used to detect cell invasion and migration. Cell cycle alterations were assessed by flow cytometry. The relationship between FOXL2 and miR-133b was verified by dual-luciferase reporter assays. In vivo metastasis was monitored in the tail vein-injected mice. RESULTS FOXL2 was upregulated in NSCLC cells and tissues. Downregulation of FOXL2 restrained cell proliferation, migration, and invasion and arrested the cell cycle of NSCLC cells. Moreover, FOXL2 promoted the epithelial-mesenchymal transition (EMT) process of NSCLC cells by inducing the transforming growth factor-β (TGF-β)/Smad signaling pathway. miR-133b directly targeted the 3'-UTR of FOXL2 and negatively regulated FOXL2 expression. Knockdown of FOXL2 blocked metastasis in vivo. CONCLUSIONS miR-133b downregulates FOXL2 by targeting the 3'-UTR of FOXL2, thereby inhibiting cell proliferation, EMT and metastasis induced by the TGF-β/Smad signaling pathway in NSCLC. FOXL2 may be a potential molecular target for treating NSCLC.
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Affiliation(s)
- Juan Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China.,Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Lirong Gao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China
| | - Anqi Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China
| | - Huiwen Qian
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianjie Zhu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China.,Institute of Respiratory Diseases, Soochow University, Suzhou, China
| | - Shundong Ji
- Jiangsu Institute of Hematology, MOH Key Laboratory of Thrombosis and Hemostasis, Collaborative Innovation Center of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zeyi Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China.,Institute of Respiratory Diseases, Soochow University, Suzhou, China
| | - Cheng Ji
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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72
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Ismailova A, Salehi-Tabar R, Dimitrov V, Memari B, Barbier C, White JH. Identification of a forkhead box protein transcriptional network induced in human neutrophils in response to inflammatory stimuli. Front Immunol 2023; 14:1123344. [PMID: 36756115 PMCID: PMC9900176 DOI: 10.3389/fimmu.2023.1123344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023] Open
Abstract
Introduction Neutrophils represent the largest proportion of circulating leukocytes and, in response to inflammatory stimuli, are rapidly recruited to sites of infection where they neutralize pathogens. Methods and results We have identified a novel neutrophil transcription network induced in response to inflammatory stimuli. We performed the first RNAseq analysis of human neutrophils exposed to lipopolysaccharide (LPS), followed by a meta-analysis of our dataset and previously published studies of LPS-challenged neutrophils. This revealed a robustly enhanced transcriptional network driven by forkhead box (FOX) transcription factors. The network is enriched in genes encoding proinflammatory cytokines and transcription factors, including MAFF and ATF3, which are implicated in responses to stress, survival and inflammation. Expression of transcription factors FOXP1 and FOXP4 is induced in neutrophils exposed to inflammatory stimuli, and potential FOXP1/FOXP4 binding sites were identified in several genes in the network, all located in chromatin regions consistent with neutrophil enhancer function. Chromatin immunoprecipitation (ChIP) assays in neutrophils confirmed enhanced binding of FOXP4, but not FOXP1, to multiple sites in response to LPS. Binding to numerous motifs and transactivation of network genes were also observed when FOXP proteins were transiently expressed in HEK293 cells. In addition to LPS, the transcriptional network is induced by other inflammatory stimuli, indicating it represents a general neutrophil response to inflammation. Discussion Collectively, these findings reveal a role for the FOXP4 transcription network as a regulator of responses to inflammatory stimuli in neutrophils.
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Affiliation(s)
- Aiten Ismailova
- Department of Physiology, McGill University, Montreal, QC, Canada
| | | | - Vassil Dimitrov
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Babak Memari
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Camille Barbier
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - John H. White
- Department of Physiology, McGill University, Montreal, QC, Canada,Department of Medicine, McGill University, Montreal, QC, Canada,*Correspondence: John H. White,
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73
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Chang R, Zhang Y, Sun J, Xu K, Li C, Zhang J, Mei W, Zhang H, Zhang J. Maternal pre-pregnancy body mass index and offspring with overweight/obesity at preschool age: The possible role of epigenome-wide DNA methylation changes in cord blood. Pediatr Obes 2023; 18:e12969. [PMID: 36102013 DOI: 10.1111/ijpo.12969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Epigenome-wide association studies have identified some DNA methylation sites associated with body mass index (BMI) or obesity. Studies in the Asian population are lacking. OBJECTIVE To examine the association of cord blood genome-wide DNA methylation (GWDm) changes with maternal pre-pregnancy BMI and children's BMI-z score at preschool age. Additionally, we also explored the genome-wide differentially methylated regions and differentially methylated probes between preschoolers with overweight/obesity and normal-weight counterparts. METHODS This two-stage study design included (1) a GWDm analysis of 30 mother-child pairs from 633 participants of the Zhuhai birth cohort with data on newborn cord blood, maternal pre-pregnancy BMI, and children's BMI at 3 years of age; and (2) a targeted validation analysis of the cord blood of ten children with overweight/obesity and ten matched controls to validate the CpG sites. RESULTS In the first stage, no significant CpG sites were found to be associated with children's BMI-z score at preschool age after FDR correction with the p-values of the CpG sites in FOXN3 (cg23501836) and ZNF264 (cg27437574) being close to 1 × 10-6 . In the second stage, a significant difference of CpG sites in AHRR (chr5:355067-355068) and FOXN3 (chr14: 89630264-89630272 and chr14: 89630387-89630388) was found between the ten children with overweight/obesity and ten controls (p < 0.05). The CpG sites in FOXN3 (chr14:89630264-89630272 and chr14:89630295-89630296) and ZNF264 (chr19: 57703104-57703107 and chr19: 57703301-57703307) were associated with children's BMI-z score; and the CpG sites in FOXN3 (chr14: 89630264-89630272 and chr14: 89630387-89630388) were associated with maternal pre-pregnancy BMI. CONCLUSIONS DNA methylation in FOXN3 and AHRR is associated with overweight/obesity in preschool-aged children, and the methylation in FOXN3 and ZNF264 might be associated with children's BMI-z score. FOXN3 methylation may be associated with maternal pre-pregnancy BMI, suggesting its potential role in the children's BMI-z score or overweight/obesity. Our results provide novel insights into the mechanisms of children's obesity.
