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Li L, Lu L, Xiao Z, Lv J, Huang H, Wu B, Zhao T, Li C, Wang W, Wang H. Deamidation enables pathogenic SMAD6 variants to activate the BMP signaling pathway. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1915-1927. [PMID: 38913236 DOI: 10.1007/s11427-023-2532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/23/2024] [Indexed: 06/25/2024]
Abstract
The BMP signaling pathway plays a crucial role in regulating early embryonic development and tissue homeostasis. SMAD6 encodes a negative regulator of BMP, and rare variants of SMAD6 are recurrently found in individuals with birth defects. However, we observed that a subset of rare pathogenic variants of SMAD6 consistently exhibited positive regulatory effects instead of the initial negative effects on the BMP signaling pathway. We sought to determine whether these SMAD6 variants have common pathogenic mechanisms. Here, we showed that pathogenic SMAD6 variants accompanying this functional reversal exhibit similar increases in deamidation. Mechanistically, increased deamidation of SMAD6 variants promotes the accumulation of the BMP receptor BMPR1A and the formation of new complexes, both of which lead to BMP signaling pathway activation. Specifically, two residues, N262 and N404, in SMAD6 were identified as the crucial sites of deamidation, which was catalyzed primarily by glutamine-fructose-6-phosphate transaminase 2 (GFPT2). Additionally, treatment of cells harboring SMAD6 variants with a deamidase inhibitor restored the inhibitory effect of SMAD6 on the BMP signaling pathway. Conversely, when wild-type SMAD6 was manually simulated to mimic the deamidated state, the reversed function of activating BMP signaling was reproduced. Taken together, these findings show that deamidation of SMAD6 plays a crucial role in the functional reversal of BMP signaling activity, which can be induced by a subset of various SMAD6 variants. Our study reveals a common pathogenic mechanism shared by these variants and provides a potential strategy for preventing birth defects through deamidation regulation, which might prevent the off-target effects of gene editing.
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Affiliation(s)
- Ling Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China
| | - Lei Lu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China.
| | - Ziqi Xiao
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
| | - Jingyi Lv
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China
| | - Bo Wu
- Prenatal Diagnosis Center of Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, 518028, China
| | - Tongjin Zhao
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China
| | - Chengtao Li
- Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Weimin Wang
- Department of Pharmacy, College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, Institute of Reproduction and Development, and Children's Hospital, Fudan University, Shanghai, 200090, China.
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200438, China.
- Prenatal Diagnosis Center of Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, 518028, China.
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La Tour S, Shaikh H, Beardwood JH, Augustynski AS, Wood MA, Keiser AA. The weekend warrior effect: Consistent intermittent exercise induces persistent cognitive benefits. Neurobiol Learn Mem 2024; 214:107971. [PMID: 39137861 DOI: 10.1016/j.nlm.2024.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/26/2024] [Accepted: 08/10/2024] [Indexed: 08/15/2024]
Abstract
Exercise provides a range of cognitive benefits, including improved memory performance. Previously, we demonstrated that 14 days of continuous voluntary wheel-running exercise enables learning in a hippocampus-dependent Object Location Memory (OLM) task under insufficient, subthreshold training conditions in adult mice. Whether similar exercise benefits can be obtained from consistent intermittent exercise as continuous exercise is unknown. Here, we examine whether intermittent exercise (the weekend warrior effect: 2 days of exercise a week for 7 weeks) displays similar or distinct cognitive benefits as previously examined with 14 days of continuous exercise. We find that both continuous and intermittent exercise parameters similarly enable hippocampus-dependent OLM compared to the 2-day exercise control group. Mice receiving intermittent exercise maintained cognitive benefits following a 7-day sedentary delay, whereas mice that underwent 14 continuous days of exercise showed diminished cognitive benefits as previously reported. Further, compared to continuous exercise, intermittent exercise mice exhibited persistently elevated levels of the genes Acvr1c and Bdnf which we know to be critically involved in hippocampus-dependent long-term memory in the dorsal hippocampus. Together findings suggest that consistent intermittent exercise persistently enables hippocampal-dependent long-term memory. Understanding the optimal parameters for persistent cognitive function and the mechanisms mediating persistent effects will aid in therapeutic pursuits investigating the mitigation of cognitive ailments.
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Affiliation(s)
- Scott La Tour
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory (CNLM), University of California Irvine, Irvine, CA 92697, USA
| | - Hassan Shaikh
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory (CNLM), University of California Irvine, Irvine, CA 92697, USA
| | - Joy H Beardwood
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory (CNLM), University of California Irvine, Irvine, CA 92697, USA
| | - Agatha S Augustynski
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory (CNLM), University of California Irvine, Irvine, CA 92697, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory (CNLM), University of California Irvine, Irvine, CA 92697, USA.
| | - Ashley A Keiser
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory (CNLM), University of California Irvine, Irvine, CA 92697, USA.
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Wieteska Ł, Taylor AB, Punch E, Coleman JA, Conway IO, Lin YF, Byeon CH, Hinck CS, Krzysiak T, Ishima R, López-Casillas F, Cherepanov P, Bernard DJ, Hill CS, Hinck AP. Structures of TGF-β with betaglycan and the signaling receptors reveal the mechanism whereby betaglycan potentiates receptor complex assembly and signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604101. [PMID: 39091787 PMCID: PMC11291015 DOI: 10.1101/2024.07.19.604101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development and tissue homeostasis and fertility in adults. It functions by enabling binding of the three TGF-β isoforms to their signaling receptors and is additionally required for inhibin A (InhA) activity. Despite its requirement for the functions of TGF-βs and InhA in vivo, structural information explaining BG ligand selectivity and its mechanism of action is lacking. Here, we determine the structure of TGF-β bound both to BG and the signaling receptors, TGFBR1 and TGFBR2. We identify key regions responsible for ligand engagement, which has revealed novel binding interfaces that differ from those described for the closely related co-receptor of the TGF-β family, endoglin, thus demonstrating remarkable evolutionary adaptation to enable ligand selectivity. Finally, we provide a structural explanation for the hand-off mechanism underlying TGF-β signal potentiation.