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Affiliation(s)
- Ruixia Chang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Sun
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Xu
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunan Li
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingli Zhang
- Traditional Chinese Medicine Hospital, Zhuhai, Guangdong, China
| | - Wenhua Mei
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
| | - Hongzhong Zhang
- Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China
| | - Jianduan Zhang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Role of FOXO3a Transcription Factor in the Regulation of Liver Oxidative Injury. Antioxidants (Basel) 2022; 11:antiox11122478. [PMID: 36552685 PMCID: PMC9774119 DOI: 10.3390/antiox11122478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Oxidative stress has been identified as a key mechanism in liver damage caused by various chemicals. The transcription factor FOXO3a has emerged as a critical regulator of redox imbalance. Multiple post-translational changes and epigenetic processes closely regulate the activity of FOXO3a, resulting in synergistic or competing impacts on its subcellular localization, stability, protein-protein interactions, DNA binding affinity, and transcriptional programs. Depending on the chemical nature and subcellular context, the oxidative-stress-mediated activation of FOXO3a can induce multiple transcriptional programs that play crucial roles in oxidative injury to the liver by chemicals. Here, we mainly review the role of FOXO3a in coordinating programs of genes that are essential for cellular homeostasis, with an emphasis on exploring the regulatory mechanisms and potential application of FOXO3a as a therapeutic target to prevent and treat liver oxidative injury.
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75
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Liao L, Yao Z, Kong J, Zhang X, Li H, Chen W, Xie Q. Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo. BMC Genomics 2022; 23:825. [PMID: 36513979 PMCID: PMC9746114 DOI: 10.1186/s12864-022-09054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo. RESULTS In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified. CONCLUSION Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
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Affiliation(s)
- Liqin Liao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Ziqi Yao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China
| | - Jie Kong
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Xinheng Zhang
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Hongxin Li
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Weiguo Chen
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Qingmei Xie
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
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76
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Czerny CC, Borschel A, Cai M, Otto M, Hoyer-Fender S. FOXA1 is a transcriptional activator of Odf2/Cenexin and regulates primary ciliation. Sci Rep 2022; 12:21468. [PMID: 36509813 PMCID: PMC9744847 DOI: 10.1038/s41598-022-25966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Primary cilia are sensory organelles essential for embryonic and postnatal development, and tissue homeostasis in adulthood. They are generated in a cell cycle-dependent manner and found on most cells of the body. Although cilia formation is intensively investigated virtually nothing is known about the transcriptional regulation of primary ciliation. We used here Odf2/Cenexin, encoding a protein of the mother centriole and the basal body that is mandatory for primary cilia formation, as the target gene for the identification of transcriptional activators. We identified a consensus binding site for Fox transcription factors (TFs) in its promoter region and focused here on the Fox family. We found transcriptional activation of Odf2 neither by FOXO TFs nor by the core TF for multiciliation, FOXJ1. However, we identified FOXA1 as a transcriptional activator of Odf2 by reporter gene assays and qRT-PCR, and showed by qWB that Foxa1 knockdown caused a decrease in ODF2 and CP110 proteins. We verified the binding sequence of FOXA1 in the Odf2 promoter by ChIP. Finally, we demonstrated that knockdown of FOXA1 affected primary cilia formation. We, thus, showed for the first time, that FOXA1 regulates primary ciliation by transcriptional activation of ciliary genes.
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Affiliation(s)
- Christian Carl Czerny
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Anett Borschel
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Mingfang Cai
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Madeline Otto
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany ,grid.424957.90000 0004 0624 9165Present Address: Thermo Fisher Scientific GENEART, Regensburg, Germany
| | - Sigrid Hoyer-Fender
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
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77
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Singh A, Rajeevan A, Gopalan V, Agrawal P, Day CP, Hannenhalli S. Broad misappropriation of developmental splicing profile by cancer in multiple organs. Nat Commun 2022; 13:7664. [PMID: 36509773 PMCID: PMC9744839 DOI: 10.1038/s41467-022-35322-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Oncogenesis mimics key aspects of embryonic development. However, the underlying mechanisms are incompletely understood. Here, we demonstrate that the splicing events specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. Such events are associated with key oncogenic processes and predict proliferation rates in cancer cell lines as well as patient survival. Such events preferentially target nitrosylation and transmembrane-region domains, whose coordinated splicing in multiple genes respectively affect intracellular transport and N-linked glycosylation. We infer critical splicing factors potentially regulating embryonic splicing events and show that such factors are potential oncogenic drivers and are upregulated specifically in malignant cells. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of critical splicing factors in brain and liver. Our study provides a comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest anti-cancer targets including splicing events, and their upstream splicing and transcriptional regulators.
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Affiliation(s)
- Arashdeep Singh
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Arati Rajeevan
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Vishaka Gopalan
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Piyush Agrawal
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Chi-Ping Day
- grid.94365.3d0000 0001 2297 5165Laboratory of Cancer Biology and Genetics National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Sridhar Hannenhalli
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
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78
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Using Dextran Instead of Egg Yolk in Extender for Cryopreservation of Spermatozoa of Dogs of Different Ages. Animals (Basel) 2022; 12:ani12243480. [PMID: 36552399 PMCID: PMC9774612 DOI: 10.3390/ani12243480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Egg yolk is a very common supplement of extenders aimed to protect sperm from cryoinjury, but due to their biological risks and difficulties with media standardization, there is a search for alternative. In addition, sperm cryoresistance can be affected by the initial decrease of their functional characteristics caused by age. The aim of this work was to evaluate the efficiency of using dextran (molecular weight 500 kDa) in the extenders instead of egg yolk for the cryopreservation of spermatozoa of dogs (Chinese Crested breed) of different ages. The obtained ejaculates were divided into three groups depending on the animal's age: 1-3, 4-6 and 7-10 years old. Sperm was cryopreserved by using 7% glycerol and 20% egg yolk, or 20% dextran. The cryoresistance of spermatozoa of the oldest age category was dramatically decreased, which was manifested in their morphology, motility, and DNA fragmentation rate. There were no differences between the cryoprotectant effect of the dextran-based extender on spermatozoa and the egg yolk-based extender in all age categories of dogs. However, given the benefits of dextran-containing media, its use for the cryopreservation of canine spermatozoa has potential benefits that need to be confirmed by sperm fertilization outcomes.