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Horvat Mercnik M, Schliefsteiner C, Sanchez-Duffhues G, Wadsack C. TGFβ signalling: a nexus between inflammation, placental health and preeclampsia throughout pregnancy. Hum Reprod Update 2024; 30:442-471. [PMID: 38519450 PMCID: PMC11215164 DOI: 10.1093/humupd/dmae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/16/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The placenta is a unique and pivotal organ in reproduction, controlling crucial growth and cell differentiation processes that ensure a successful pregnancy. Placental development is a tightly regulated and dynamic process, in which the transforming growth factor beta (TGFβ) superfamily plays a central role. This family of pleiotropic growth factors is heavily involved in regulating various aspects of reproductive biology, particularly in trophoblast differentiation during the first trimester of pregnancy. TGFβ signalling precisely regulates trophoblast invasion and the cell transition from cytotrophoblasts to extravillous trophoblasts, which is an epithelial-to-mesenchymal transition-like process. Later in pregnancy, TGFβ signalling ensures proper vascularization and angiogenesis in placental endothelial cells. Beyond its role in trophoblasts and endothelial cells, TGFβ signalling contributes to the polarization and function of placental and decidual macrophages by promoting maternal tolerance of the semi-allogeneic foetus. Disturbances in early placental development have been associated with several pregnancy complications, including preeclampsia (PE) which is one of the severe complications. Emerging evidence suggests that TGFβ is involved in the pathogenesis of PE, thereby offering a potential target for intervention in the human placenta. OBJECTIVE AND RATIONALE This comprehensive review aims to explore and elucidate the roles of the major members of the TGFβ superfamily, including TGFβs, bone morphogenetic proteins (BMPs), activins, inhibins, nodals, and growth differentiation factors (GDFs), in the context of placental development and function. The review focusses on their interactions within the major cell types of the placenta, namely trophoblasts, endothelial cells, and immune cells, in both normal pregnancies and pregnancies complicated by PE throughout pregnancy. SEARCH METHODS A literature search was carried out using PubMed and Google Scholar, searching terms: 'TGF signalling preeclampsia', 'pregnancy TGF signalling', 'preeclampsia tgfβ', 'preeclampsia bmp', 'preeclampsia gdf', 'preeclampsia activin', 'endoglin preeclampsia', 'endoglin pregnancy', 'tgfβ signalling pregnancy', 'bmp signalling pregnancy', 'gdf signalling pregnancy', 'activin signalling pregnancy', 'Hofbauer cell tgfβ signalling', 'placental macrophages tgfβ', 'endothelial cells tgfβ', 'endothelium tgfβ signalling', 'trophoblast invasion tgfβ signalling', 'trophoblast invasion Smad', 'trophoblast invasion bmp', 'trophoblast invasion tgfβ', 'tgfβ preeclampsia', 'tgfβ placental development', 'TGFβ placental function', 'endothelial dysfunction preeclampsia tgfβ signalling', 'vascular remodelling placenta TGFβ', 'inflammation pregnancy tgfβ', 'immune response pregnancy tgfβ', 'immune tolerance pregnancy tgfβ', 'TGFβ pregnancy NK cells', 'bmp pregnancy NK cells', 'bmp pregnancy tregs', 'tgfβ pregnancy tregs', 'TGFβ placenta NK cells', 'TGFβ placenta tregs', 'NK cells preeclampsia', 'Tregs preeclampsia'. Only articles published in English until 2023 were used. OUTCOMES A comprehensive understanding of TGFβ signalling and its role in regulating interconnected cell functions of the main placental cell types provides valuable insights into the processes essential for successful placental development and growth of the foetus during pregnancy. By orchestrating trophoblast invasion, vascularization, immune tolerance, and tissue remodelling, TGFβ ligands contribute to the proper functioning of a healthy maternal-foetal interface. However, dysregulation of TGFβ signalling has been implicated in the pathogenesis of PE, where the shallow trophoblast invasion, defective vascular remodelling, decreased uteroplacental perfusion, and endothelial cell and immune dysfunction observed in PE, are all affected by an altered TGFβ signalling. WIDER IMPLICATIONS The dysregulation of TGFβ signalling in PE has important implications for research and clinical practice. Further investigation is required to understand the underlying mechanisms, including the role of different ligands and their regulation under pathophysiological conditions, in order to discover new therapeutic targets. Distinguishing between clinically manifested subtypes of PE and studying TGFβ signalling in different placental cell types holistically is an important first step. To put this knowledge into practice, pre-clinical animal models combined with new technologies are needed. This may also lead to improved human research models and identify potential therapeutic targets, ultimately improving outcomes for affected pregnancies and reducing the burden of PE.