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79
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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80
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Zangouei AS, Tolue Ghasaban F, Dalili A, Akhlaghipour I, Moghbeli M. MicroRNAs as the pivotal regulators of Forkhead box protein family during gastrointestinal tumor progression and metastasis. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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81
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Zhou J, Yang YJ, Gan RH, Wang Y, Li Z, Zhang XJ, Gui JF, Zhou L. Foxl2a and Foxl2b are involved in midbrain-hindbrain boundary development in zebrafish. Gene Expr Patterns 2022; 46:119286. [PMID: 36341978 DOI: 10.1016/j.gep.2022.119286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/23/2022] [Accepted: 10/24/2022] [Indexed: 11/04/2022]
Abstract
Foxl2 plays conserved central function in ovarian differentiation and maintenance in several fish species. However, its expression pattern and function in fish embryogenesis are still largely unknown. In this study, we first presented a sequential expression pattern of zebrafish foxl2a and foxl2b during embryo development. They were predominantly expressed in the cranial paraxial mesoderm (CPM) and cranial venous vasculature (CVV) during somitogenesis and subsequently expressed in the pharyngeal arches after 48 h post-fertilization (hpf). Then, we compared the brain structures among zebrafish wildtype (WT) and three homozygous foxl2 mutants (foxl2a-/-, foxl2b-/- and foxl2a-/-;foxl2b-/-) and found the reduction of the fourth ventricle in the three foxl2 mutants, especially in foxl2a-/-;foxl2b-/- mutant. Finally, we detected several key transcription factors involved in the gene regulatory network of midbrain-hindbrain boundary (MHB) patterning, such as wnt1, en1b and pax2a. Their expression levels were obviously downregulated in MHB of foxl2a-/- and foxl2a-/-;foxl2b-/- mutants. Thus, we suggest that Foxl2a and Foxl2b are involved in MHB and the fourth ventricle development in zebrafish. The current study provides insights into the molecular mechanism underlying development of brain ventricular system.
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Affiliation(s)
- Jian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Jing Yang
- College of Fisheries, Tianjin Agricultural University, China
| | - Rui-Hai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
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82
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Sher G, Masoodi T, Patil K, Akhtar S, Kuttikrishnan S, Ahmad A, Uddin S. Dysregulated FOXM1 signaling in the regulation of cancer stem cells. Semin Cancer Biol 2022; 86:107-121. [PMID: 35931301 DOI: 10.1016/j.semcancer.2022.07.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 07/31/2022] [Indexed: 01/27/2023]
Abstract
Since the introduction of the cancer stem cell (CSC) paradigm, significant advances have been made in understanding the functional and biological plasticity of these elusive components in malignancies. Endowed with self-renewing abilities and multilineage differentiation potential, CSCs have emerged as cellular drivers of virtually all facets of tumor biology, including metastasis, tumor recurrence/relapse, and drug resistance. The functional and biological characteristics of CSCs, such as self-renewal, cell fate decisions, survival, proliferation, and differentiation are regulated by an array of extracellular factors, signaling pathways, and pluripotent transcriptional factors. Besides the well-characterized regulatory role of transcription factors OCT4, SOX2, NANOG, KLF4, and MYC in CSCs, evidence for the central role of Forkhead box transcription factor FOXM1 in the establishment, maintenance, and functions of CSCs is accumulating. Conventionally identified as a master regulator of the cell cycle, a comprehensive understanding of this molecule has revealed its multifarious oncogenic potential and uncovered its role in angiogenesis, invasion, migration, self-renewal, and drug resistance. This review compiles the large body of literature that has accumulated in recent years that provides evidence for the mechanisms by which FOXM1 expression promotes stemness in glioblastoma, breast, colon, ovarian, lung, hepatic, and pancreatic carcinomas. We have also compiled the data showing the association of stem cell mediators with FOXM1 using TCGA mRNA expression data. Further, the prognostic importance of FOXM1 and other stem cell markers is presented. The delineation of FOXM1-mediated regulation of CSCs can aid in the development of molecularly targeted pharmacological approaches directed at the selective eradication of CSCs in several human malignancies.
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Affiliation(s)
- Gulab Sher
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Tariq Masoodi
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, Doha 26999, Qatar
| | - Kalyani Patil
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Sabah Akhtar
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Aamir Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Laboratory Animal Research Center, Qatar University, Doha 2713, Qatar.
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83
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Mitchell AV, Wu L, James Block C, Zhang M, Hackett J, Craig DB, Chen W, Zhao Y, Zhang B, Dang Y, Zhang X, Zhang S, Wang C, Gibson H, Pile LA, Kidder B, Matherly L, Yang Z, Dou Y, Wu G. FOXQ1 recruits the MLL complex to activate transcription of EMT and promote breast cancer metastasis. Nat Commun 2022; 13:6548. [PMID: 36319643 PMCID: PMC9626503 DOI: 10.1038/s41467-022-34239-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Aberrant expression of the Forkhead box transcription factor, FOXQ1, is a prevalent mechanism of epithelial-mesenchymal transition (EMT) and metastasis in multiple carcinoma types. However, it remains unknown how FOXQ1 regulates gene expression. Here, we report that FOXQ1 initiates EMT by recruiting the MLL/KMT2 histone methyltransferase complex as a transcriptional coactivator. We first establish that FOXQ1 promoter recognition precedes MLL complex assembly and histone-3 lysine-4 trimethylation within the promoter regions of critical genes in the EMT program. Mechanistically, we identify that the Forkhead box in FOXQ1 functions as a transactivation domain directly binding the MLL core complex subunit RbBP5 without interrupting FOXQ1 DNA binding activity. Moreover, genetic disruption of the FOXQ1-RbBP5 interaction or pharmacologic targeting of KMT2/MLL recruitment inhibits FOXQ1-dependent gene expression, EMT, and in vivo tumor progression. Our study suggests that targeting the FOXQ1-MLL epigenetic axis could be a promising strategy to combat triple-negative breast cancer metastatic progression.
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Affiliation(s)
- Allison V Mitchell
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Ling Wu
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - C James Block
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Mu Zhang
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Justin Hackett
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Douglas B Craig
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Wei Chen
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiaohong Zhang
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Shengping Zhang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 650 Xinsongjiang Road, Songjiang District, Shanghai, 201620, China
| | - Chuangui Wang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 650 Xinsongjiang Road, Songjiang District, Shanghai, 201620, China
| | - Heather Gibson
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Lori A Pile
- The Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Benjamin Kidder
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Larry Matherly
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Zhe Yang
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Guojun Wu
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA.
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84
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Andreas A, Maloy A, Nyunoya T, Zhang Y, Chandra D. The FoxP1 gene regulates lung function, production of matrix metalloproteinases and inflammatory mediators, and viability of lung epithelia. Respir Res 2022; 23:281. [PMID: 36221131 PMCID: PMC9554985 DOI: 10.1186/s12931-022-02213-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Background Genes involved in lung development may become dysregulated in adult life and contribute to the pathogenesis of lung diseases. Multiple genes regulate lung development, including Forkhead box protein P1-4 (FoxP1-4). Methods We examined the association between variants in the FoxP1-4 genes and lung function using data from a GWAS that included close to 400,000 individuals and 20 million SNPs. Results More than 100 variants in the FoxP1 gene, but none in the FoxP2-4 genes, are associated with lung function. The sentinel variant in the FoxP1 gene associated with FEV1 was rs1499894 (C > T), while the sentinel variant in the FoxP1 gene associated with FVC was rs35480566 (A > G). Those with the T allele instead of the C allele for rs1499894, or the G allele instead of the A allele for rs35480566 had increased FoxP1 mRNA levels in transcriptomic data, higher FEV1 and FVC, and reduced odds of being diagnosed with idiopathic pulmonary fibrosis. Further, knockdown of FoxP1 in lung epithelial cells by RNA interference led to increased mRNA levels for matrix metalloproteinases 1, 2, 3 and pro-inflammatory cytokines IL-6 & IL-8, as well as reduced cell viability after exposure to cigarette smoke—all processes implicated in the pathogenesis of COPD and IPF. Conclusions Our results suggest that the protein encoded by the FoxP1 gene may protect against the development of COPD and IPF. A causal role for FoxP1 in the pathogenesis of COPD and IPF may warrant further investigation, and FoxP1 may be a novel therapeutic target for these lung disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02213-4.
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Affiliation(s)
- Alexis Andreas
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Abby Maloy
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Toru Nyunoya
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA.,Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Divay Chandra
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA. .,Pulmonary, Allergy, and Critical Care Medicine, UPMC Montefiore Hospital-NW628, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA.
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85
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Seudre O, Martín-Zamora FM, Rapisarda V, Luqman I, Carrillo-Baltodano AM, Martín-Durán JM. The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia. Genome Biol Evol 2022; 14:evac139. [PMID: 36099507 PMCID: PMC9539403 DOI: 10.1093/gbe/evac139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia-a large clade of invertebrate animals including molluscs and annelids-are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterize the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids. The genome of O. fusiformis contains at least a single ortholog for 20 of the 22 Fox gene classes that are ancestral to Bilateria, including an ortholog of the recently discovered foxT class. Temporal and spatial expression dynamics reveal a conserved role of Fox genes in gut formation, mesoderm patterning, and apical organ and cilia formation in Annelida and Spiralia. Moreover, we uncover an ancestral expansion of foxQ2 genes in Spiralia, represented by 11 paralogs in O. fusiformis. Notably, although all foxQ2 copies have apical expression in O. fusiformis, they show variable spatial domains and staggered temporal activation, which suggest cooperation and sub-functionalization among foxQ2 genes for the development of apical fates in this annelid. Altogether, our study informs the evolution and developmental roles of Fox genes in Annelida and Spiralia generally, providing the basis to explore how regulatory changes in Fox gene expression might have contributed to developmental and morphological diversification in Spiralia.
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Affiliation(s)
- Océane Seudre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Valentina Rapisarda
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Imran Luqman
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
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86
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Yuan H, Hatleberg WL, Degnan BM, Degnan SM. Gene activation of metazoan Fox transcription factors at the onset of metamorphosis in the marine demosponge Amphimedon queenslandica. Dev Growth Differ 2022; 64:455-468. [PMID: 36155915 PMCID: PMC9828451 DOI: 10.1111/dgd.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 01/12/2023]
Abstract
Transcription factors encoded by the Forkhead (Fox) gene family have diverse, sometimes conserved, regulatory roles in eumetazoan development, immunity, and physiology. Although this gene family includes members that predate the origin of the animal kingdom, the majority of metazoan Fox genes evolved after the divergence of animals and choanoflagellates. Here, we characterize the composition, structure, and expression of Fox genes in the marine demosponge Amphimedon queenslandica to better understand the origin and evolution of this family. The Fox gene repertoire in A. queenslandica appears to be similar to the ancestral metazoan Fox gene family. All 17 A. queenslandica Fox genes are differentially expressed during development and in adult cell types. Remarkably, eight of these, all of which appear to be metazoan-specific, are induced within just 1 h of larval settlement and commencement of metamorphosis. Gene co-expression analyses suggest that these eight Fox genes regulate developmental and physiological processes similar to their roles in other animals. These findings are consistent with Fox genes playing deeply ancestral roles in animal development and physiology, including in response to changes in the external environment.
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Affiliation(s)
- Huifang Yuan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
| | - William L. Hatleberg
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia,Present address:
Department of Biological SciencesCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Bernard M. Degnan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Sandie M. Degnan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
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87
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Wei Y, Huang X, Ma Y, Dai L. FOXC1‑mediated TRIM22 regulates the excessive proliferation and inflammation of fibroblast‑like synoviocytes in rheumatoid arthritis via NF‑κB signaling pathway. Mol Med Rep 2022; 26:304. [PMID: 35946462 PMCID: PMC9434987 DOI: 10.3892/mmr.2022.12820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/15/2022] [Indexed: 11/10/2022] Open
Abstract
Rheumatoid arthritis (RA) is a common systemic autoimmune disorder of unknown etiology, which threatens public health. The regulatory role of tripartite motif-containing 22 (TRIM22) has been reported in multiple types of cancers and disease, but not in RA. The aim of the present study was therefore to elucidate the potential roles and underlying mechanisms of TRIM22 in fibroblast-like synoviocytes (FLSs) in RA. The Gene Expression Omnibus database was used to examine TRIM22 mRNA expression levels in synovial tissue samples of patients with RA and healthy controls. TRIM22 and forkhead box C1 (FOXC1) mRNA and protein expression levels in normal FLSs and RA-FLSs were assessed using reverse transcription-quantitative PCR (RT-qPCR) and western blotting, respectively. The Cell Counting Kit-8 assay was used to assess cell proliferation. Cell apoptosis was analyzed using flow cytometry. The migratory and invasive abilities of RA-FLSs were assessed using Transwell assays. Western blotting was used to analyze the protein expression levels of apoptosis-related factors, MMP2, MMP9 and NF-κB signaling pathway-related proteins. Inflammatory factors levels were assessed via ELISA and RT-qPCR. Furthermore, the JASPAR database, chromatin immunoprecipitation and the dual-luciferase reporter assays were used to determine the interaction between FOXC1 and the TRIM22 promoter. The results of the present study demonstrated that TRIM22 expression levels were significantly elevated in the synovial tissue samples of patients with RA and RA-FLSs. Moreover, FOXC1 was also significantly overexpressed in RA-FLSs. TRIM22 knockdown significantly reduced cell proliferation, migration, invasion and the inflammatory response, whereas cell apoptosis was significantly increased. Furthermore, the results demonstrated that FOXC1 may have positively mediated TRIM22 expression via binding to the TRIM22 promoter. Moreover, FOXC1 overexpression significantly reversed the outcome of TRIM22 knockdown on the proliferation, apoptosis, migration, invasion and inflammation of RA-FLSs. FOXC1 overexpression also significantly reversed the inactivation of the NF-κB signaling pathway caused by TRIM22 knockdown. In summary, the present study demonstrated that TRIM22 was potentially activated via FOXC1, which contributed to the progression of RA via the NF-κB signaling pathway.