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Affiliation(s)
| | | | - Gonzalo Sanchez-Duffhues
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Tissue-Specific BMP Signalling ISPA-HUCA, Oviedo, Spain
| | - Christian Wadsack
- Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Tanzi E, Di Modica SM, Bordini J, Olivari V, Pagani A, Furiosi V, Silvestri L, Campanella A, Nai A. Bone marrow Tfr2 deletion improves the therapeutic efficacy of the activin-receptor ligand trap RAP-536 in β-thalassemic mice. Am J Hematol 2024; 99:1313-1325. [PMID: 38629683 DOI: 10.1002/ajh.27336] [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: 11/23/2023] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 06/12/2024]
Abstract
β-thalassemia is a disorder characterized by anemia, ineffective erythropoiesis (IE), and iron overload, whose treatment still requires improvement. The activin receptor-ligand trap Luspatercept, a novel therapeutic option for β-thalassemia, stimulates erythroid differentiation inhibiting the transforming growth factor β pathway. However, its exact mechanism of action and the possible connection with erythropoietin (Epo), the erythropoiesis governing cytokine, remain to be clarified. Moreover, Luspatercept does not correct all the features of the disease, calling for the identification of strategies that enhance its efficacy. Transferrin receptor 2 (TFR2) regulates systemic iron homeostasis in the liver and modulates the response to Epo of erythroid cells, thus balancing red blood cells production with iron availability. Stimulating Epo signaling, hematopoietic Tfr2 deletion ameliorates anemia and IE in Hbbth3/+ thalassemic mice. To investigate whether hematopoietic Tfr2 inactivation improves the efficacy of Luspatercept, we treated Hbbth3/+ mice with or without hematopoietic Tfr2 (Tfr2BMKO/Hbbth3/+) with RAP-536, the murine analog of Luspatercept. As expected, both hematopoietic Tfr2 deletion and RAP-536 significantly ameliorate IE and anemia, and the combined approach has an additive effect. Since RAP-536 has comparable efficacy in both Hbbth3/+ and Tfr2BMKO/Hbbth3/+ animals, we propose that the drug promotes erythroid differentiation independently of TFR2 and EPO stimulation. Notably, the lack of Tfr2, but not RAP-536, can also attenuate iron-overload and related complications. Overall, our results shed further light on the mechanism of action of Luspatercept and suggest that strategies aimed at inhibiting hematopoietic TFR2 might improve the therapeutic efficacy of activin receptor-ligand traps.
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Affiliation(s)
- Emanuele Tanzi
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Simona Maria Di Modica
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jessica Bordini
- Vita-Salute San Raffaele University, Milan, Italy
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Violante Olivari
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Alessia Pagani
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Valeria Furiosi
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Laura Silvestri
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandro Campanella
- Vita-Salute San Raffaele University, Milan, Italy
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Antonella Nai
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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Lan XQ, Deng CJ, Wang QQ, Zhao LM, Jiao BW, Xiang Y. The role of TGF-β signaling in muscle atrophy, sarcopenia and cancer cachexia. Gen Comp Endocrinol 2024; 353:114513. [PMID: 38604437 DOI: 10.1016/j.ygcen.2024.114513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/24/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Skeletal muscle, comprising a significant proportion (40 to 50 percent) of total body weight in humans, plays a critical role in maintaining normal physiological conditions. Muscle atrophy occurs when the rate of protein degradation exceeds protein synthesis. Sarcopenia refers to age-related muscle atrophy, while cachexia represents a more complex form of muscle wasting associated with various diseases such as cancer, heart failure, and AIDS. Recent research has highlighted the involvement of signaling pathways, including IGF1-Akt-mTOR, MuRF1-MAFbx, and FOXO, in regulating the delicate balance between muscle protein synthesis and breakdown. Myostatin, a member of the TGF-β superfamily, negatively regulates muscle growth and promotes muscle atrophy by activating Smad2 and Smad3. It also interacts with other signaling pathways in cachexia and sarcopenia. Inhibition of myostatin has emerged as a promising therapeutic approach for sarcopenia and cachexia. Additionally, other TGF-β family members, such as TGF-β1, activin A, and GDF11, have been implicated in the regulation of skeletal muscle mass. Furthermore, myostatin cooperates with these family members to impair muscle differentiation and contribute to muscle loss. This review provides an overview of the significance of myostatin and other TGF-β signaling pathway members in muscular dystrophy, sarcopenia, and cachexia. It also discusses potential novel therapeutic strategies targeting myostatin and TGF-β signaling for the treatment of muscle atrophy.
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Affiliation(s)
- Xin-Qiang Lan
- Metabolic Control and Aging Group, Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Cheng-Jie Deng
- Department of Biochemistry and Molecular Biology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Qi-Quan Wang
- Metabolic Control and Aging Group, Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Li-Min Zhao
- Senescence and Cancer Group, Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Bao-Wei Jiao
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yang Xiang
- Metabolic Control and Aging Group, Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, Nanchang 330031, Jiangxi, China.
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Oliviero G, Wynne K, Andrews D, Crean J, Kolch W, Cagney G. Expression Proteomics and Histone Analysis Reveal Extensive Chromatin Network Changes and a Role for Histone Tail Trimming during Cellular Differentiation. Biomolecules 2024; 14:747. [PMID: 39062462 PMCID: PMC11274982 DOI: 10.3390/biom14070747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
In order to understand the coordinated proteome changes associated with differentiation of a cultured cell pluripotency model, protein expression changes induced by treatment of NT2 embryonal carcinoma cells with retinoic acid were monitored by mass spectrometry. The relative levels of over 5000 proteins were mapped across distinct cell fractions. Analysis of the chromatin fraction revealed major abundance changes among chromatin proteins and epigenetic pathways between the pluripotent and differentiated states. Protein complexes associated with epigenetic regulation of gene expression, chromatin remodelling (e.g., SWI/SNF, NuRD) and histone-modifying enzymes (e.g., Polycomb, MLL) were found to be extensively regulated. We therefore investigated histone modifications before and after differentiation, observing changes in the global levels of lysine acetylation and methylation across the four canonical histone protein families, as well as among variant histones. We identified the set of proteins with affinity to peptides housing the histone marks H3K4me3 and H3K27me3, and found increased levels of chromatin-associated histone H3 tail trimming following differentiation that correlated with increased expression levels of cathepsin proteases. We further found that inhibition of cathepsins B and D reduces histone H3 clipping. Overall, the work reveals a global reorganization of the cell proteome congruent with differentiation, highlighting the key role of multiple epigenetic pathways, and demonstrating a direct link between cathepsin B and D activity and histone modification.
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Affiliation(s)
- Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - Darrell Andrews
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - John Crean
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - Gerard Cagney
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
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Vora M, Dietz J, Wing Z, Liu J, Rongo C, Savage-Dunn C. Genome-wide analysis of Smad and Schnurri transcription factors in C. elegans demonstrates widespread interaction and a function in collagen secretion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597576. [PMID: 38895257 PMCID: PMC11185707 DOI: 10.1101/2024.06.05.597576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Smads and their transcription factor partners mediate the transcriptional responses of target cells to secreted ligands of the Transforming Growth Factor-β (TGF-β) family, including those of the conserved bone morphogenetic protein (BMP) family, yet only a small number of direct target genes have been well characterized. In C. elegans, the BMP2/4 ortholog DBL-1 regulates multiple biological functions, including body size, via a canonical receptor-Smad signaling cascade. Here, we identify functional binding sites for SMA-3/Smad and its transcriptional partner SMA-9/Schnurri based on ChIP-seq peaks (identified by modEncode) and expression differences of nearby genes identified from RNA-seq analysis of corresponding mutants. We found that SMA-3 and SMA-9 have both overlapping and unique target genes. At a genome-wide scale, SMA-3/Smad acts as a transcriptional activator, whereas SMA-9/Schnurri direct targets include both activated and repressed genes. Mutations in sma-9 partially suppress the small body size phenotype of sma-3, suggesting some level of antagonism between these factors and challenging the prevailing model for Schnurri function. A functional analysis of target genes revealed a novel role in body size for genes involved in one-carbon metabolism and in the endoplasmic reticulum (ER) secretory pathway, including the disulfide reductase dpy-11. Our findings indicate that Smads and SMA-9/Schnurri have previously unappreciated complex genetic and genomic regulatory interactions that in turn regulate the secretion of extracellular components like collagen into the cuticle to mediate body size regulation.
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Affiliation(s)
- Mehul Vora
- Waksman Institute, Dept. of Genetics, Rutgers University, NJ, USA
- ModOmics Ltd, Southampton, UK
| | - Jonathan Dietz
- Waksman Institute, Dept. of Genetics, Rutgers University, NJ, USA
| | - Zachary Wing
- Department of Biology, Queens College, CUNY, NY, USA
| | - Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, NY, USA
| | | | - Cathy Savage-Dunn
- Department of Biology, Queens College, CUNY, NY, USA
- PhD Program in Biology, the Graduate Center, CUNY, NY, USA
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9
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Mörsdorf D, Knabl P, Genikhovich G. Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria. Dev Genes Evol 2024; 234:1-19. [PMID: 38472535 PMCID: PMC11226491 DOI: 10.1007/s00427-024-00714-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Bilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.
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Affiliation(s)
- David Mörsdorf
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria.
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Kruger RE, Frum T, Brumm AS, Hickey SL, Niakan KK, Aziz F, Shammami MA, Roberts JG, Ralston A. Smad4 is essential for epiblast scaling and morphogenesis after implantation, but nonessential before implantation. Development 2024; 151:dev202377. [PMID: 38752427 PMCID: PMC11190579 DOI: 10.1242/dev.202377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/03/2024] [Indexed: 05/28/2024]
Abstract
Bone morphogenic protein (BMP) signaling plays an essential and highly conserved role in embryo axial patterning in animal species. However, in mammalian embryos, which develop inside the mother, early development includes a preimplantation stage, which does not occur in externally developing embryos. During preimplantation, the epiblast is segregated from extra-embryonic lineages that enable implantation and development in utero. Yet, the requirement for BMP signaling is imprecisely defined in mouse early embryos. Here, we show that, in contrast to previous reports, BMP signaling (SMAD1/5/9 phosphorylation) is not detectable until implantation when it is detected in the primitive endoderm - an extra-embryonic lineage. Moreover, preimplantation development appears to be normal following deletion of maternal and zygotic Smad4, an essential effector of canonical BMP signaling. In fact, mice lacking maternal Smad4 are viable. Finally, we uncover a new requirement for zygotic Smad4 in epiblast scaling and cavitation immediately after implantation, via a mechanism involving FGFR/ERK attenuation. Altogether, our results demonstrate no role for BMP4/SMAD4 in the first lineage decisions during mouse development. Rather, multi-pathway signaling among embryonic and extra-embryonic cell types drives epiblast morphogenesis postimplantation.
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Affiliation(s)
- Robin E. Kruger
- Cell and Molecular Biology Ph.D. Program, Michigan State University, East Lansing, MI 48824, USA
- Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI 48824, USA
| | - Tristan Frum
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - A. Sophie Brumm
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute,London NW1 1AT, UK
| | - Stephanie L. Hickey
- Research Technology Support Facility, Michigan State University, East Lansing, MI 48824, USA
| | - Kathy K. Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute,London NW1 1AT, UK
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Farina Aziz
- Cell and Molecular Biology Ph.D. Program, Michigan State University, East Lansing, MI 48824, USA
| | - Marcelio A. Shammami
- Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI 48824, USA
- Genetics and Genome Sciences Ph.D. Program, Michigan State University, East Lansing, MI 48824, USA
| | - Jada G. Roberts
- Molecular, Cellular, and Integrative Physiology Ph.D. Program, Michigan State University, East Lansing, MI 48824, USA
| | - Amy Ralston
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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11
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Asoka AS, Kolikkandy A, Nair B, Kamath AJ, Sethi G, Nath LR. Role of Culinary Indian Spices in the Regulation of TGF-β Signaling Pathway in Inflammation-Induced Liver Cancer. Mol Nutr Food Res 2024; 68:e2300793. [PMID: 38766929 DOI: 10.1002/mnfr.202300793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/29/2023] [Indexed: 05/22/2024]
Abstract
SCOPE Hepatocellular carcinoma (HCC) results from various etiologies, such as Hepatitis B and C, Alcoholic and Non-alcoholic fatty liver disorders, fibrosis, and cirrhosis. About 80 to 90% of HCC cases possess cirrhosis, which is brought on by persistent liver inflammation. TGF-β is a multifunctional polypeptide molecule that acts as a pro-fibrogenic marker, inflammatory cytokine, immunosuppressive agent, and pro-carcinogenic growth factor during the progression of HCC. The preclinical and clinical evidence illustrates that TGF-β can induce epithelial-to-mesenchymal transition, promoting progression and hepatocyte immune evasion. Therefore, targeting the TGF-β pathway can be a promising therapeutic option against HCC. METHODS AND RESULTS We carry out a systemic analysis of eight potentially selected culinary Indian spices: Turmeric, Black pepper, Ginger, Garlic, Fenugreek, Red pepper, Clove, Cinnamon, and their bioactives in regulation of the TGF-β pathway against liver cancer. CONCLUSION Turmeric and its active constituent, curcumin, possess the highest therapeutic potential in treating inflammation-induced HCC and they also have the maximum number of ongoing in-vivo and in-vitro studies.