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Affiliation(s)
- Yazhi Wei
- Department of Clinical Laboratory, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, Guangdong 518040, P.R. China
| | - Xinmin Huang
- Department of Rheumatology, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, Guangdong 518040, P.R. China
| | - Yanmei Ma
- The Science and education division, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, Guangdong 518040, P.R. China
| | - Liping Dai
- Department of Rheumatology, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, Guangdong 518040, P.R. China
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88
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An Integrated Study on the Differential Expression of the FOX Gene Family in Cancer and Their Response to Chemotherapy Drugs. Genes (Basel) 2022; 13:genes13101754. [PMID: 36292640 PMCID: PMC9602029 DOI: 10.3390/genes13101754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
The Forkhead-box (FOX) transcription factors, as one of the largest gene families in humans, play key roles in cancer. Although studies have suggested that several FOX transcription factors have a significant impact on cancer, the functions of most of the FOX genes in cancer remain elusive. In the study, the expression of 43 FOX genes in 63 kinds of cancer diseases (including many subtypes of same cancer) and in response to 60 chemical substances was obtained from the Gene Expression Atlas database of the European Bioinformatics Institute. Based on the high degree of overlap in FOXO family members differentially expressed in various cancers and their particular responses to chemotherapeutic drugs, our data disclosed the FOX genes that played an important role in the development and progression of cancer. More importantly, we predicted the role of one or several combinatorial FOX genes in the diagnosis and prognostic assessment of a specific cancer and evaluated the potential of a certain anticancer drug therapy for this type of cancer by integrating patterns of FOX genes expression with anticancer drugs sensitivity.
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89
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Zheng B, Seltzsam S, Wang C, Schierbaum L, Schneider S, Wu CHW, Dai R, Connaughton DM, Nakayama M, Mann N, Stajic N, Mane S, Bauer SB, Tasic V, Nam HJ, Shril S, Hildebrandt F. Whole-exome sequencing identifies FOXL2, FOXA2 and FOXA3 as candidate genes for monogenic congenital anomalies of the kidneys and urinary tract. Nephrol Dial Transplant 2022; 37:1833-1843. [PMID: 34473308 PMCID: PMC9755999 DOI: 10.1093/ndt/gfab253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the most common cause of chronic kidney disease in the first three decades of life. Variants in four Forkhead box (FOX) transcription factors have been associated with CAKUT. We hypothesized that other FOX genes, if highly expressed in developing kidneys, may also represent monogenic causes of CAKUT. METHODS We here performed whole-exome sequencing (WES) in 541 families with CAKUT and generated four lists of CAKUT candidate genes: (A) 36 FOX genes showing high expression during renal development, (B) 4 FOX genes known to cause CAKUT to validate list A, (C) 80 genes that we identified as unique potential novel CAKUT candidate genes when performing WES in 541 CAKUT families and (D) 175 genes identified from WES as multiple potential novel CAKUT candidate genes. RESULTS To prioritize potential novel CAKUT candidates in the FOX gene family, we overlapped 36 FOX genes (list A) with lists C and D of WES-derived CAKUT candidates. Intersection with list C identified a de novo FOXL2 in-frame deletion in a patient with eyelid abnormalities and ureteropelvic junction obstruction, and a homozygous FOXA2 missense variant in a patient with horseshoe kidney. Intersection with list D identified a heterozygous FOXA3 missense variant in a CAKUT family with multiple affected individuals. CONCLUSIONS We hereby identified FOXL2, FOXA2 and FOXA3 as novel monogenic candidate genes of CAKUT, supporting the utility of a paralog-based approach to discover mutated genes associated with human disease.
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Affiliation(s)
- Bixia Zheng
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chunyan Wang
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Luca Schierbaum
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sophia Schneider
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rufeng Dai
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dervla M Connaughton
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Natasa Stajic
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Stuart B Bauer
- Department of Urology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Hyun Joo Nam
- Department of Biological and Environmental Science, Texas A&M University at Commerce, Commerce, TX, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
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90
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Xu L, Yang Z, Zhao Q, Feng H, Kuang J, Liu Z, Chen L, Zhan L, Yan J, Cai W, Qiu W. Effect of FOXP2 transcription factor on immune infiltration of thyroid cancer and its potential clinical value. Front Immunol 2022; 13:982812. [PMID: 36203616 PMCID: PMC9531268 DOI: 10.3389/fimmu.2022.982812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Background The clinical outcomes are not always favorable in certain thyroid cancer patients. The effect of Forkhead-box family on immune cells infiltration and tumor microenvironment in thyroid cancer was explored. The role of FOXP2 in tumor invasion and recurrence was investigated consequently. Methods TIMER and GEPIA were firstly employed to compare FOXPs expression in normal and cancer tissues from multiple human cancers. The results from database were confirmed by quantitative Real Time-PCR and Western blot in matched thyroid cancer and adjacent normal tissues, in addition to a panel of thyroid cancer cell lines and normal thyroid cell. GEPIA platform was employed to discover the possibility of FOXPs as prognostic indicator. TISIBD and UACLCAN were then employed to estimate the influence of FOXPs on lymph node metastasis and tumor staging. GEPIA analysis was initially employed to analyze correlation of FOXPs and tumor immune infiltrating cells, and TIMER dataset was then included for standardization according to tumor purity. Result Different member of FOXPs showed divergence in expression in various cancer tissues. Lower FOXP1, FOXP2 and higher FOXP3, FOXP4 levels could be identified in thyroid cancer tissues when compared with matched normal tissue. There was an inverse correlation between FOXP2, FOXP4 and immune invasion, whereas FOXP1 and FOXP3 were positively correlated. FOXPs showed remarkable correlations with multiply immune cells. More importantly, only FOXP2 showed the significant effect on recurrence and tumor staging. Conclusion As immune regulatory factor, the reduction of FOXP2 may affect tumor microenvironments and immune cells infiltration, enhance tumor immune escape, and promote recurrence of thyroid cancer. FOXP2 could be a new potential diagnostic and prognostic marker.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jiqi Yan
- *Correspondence: Jiqi Yan, ; Wei Cai, ; Weihua Qiu,
| | - Wei Cai
- *Correspondence: Jiqi Yan, ; Wei Cai, ; Weihua Qiu,
| | - Weihua Qiu
- *Correspondence: Jiqi Yan, ; Wei Cai, ; Weihua Qiu,
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91
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Wang J, Ge F, Yuan T, Qian M, Yan F, Yang B, He Q, Zhu H. The molecular mechanisms and targeting strategies of transcription factors in cholangiocarcinoma. Expert Opin Ther Targets 2022; 26:781-789. [PMID: 36243001 DOI: 10.1080/14728222.2022.2137020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/13/2022] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Cholangiocarcinoma consists of a cluster of malignant biliary tumors that tend to have a poor prognosis, ranking as the second most prevalent type of liver cancer, and their incidence rate has increased globally recently. The high-frequency driving mutations of cholangiocarcinoma, such as KRAS/IDH1/ARID1A/P53, imply the epigenetic instability of cholangiocarcinoma, leading to the dysregulation of various related transcription factors, thus affecting the occurrence and development of cholangiocarcinoma. Increasingly evidence indicates that the high heterogeneity and malignancy of cholangiocarcinoma are closely related to the dysregulation of transcription factors which promote cell proliferation, invasion, migration, angiogenesis, and drug resistance through reprogrammed transcriptional networks. It is of great significance to further explore and summarize the role of transcription factors in cholangiocarcinoma. AREAS COVERED This review summarizes the oncogenic or tumor suppressive roles of key transcription factors in regulating cholangiocarcinoma progression and the potential targeting strategies of transcription factors in cholangiocarcinoma. EXPERT OPINION Cholangiocarcinoma is a type of cancer highly influenced by transcriptional regulation, specifically transcription factors and epigenetic regulatory factors. Targeting transcription factors could be a potential and important strategy that is likely to impact future cholangiocarcinoma treatment.
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Affiliation(s)
- Jiao Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fujing Ge
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Yuan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Meijia Qian
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fangjie Yan
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- The Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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92
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Cui G, Feng S, Yan Y, Wang L, He X, Li X, Duan Y, Chen J, Tang K, Zheng P, Tam PPL, Si W, Jing N, Peng G. Spatial molecular anatomy of germ layers in the gastrulating cynomolgus monkey embryo. Cell Rep 2022; 40:111285. [PMID: 36044859 DOI: 10.1016/j.celrep.2022.111285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/31/2022] [Accepted: 08/05/2022] [Indexed: 12/18/2022] Open
Abstract
During mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors, and germ layer morphogenesis. While the mouse model has been instrumental for understanding mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a spatial and temporal survey of the molecular dynamics of cell types populating the non-human primate embryos during gastrulation. We reconstructed three-dimensional digital models from serial sections of cynomolgus monkey (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21. Spatial transcriptomics identifies gene expression profiles unique to the germ layers. Cross-species comparison reveals a developmental coordinate of germ layer segregation between mouse and primates, and species-specific transcription programs during gastrulation. These findings offer insights into evolutionarily conserved and divergent processes during mammalian gastrulation.
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Affiliation(s)
- Guizhong Cui
- Bioland Laboratory/Guangzhou Laboratory, Guangzhou 510005, China
| | - Su Feng
- Bioland Laboratory/Guangzhou Laboratory, Guangzhou 510005, China
| | - Yaping Yan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Li Wang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiechao He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xi Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yanchao Duan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Jun Chen
- Department of Endocrinology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Patrick P L Tam
- Embryology Research Unit, Children's Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Wei Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
| | - Naihe Jing
- Bioland Laboratory/Guangzhou Laboratory, Guangzhou 510005, China; Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Guangdun Peng
- Bioland Laboratory/Guangzhou Laboratory, Guangzhou 510005, China; Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Guangzhou 510530, China.
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93
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Nagel S, Pommerenke C, Quentmeier H, Meyer C, Kaufmann M, MacLeod RAF. Genomic Aberrations Generate Fusion Gene FOXK2::TP63 and Activate NFKB1 in Cutaneous T-Cell Lymphoma. Biomedicines 2022; 10:biomedicines10082038. [PMID: 36009586 PMCID: PMC9406051 DOI: 10.3390/biomedicines10082038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is a severe lymphoid malignancy with a worse prognosis lacking curative treatment regimens. Several gene mutations and deregulated pathways, including NFkB signaling, have been implicated in its pathogenesis. Accordingly, CTCL cell line HUT-78 reportedly contains mutated NFKB2, which is constitutively activated via partial gene deletion, also demonstrating that genomic rearrangements cause driving mutations in this malignancy. Here, along with HUT-78, we analyzed CTCL cell line HH to identify additional aberrations underlying gene deregulation. Karyotyping and genomic profiling of HH showed several rearrangements worthy of detailed investigation. Corresponding to the established karyotype, RNA-seq data and PCR analysis confirmed the presence of t(3;17)(q28;q25), generating a novel fusion gene, FOXK2::TP63. Furthermore, chromosomal rearrangement t(1;4)(p32;q25) was connected to amplification at 4q24–26, affecting aberrant NFKB1 overexpression thereat. Transcription factor binding-site analysis and knockdown experiments demonstrated that IRF4 contributed to NFKB1 expression. Within the same amplicon, we identified amplification and overexpression of NFkB signaling activator CAMK2D (4q26) and p53-inhibitor UBE2D3 (4q24). Genomic profiling data for HUT-78 detailed a deletion at 10q25 underlying reported NFKB2 activation. Moreover, amplifications of ID1 (20q11) and IKZF2 (2q34) in this cell line drove overexpression of these NK cell differentiation factors and possibly thus formed corresponding lineage characteristics. Target gene analysis for NFKB1 via siRNA-mediated knockdown in HH revealed activation of TP63, MIR155, and NOTCH pathway component RBPJ. Finally, treatment of HH with NFkB inhibitor demonstrated a role for NFkB in supporting proliferation, while usage of inhibitor DAPT showed significant survival effects via the NOTCH pathway. Collectively, our data suggest that NFkB and/or NOTCH inhibitors may represent reasonable treatment options for subsets of CTCL patients.