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Affiliation(s)
- Ajay Sarija Asoka
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
| | - Anusha Kolikkandy
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
| | - Bhagyalakshmi Nair
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
| | - Adithya J Kamath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
- Department of Pharmaceutics, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Lekshmi R Nath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara, P.O., Kochi, Kerala, 682041, India
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12
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Moraes-Lacerda T, Garcia-Fossa F, de Jesus MB. Exploring the interplay between the TGF- βpathway and SLN-mediated transfection: implications for gene delivery efficiency in prostate cancer and non-cancer cells. NANOTECHNOLOGY 2024; 35:325102. [PMID: 38688253 DOI: 10.1088/1361-6528/ad4556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/30/2024] [Indexed: 05/02/2024]
Abstract
Solid lipid nanoparticles (SLN) are widely recognized for their biocompatibility, scalability, and long-term stability, making them versatile formulations for drug and gene delivery. Cellular interactions, governed by complex endocytic and signaling pathways, are pivotal for successfully applying SLN as a therapeutic agent. This study aims to enhance our understanding of the intricate interplay between SLN and cells by investigating the influence of specific endocytic and cell signaling pathways, with a focus on the impact of the TGF-βpathway on SLN-mediated cell transfection in both cancerous and non-cancerous prostate cells. Here, we systematically explored the intricate mechanisms governing the interactions between solid lipid nanoparticles and cells. By pharmacologically manipulating endocytic and signaling pathways, we analyzed alterations in SLNplex internalization, intracellular traffic, and cell transfection dynamics. Our findings highlight the significant role of macropinocytosis in the internalization and transfection processes of SLNplex in both cancer and non-cancer prostate cells. Moreover, we demonstrated that the TGF-βpathway is an important factor influencing endosomal release, potentially impacting gene expression and modulating cell transfection efficiency. This study provides novel insights into the dynamic mechanisms governing the interaction between cells and SLN, emphasizing the pivotal role of TGF-βsignaling in SLN-mediated transfection, affecting internalization, intracellular transport, and release of the genetic cargo. These findings provide valuable insight for the optimization of SLN-based therapeutic strategies in prostate-related applications.
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Affiliation(s)
- Thaís Moraes-Lacerda
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, São Paulo 13083862, Brazil
| | - Fernanda Garcia-Fossa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, São Paulo 13083862, Brazil
| | - Marcelo Bispo de Jesus
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, São Paulo 13083862, Brazil
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13
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Keiser AA, Dong TN, Kramár EA, Butler CW, Chen S, Matheos DP, Rounds JS, Rodriguez A, Beardwood JH, Augustynski AS, Al-Shammari A, Alaghband Y, Alizo Vera V, Berchtold NC, Shanur S, Baldi P, Cotman CW, Wood MA. Specific exercise patterns generate an epigenetic molecular memory window that drives long-term memory formation and identifies ACVR1C as a bidirectional regulator of memory in mice. Nat Commun 2024; 15:3836. [PMID: 38714691 PMCID: PMC11076285 DOI: 10.1038/s41467-024-47996-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/15/2024] [Indexed: 05/10/2024] Open
Abstract
Exercise has beneficial effects on cognition throughout the lifespan. Here, we demonstrate that specific exercise patterns transform insufficient, subthreshold training into long-term memory in mice. Our findings reveal a potential molecular memory window such that subthreshold training within this window enables long-term memory formation. We performed RNA-seq on dorsal hippocampus and identify genes whose expression correlate with conditions in which exercise enables long-term memory formation. Among these genes we found Acvr1c, a member of the TGF ß family. We find that exercise, in any amount, alleviates epigenetic repression at the Acvr1c promoter during consolidation. Additionally, we find that ACVR1C can bidirectionally regulate synaptic plasticity and long-term memory in mice. Furthermore, Acvr1c expression is impaired in the aging human and mouse brain, as well as in the 5xFAD mouse model, and over-expression of Acvr1c enables learning and facilitates plasticity in mice. These data suggest that promoting ACVR1C may protect against cognitive impairment.
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Affiliation(s)
- Ashley A Keiser
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Tri N Dong
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Enikö A Kramár
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Christopher W Butler
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
- Department of Neurology, University of California Irvine, Irvine, CA, 92697, USA
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, School of Information and Computer Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Dina P Matheos
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Jacob S Rounds
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Alyssa Rodriguez
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Joy H Beardwood
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Agatha S Augustynski
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Ameer Al-Shammari
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Yasaman Alaghband
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Vanessa Alizo Vera
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Nicole C Berchtold
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
- Department of Neurology, University of California Irvine, Irvine, CA, 92697, USA
| | - Sharmin Shanur
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Carl W Cotman
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA
- Department of Neurology, University of California Irvine, Irvine, CA, 92697, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, USA.
- Center for the Neurobiology of Learning and Memory (CNLM), University of California, Irvine, Irvine, CA, 92697, USA.
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), University of California, Irvine, Irvine, CA, 92697, USA.