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94
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Jing J, Feng J, Yuan Y, Guo T, Lei J, Pei F, Ho TV, Chai Y. Spatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis. Nat Commun 2022; 13:4803. [PMID: 35974052 PMCID: PMC9381504 DOI: 10.1038/s41467-022-32490-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
Cranial neural crest cells are an evolutionary innovation of vertebrates for craniofacial development and function, yet the mechanisms that govern the cell fate decisions of postmigratory cranial neural crest cells remain largely unknown. Using the mouse molar as a model, we perform single-cell transcriptome profiling to interrogate the cell fate diversification of postmigratory cranial neural crest cells. We reveal the landscape of transcriptional heterogeneity and define the specific cellular domains during the progression of cranial neural crest cell-derived dental lineage diversification, and find that each domain makes a specific contribution to distinct molar mesenchymal tissues. Furthermore, IGF signaling-mediated cell-cell interaction between the cellular domains highlights the pivotal role of autonomous regulation of the dental mesenchyme. Importantly, we reveal cell-type-specific gene regulatory networks in the dental mesenchyme and show that Foxp4 is indispensable for the differentiation of periodontal ligament. Our single-cell atlas provides comprehensive mechanistic insight into the cell fate diversification process of the cranial neural crest cell-derived odontogenic populations.
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Affiliation(s)
- Junjun Jing
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA ,grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Chengdu, Sichuan 610041 China
| | - Jifan Feng
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Yuan Yuan
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Tingwei Guo
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Jie Lei
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Fei Pei
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Thach-Vu Ho
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA.
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95
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Zhang Z, Liu W, Bao X, Sun T, Wang J, Li M, Liu C. USP39 facilitates breast cancer cell proliferation through stabilization of FOXM1. Am J Cancer Res 2022; 12:3644-3661. [PMID: 36119839 PMCID: PMC9442023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/09/2022] [Indexed: 06/15/2023] Open
Abstract
Deubiquitinating enzyme dysregulation has been linked to the development of a variety of human malignancies, including breast cancer. However, the exact involvement of the deubiquitinating enzyme USP39 in the progression of breast cancer is yet unknown. Cell viability and colony formation analysis was used to assess the effects of USP39 knockdown on breast cancer cells in this study. The interaction between USP39 and FOXM1 was investigated using co-immunoprecipitation (co-IP) and in vitro deubiquitination analysis. The expression of USP39 and FOXM1 in breast cancer tissues was studied using the TCGA database. According to our findings, USP39 deubiquitinates and stabilizes FOXM1, promoting breast cancer cell proliferation, colony formation, and tumor growth in vivo. Furthermore, elevated USP39 expression lowers FOXM1 ubiquitination, resulting in increased transcriptional activity. In addition, the high expression of USP39 reduces the ubiquitination of FOXM1, thereby enhancing the transcriptional activity of FOXM1 and regulating the expression of downstream genes Cdc25b and Plk1. USP39 is positively correlated with the expression level of FOXM1 in breast cancer cells. In general, our research revealed the USP39-FOXM1 axis as a critical driver of breast cancer cell proliferation and provided a theoretical foundation for targeting the USP39-FOXM1 axis for pancreatic cancer treatment.
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Affiliation(s)
- Zhenwang Zhang
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and TechnologyXianning 437000, Hubei, China
- Hubei University of Science and Technology of Medicine, Xianning Medical CollegeXianning 437000, Hubei, China
| | - Wu Liu
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and TechnologyXianning 437000, Hubei, China
- Hubei University of Science and Technology of Medicine, Xianning Medical CollegeXianning 437000, Hubei, China
| | - Xiajun Bao
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and TechnologyXianning 437000, Hubei, China
- Hubei University of Science and Technology of Medicine, Xianning Medical CollegeXianning 437000, Hubei, China
| | - Tian Sun
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and TechnologyXianning 437000, Hubei, China
- Hubei University of Science and Technology of Medicine, Xianning Medical CollegeXianning 437000, Hubei, China
| | - Jiawei Wang
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and TechnologyXianning 437000, Hubei, China
- Hubei University of Science and Technology of Medicine, Xianning Medical CollegeXianning 437000, Hubei, China
| | - Mengxi Li
- Science and Technology Industry Management Office, Hubei University of Science and TechnologyXianning 437000, Hubei, China
| | - Chao Liu
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and TechnologyXianning 437000, Hubei, China
- Hubei University of Science and Technology of Medicine, Xianning Medical CollegeXianning 437000, Hubei, China
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96
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Yánez DC, Lau CI, Papaioannou E, Chawda MM, Rowell J, Ross S, Furmanski A, Crompton T. The Pioneer Transcription Factor Foxa2 Modulates T Helper Differentiation to Reduce Mouse Allergic Airway Disease. Front Immunol 2022; 13:890781. [PMID: 36003391 PMCID: PMC9393229 DOI: 10.3389/fimmu.2022.890781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/18/2022] [Indexed: 12/17/2022] Open
Abstract
Foxa2, a member of the Forkhead box (Fox) family of transcription factors, plays an important role in the regulation of lung function and lung tissue homeostasis. FOXA2 expression is reduced in the lung and airways epithelium of asthmatic patients and in mice absence of Foxa2 from the lung epithelium contributes to airway inflammation and goblet cell hyperplasia. Here we demonstrate a novel role for Foxa2 in the regulation of T helper differentiation and investigate its impact on lung inflammation. Conditional deletion of Foxa2 from T-cells led to increased Th2 cytokine secretion and differentiation, but decreased Th1 differentiation and IFN-γ expression in vitro. Induction of mouse allergic airway inflammation resulted in more severe disease in the conditional Foxa2 knockout than in control mice, with increased cellular infiltration to the lung, characterized by the recruitment of eosinophils and basophils, increased mucus production and increased production of Th2 cytokines and serum IgE. Thus, these experiments suggest that Foxa2 expression in T-cells is required to protect against the Th2 inflammatory response in allergic airway inflammation and that Foxa2 is important in T-cells to maintain the balance of effector cell differentiation and function in the lung.