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14
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Du X, Duan M, Kan S, Yang Y, Xu S, Wei J, Li J, Chen H, Zhou X, Xie J. TGF-β3 mediates mitochondrial dynamics through the p-Smad3/AMPK pathway. Cell Prolif 2024; 57:e13579. [PMID: 38012096 PMCID: PMC11056712 DOI: 10.1111/cpr.13579] [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: 09/06/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
It is well recognized that mitochondrial dynamics plays a vital role in cartilage physiology. Any perturbation in mitochondrial dynamics could cause disorders in cartilage metabolism and even lead to the occurrence of cartilage diseases such as osteoarthritis (OA). TGF-β3, as an important growth factor that appears in the joints of OA disease, shows its great potential in chondrocyte growth and metabolism. Nevertheless, the role of TGF-β3 on mitochondrial dynamics is still not well understood. Here we aimed to investigate the effect of TGF-β3 on mitochondrial dynamics of chondrocytes and reveal its underlying bio-mechanism. By using transmission electron microscopy (TEM) for the number and morphology of mitochondria, western blotting for the protein expressions, immunofluorescence for the cytoplasmic distributions of proteins, and RNA sequencing for the transcriptome changes related to mitochondrial dynamics. We found that TGF-β3 could increase the number of mitochondria in chondrocytes. TGF-β3-enhanced mitochondrial number was via promoting the mitochondrial fission. The mitochondrial fission induced by TGF-β3 was mediated by AMPK signaling. TGF-β3 activated canonical p-Smad3 signaling and resultantly mediated AMPK-induced mitochondrial fission. Taken together, these results elucidate an understanding of the role of TGF-β3 on mitochondrial dynamics in chondrocytes and provide potential cues for therapeutic strategies in cartilage injury and OA disease in terms of energy metabolism.
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Affiliation(s)
- Xinmei Du
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Mengmeng Duan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Shiyi Kan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Yueyi Yang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Siqun Xu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Jieya Wei
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Jiazhou Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Hao Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
| | - Jing Xie
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of StomatologySichuan UniversityChengduSichuanChina
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15
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Skok Gibbs C, Mahmood O, Bonneau R, Cho K. PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization. Genome Biol 2024; 25:88. [PMID: 38589899 PMCID: PMC11003171 DOI: 10.1186/s13059-024-03226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
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Affiliation(s)
| | - Omar Mahmood
- Center for Data Science, New York University, New York, NY, 10011, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, 10011, USA
- Prescient Design, Genentech, New York, NY, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, 10011, USA.
- Prescient Design, Genentech, New York, NY, 10010, USA.
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16
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Zhang E, Sun Q, Zhang C, Ma H, Zhang J, Ding Y, Wang G, Jin C, Jin C, Fu Y, Yan C, Zhu M, Wang C, Dai J, Jin G, Hu Z, Shen H, Ma H. Comprehensive functional interrogation of susceptibility loci in GWASs identified KIAA0391 as a novel oncogenic driver via regulating pyroptosis in NSCLC. Cancer Lett 2024; 585:216646. [PMID: 38262497 DOI: 10.1016/j.canlet.2024.216646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/23/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024]
Abstract
Approximately 51 non-small-cell lung cancer (NSCLC) risk loci have been identified by genome-wide association studies (GWASs). We conducted a high throughput RNA-interference (RNAi) screening to identify the candidate causal genes in NSCLC risk loci. KIAA0391 at 14q13.1 had the highest score and could promote proliferation and metastasis of NSCLC in vitro and in vivo. We next prioritized rs3783313 as a causal variant at 14q13.1, by integrating a large-scale population study consisting of 27,120 lung cancer cases and 27,355 controls, functional annotation, and expression quantitative trait locus (eQTL) analysis. Then we found that rs3783313 could facilitate a promoter-enhancer interaction to upregulate KIAA0391 expression by affecting the affinity of transcription factor NFYA. Mechanistically, KIAA0391 knockdown dramatically influenced pyroptosis-related pathways and increased the expression of CASP1. And KIAA0391 transcriptionally repressed CASP1 by binding to SMAD2 and induced an anti-pyroptosis phenotype, promoting tumorigenesis of NSCLC, which provides new insights and potential target for NSCLC.
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Affiliation(s)
- Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qi Sun
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chang Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing 211166, China
| | - Huimin Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jing Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yue Ding
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guoqing Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chen Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Chenying Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yating Fu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Research Unit of Prospective Cohort of Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100142, China.
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Research Unit of Prospective Cohort of Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100142, China.
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17
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Runa F, Ortiz-Soto G, de Barros NR, Kelber JA. Targeting SMAD-Dependent Signaling: Considerations in Epithelial and Mesenchymal Solid Tumors. Pharmaceuticals (Basel) 2024; 17:326. [PMID: 38543112 PMCID: PMC10975212 DOI: 10.3390/ph17030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 04/01/2024] Open
Abstract
SMADs are the canonical intracellular effector proteins of the TGF-β (transforming growth factor-β). SMADs translocate from plasma membrane receptors to the nucleus regulated by many SMAD-interacting proteins through phosphorylation and other post-translational modifications that govern their nucleocytoplasmic shuttling and subsequent transcriptional activity. The signaling pathway of TGF-β/SMAD exhibits both tumor-suppressing and tumor-promoting phenotypes in epithelial-derived solid tumors. Collectively, the pleiotropic nature of TGF-β/SMAD signaling presents significant challenges for the development of effective cancer therapies. Here, we review preclinical studies that evaluate the efficacy of inhibitors targeting major SMAD-regulating and/or -interacting proteins, particularly enzymes that may play important roles in epithelial or mesenchymal compartments within solid tumors.