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Affiliation(s)
- Diana C Yánez
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Ching-In Lau
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Mira M Chawda
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jasmine Rowell
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Susan Ross
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Anna Furmanski
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
| | - Tessa Crompton
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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97
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Silva-Vignato B, Cesar ASM, Afonso J, Moreira GCM, Poleti MD, Petrini J, Garcia IS, Clemente LG, Mourão GB, Regitano LCDA, Coutinho LL. Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness. Front Genet 2022; 13:935238. [PMID: 35991540 PMCID: PMC9386181 DOI: 10.3389/fgene.2022.935238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.
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Affiliation(s)
- Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food, and Nutrition, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | | | - Mirele Daiana Poleti
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
- *Correspondence: Luiz Lehmann Coutinho,
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98
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Choi Y, Luo Y, Lee S, Jin H, Yoon HJ, Hahn Y, Bae J, Lee HH. FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations. Nucleic Acids Res 2022; 50:8929-8946. [PMID: 35920317 PMCID: PMC9410875 DOI: 10.1093/nar/gkac673] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Although both the p53 and forkhead box (FOX) family proteins are key transcription factors associated with cancer progression, their direct relationship is unknown. Here, we found that FOX family proteins bind to the non-canonical homotypic cluster of the p53 promoter region (TP53). Analysis of crystal structures of FOX proteins (FOXL2 and FOXA1) bound to the p53 homotypic cluster indicated that they interact with a 2:1 stoichiometry accommodated by FOX-induced DNA allostery. In particular, FOX proteins exhibited distinct dimerization patterns in recognition of the same p53-DNA; dimer formation of FOXA1 involved protein–protein interaction, but FOXL2 did not. Biochemical and biological functional analyses confirmed the cooperative binding of FOX proteins to the TP53 promoter for the transcriptional activation of TP53. In addition, up-regulation of TP53 was necessary for FOX proteins to exhibit anti-proliferative activity in cancer cells. These analyses reveal the presence of a discrete characteristic within FOX family proteins in which FOX proteins regulate the transcription activity of the p53 tumor suppressor via cooperative binding to the TP53 promoter in alternative dimer configurations.
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Affiliation(s)
- Yuri Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Yongyang Luo
- School of Pharmacy, Chung-Ang University, Seoul 06974, Korea
| | - Seunghwa Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Hanyong Jin
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, Jilin Province, China
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Jeehyeon Bae
- School of Pharmacy, Chung-Ang University, Seoul 06974, Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
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99
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Liu R, Sun Y, Chen S, Hong Y, Lu Z. FOXD3 and GAB2 as a pair of rivals antagonistically control hepatocellular carcinogenesis. FEBS J 2022; 289:4536-4548. [DOI: 10.1111/febs.16403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/05/2021] [Accepted: 02/15/2022] [Indexed: 02/07/2023]
Affiliation(s)
- Ruimin Liu
- School of Pharmaceutical Sciences State Key Laboratory of Cellular Stress Biology Xiamen University Xiamen China
| | - Yan Sun
- School of Pharmaceutical Sciences State Key Laboratory of Cellular Stress Biology Xiamen University Xiamen China
| | - Shuai Chen
- School of Pharmaceutical Sciences State Key Laboratory of Cellular Stress Biology Xiamen University Xiamen China
| | - Yun Hong
- School of Pharmaceutical Sciences State Key Laboratory of Cellular Stress Biology Xiamen University Xiamen China
| | - Zhongxian Lu
- School of Pharmaceutical Sciences State Key Laboratory of Cellular Stress Biology Xiamen University Xiamen China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research School of Pharmaceutical Sciences Xiamen China
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100
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Hany NM, Eissa S, Basyouni M, Hasanin AH, Aboul-Ela YM, Elmagd NMA, Montasser IF, Ali MA, Skipp PJ, Matboli M. Modulation of hepatic stellate cells by Mutaflor ® probiotic in non-alcoholic fatty liver disease management. Lab Invest 2022; 20:342. [PMID: 35907883 PMCID: PMC9338485 DOI: 10.1186/s12967-022-03543-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/17/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND NAFLD and NASH are emerging as primary causes of chronic liver disease, indicating a need for an effective treatment. Mutaflor® probiotic, a microbial treatment of interest, was effective in sustaining remission in ulcerative colitis patients. OBJECTIVE To construct a genetic-epigenetic network linked to HSC signaling as a modulator of NAFLD/NASH pathogenesis, then assess the effects of Mutaflor® on this network. METHODS First, in silico analysis was used to construct a genetic-epigenetic network linked to HSC signaling. Second, an investigation using rats, including HFHSD induced NASH and Mutaflor® treated animals, was designed. Experimental procedures included biochemical and histopathologic analysis of rat blood and liver samples. At the molecular level, the expression of genetic (FOXA2, TEAD2, and LATS2 mRNAs) and epigenetic (miR-650, RPARP AS-1 LncRNA) network was measured by real-time PCR. PCR results were validated with immunohistochemistry (α-SMA and LATS2). Target effector proteins, IL-6 and TGF-β, were estimated by ELISA. RESULTS Mutaflor® administration minimized biochemical and histopathologic alterations caused by NAFLD/NASH. HSC activation and expression of profibrogenic IL-6 and TGF-β effector proteins were reduced via inhibition of hedgehog and hippo pathways. Pathways may have been inhibited through upregulation of RPARP AS-1 LncRNA which in turn downregulated the expression of miR-650, FOXA2 mRNA and TEAD2 mRNA and upregulated LATS2 mRNA expression. CONCLUSION Mutaflor® may slow the progression of NAFLD/NASH by modulating a genetic-epigenetic network linked to HSC signaling. The probiotic may be a useful modality for the prevention and treatment of NAFLD/NASH.
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Affiliation(s)
- Noha M Hany
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, P.O. box, Cairo, 11381, Egypt
| | - Sanaa Eissa
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, P.O. box, Cairo, 11381, Egypt. .,MASRI Research Institue, Ain Shams University, Cairo, Egypt.
| | - Manal Basyouni
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, P.O. box, Cairo, 11381, Egypt
| | - Amany H Hasanin
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Yasmin M Aboul-Ela
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nagwa M Abo Elmagd
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Iman F Montasser
- Department of Gastroenterology, Hepatology and Infectious Diseases, Tropical Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mahmoud A Ali
- Department of Molecular Microbiology, Military Medical Academy, Cairo, Egypt
| | - Paul J Skipp
- Centre for Proteomic Research, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Marwa Matboli
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, P.O. box, Cairo, 11381, Egypt
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