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Affiliation(s)
- Farhana Runa
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | | | | | - Jonathan A Kelber
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
- Department of Biology, Baylor University, Waco, TX 76706, USA
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18
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Pu T, Wang J, Wei J, Zeng A, Zhang J, Chen J, Yin L, Li J, Lin TP, Melamed J, Corey E, Gao AC, Wu BJ. Stromal-derived MAOB promotes prostate cancer growth and progression. SCIENCE ADVANCES 2024; 10:eadi4935. [PMID: 38335292 PMCID: PMC10857382 DOI: 10.1126/sciadv.adi4935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Prostate cancer (PC) develops in a microenvironment where the stromal cells modulate adjacent tumor growth and progression. Here, we demonstrated elevated levels of monoamine oxidase B (MAOB), a mitochondrial enzyme that degrades biogenic and dietary monoamines, in human PC stroma, which was associated with poor clinical outcomes of PC patients. Knockdown or overexpression of MAOB in human prostate stromal fibroblasts indicated that MAOB promotes cocultured PC cell proliferation, migration, and invasion and co-inoculated prostate tumor growth in mice. Mechanistically, MAOB induces a reactive stroma with activated marker expression, increased extracellular matrix remodeling, and acquisition of a protumorigenic phenotype through enhanced production of reactive oxygen species. Moreover, MAOB transcriptionally activates CXCL12 through Twist1 synergizing with TGFβ1-dependent Smads in prostate stroma, which stimulates tumor-expressed CXCR4-Src/JNK signaling in a paracrine manner. Pharmacological inhibition of stromal MAOB restricted PC xenograft growth in mice. Collectively, these findings characterize the contribution of MAOB to PC and suggest MAOB as a potential stroma-based therapeutic target.
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Affiliation(s)
- Tianjie Pu
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Jing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Jing Wei
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Alan Zeng
- Undergraduate Programs, University of Washington, Seattle, WA 98195, USA
| | - Jinglong Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Jingrui Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Lijuan Yin
- Uro-Oncology Research Program, Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jingjing Li
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Tzu-Ping Lin
- Department of Urology, Taipei Veterans General Hospital, Taipei 11217, Taiwan, Republic of China
- Department of Urology, School of Medicine and Shu-Tien Urological Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan, Republic of China
| | - Jonathan Melamed
- Department of Pathology, Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Allen C. Gao
- Department of Urologic Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Boyang Jason Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
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19
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Ridwan SM, Twillie A, Poursaeid S, Beard EK, Bener MB, Antel M, Cowan AE, Matsuda S, Inaba M. Diffusible fraction of niche BMP ligand safeguards stem-cell differentiation. Nat Commun 2024; 15:1166. [PMID: 38326318 PMCID: PMC10850516 DOI: 10.1038/s41467-024-45408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Drosophila male germline stem cells (GSCs) reside at the tip of the testis and surround a cluster of niche cells. Decapentaplegic (Dpp) is one of the well-established ligands and has a major role in maintaining stem cells located in close proximity. However, the existence and the role of the diffusible fraction of Dpp outside of the niche have been unclear. Here, using genetically-encoded nanobodies called Morphotraps, we physically block Dpp diffusion without interfering with niche-stem cell signaling and find that a diffusible fraction of Dpp is required to ensure differentiation of GSC daughter cells, opposite of its role in maintenance of GSC in the niche. Our work provides an example in which a soluble niche ligand induces opposed cellular responses in stem cells versus in differentiating descendants to ensure spatial control of the niche. This may be a common mechanism to regulate tissue homeostasis.
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Affiliation(s)
- Sharif M Ridwan
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Autumn Twillie
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Samaneh Poursaeid
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Emma Kristine Beard
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Muhammed Burak Bener
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Matthew Antel
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Ann E Cowan
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT, USA
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Shinya Matsuda
- Biozentrum, University of Basel, Basel, Switzerland.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Mayu Inaba
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA.
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20
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Shi D, Feng W, Zi Z. Machine learning unveils RNA polymerase II binding as a predictor for SMAD2-dependent transcription dynamics in response to Actvin signalling. IET Syst Biol 2024; 18:14-22. [PMID: 38193845 PMCID: PMC10860719 DOI: 10.1049/syb2.12085] [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: 08/07/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 01/10/2024] Open
Abstract
The transforming growth factor-β (TGF-β) superfamily, including Nodal and Activin, plays a critical role in various cellular processes. Understanding the intricate regulation and gene expression dynamics of TGF-β signalling is of interest due to its diverse biological roles. A machine learning approach is used to predict gene expression patterns induced by Activin using features, such as histone modifications, RNA polymerase II binding, SMAD2-binding, and mRNA half-life. RNA sequencing and ChIP sequencing datasets were analysed and differentially expressed SMAD2-binding genes were identified. These genes were classified into activated and repressed categories based on their expression patterns. The predictive power of different features and combinations was evaluated using logistic regression models and their performances were assessed. Results showed that RNA polymerase II binding was the most informative feature for predicting the expression patterns of SMAD2-binding genes. The authors provide insights into the interplay between transcriptional regulation and Activin signalling and offers a computational framework for predicting gene expression patterns in response to cell signalling.
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Affiliation(s)
- Dan Shi
- Max Planck Institute for Molecular GeneticsOtto Warburg LaboratoryBerlinGermany
| | - Weihua Feng
- Zhengzhou Tobacco Research Institute of China National Tobacco CorporationZhengzhouChina
| | - Zhike Zi
- Max Planck Institute for Molecular GeneticsOtto Warburg LaboratoryBerlinGermany
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
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21
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Ahuja S, Zaheer S. Multifaceted TGF-β signaling, a master regulator: From bench-to-bedside, intricacies, and complexities. Cell Biol Int 2024; 48:87-127. [PMID: 37859532 DOI: 10.1002/cbin.12097] [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: 06/30/2023] [Revised: 09/08/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Physiological embryogenesis and adult tissue homeostasis are regulated by transforming growth factor-β (TGF-β), an evolutionarily conserved family of secreted polypeptide factors, acting in an autocrine and paracrine manner. The role of TGF-β in inflammation, fibrosis, and cancer is complex and sometimes even contradictory, exhibiting either inhibitory or promoting effects depending on the stage of the disease. Under pathological conditions, especially fibrosis and cancer, overexpressed TGF-β causes extracellular matrix deposition, epithelial-mesenchymal transition, cancer-associated fibroblast formation, and/or angiogenesis. In this review article, we have tried to dive deep into the mechanism of action of TGF-β in inflammation, fibrosis, and carcinogenesis. As TGF-β and its downstream signaling mechanism are implicated in fibrosis and carcinogenesis blocking this signaling mechanism appears to be a promising avenue. However, targeting TGF-β carries substantial risk as this pathway is implicated in multiple homeostatic processes and is also known to have tumor-suppressor functions. There is a need for careful dosing of TGF-β drugs for therapeutic use and patient selection.
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Affiliation(s)
- Sana Ahuja
- Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Sufian Zaheer
- Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
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22
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Kruger RE, Frum T, Brumm AS, Hickey SL, Niakan KK, Aziz F, Shammami MA, Roberts JG, Ralston A. Smad4 is essential for epiblast scaling and morphogenesis after implantation, but nonessential prior to implantation in the mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576717. [PMID: 38328075 PMCID: PMC10849569 DOI: 10.1101/2024.01.23.576717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Bone Morphogenic Protein (BMP) signaling plays an essential and highly conserved role in axial patterning in embryos of many externally developing animal species. However, in mammalian embryos, which develop inside the mother, early development includes an additional stage known as preimplantation. During preimplantation, the epiblast lineage is segregated from the extraembryonic lineages that enable implantation and development in utero. Yet, the requirement for BMP signaling in mouse preimplantation is imprecisely defined. We show that, in contrast to prior reports, BMP signaling (as reported by SMAD1/5/9 phosphorylation) is not detectable until implantation, when it is detected in the primitive endoderm - an extraembryonic lineage. Moreover, preimplantation development appears normal following deletion of maternal and zygotic Smad4, an essential effector of BMP signaling. In fact, mice lacking maternal Smad4 are viable. Finally, we uncover a new requirement for zygotic Smad4 in epiblast scaling and cavitation immediately after implantation, via a mechanism involving FGFR/ERK attenuation. Altogether, our results demonstrate no role for BMP4/SMAD4 in the first lineage decisions during mouse development. Rather, multi-pathway signaling among embryonic and extraembryonic cell types drives epiblast morphogenesis post-implantation.
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Affiliation(s)
- Robin E. Kruger
- Cell and Molecular Biology Ph.D. Program, Michigan State University, East Lansing, MI, 48824, USA
- Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Tristan Frum
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Current address: Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - A. Sophie Brumm
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute; London, NW1 1AT, UK
| | - Stephanie L. Hickey
- Research Technology Support Facility, Michigan State University, East Lansing, MI, 48824, USA
| | - Kathy K. Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute; London, NW1 1AT, UK
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Farina Aziz
- Cell and Molecular Biology Ph.D. Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Marcelio A. Shammami
- Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Ph.D. Program, Michigan State University, East Lansing, MI 48824, USA
| | - Jada G. Roberts
- Molecular, Cellular, and Integrative Physiology Ph.D. Program, Michigan State University, East Lansing, MI 48824, USA
| | - Amy Ralston
- Reproductive and Developmental Sciences Training Program, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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23
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Xiao M, Wang F, Chen N, Zhang H, Cao J, Yu Y, Zhao B, Ji J, Xu P, Li L, Shen L, Lin X, Feng XH. Smad4 sequestered in SFPQ condensates prevents TGF-β tumor-suppressive signaling. Dev Cell 2024; 59:48-63.e8. [PMID: 38103553 DOI: 10.1016/j.devcel.2023.11.020] [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: 05/10/2023] [Revised: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Loss of TGF-β growth-inhibitory responses is a hallmark of human cancer. However, the molecular mechanisms underlying the TGF-β resistance of cancer cells remain to be fully elucidated. Splicing factor proline- and glutamine-rich (SFPQ) is a prion-like RNA-binding protein that is frequently upregulated in human cancers. In this study, we identified SFPQ as a potent suppressor of TGF-β signaling. The ability of SFPQ to suppress TGF-β responses depends on its prion-like domain (PrLD) that drives liquid-liquid phase separation (LLPS). Mechanistically, SFPQ physically restrained Smad4 in its condensates, which excluded Smad4 from the Smad complex and chromatin occupancy and thus functionally dampened Smad-dependent transcriptional responses. Accordingly, SFPQ deficiency or loss of phase separation activities rendered human cells hypersensitive to TGF-β responses. Together, our data identify an important function of SFPQ through LLPS that suppresses Smad transcriptional activation and TGF-β tumor-suppressive activity.
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Affiliation(s)
- Mu Xiao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Fei Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Nuo Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hanchenxi Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jin Cao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yi Yu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Bin Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Li Shen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xia Lin
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, Zhejiang 321000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China; The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310009, China.
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24
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Gonzalez V, Grant MG, Suzuki M, Christophers B, Rowland Williams J, Burdine RD. Cooperation between Nodal and FGF signals regulates zebrafish cardiac cell migration and heart morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574380. [PMID: 38260277 PMCID: PMC10802409 DOI: 10.1101/2024.01.05.574380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Asymmetric vertebrate heart development is driven by an intricate sequence of morphogenetic cell movements, the coordination of which requires precise interpretation of signaling cues by heart primordia. Here we show that Nodal functions cooperatively with FGF during heart tube formation and asymmetric placement. Both pathways act as migratory stimuli for cardiac progenitor cells (CPCs), but FGF is dispensable for directing heart tube asymmetry, which is governed by Nodal. We further find that Nodal controls CPC migration by inducing left-right asymmetries in the formation of actin-based protrusions in CPCs. Additionally, we define a developmental window in which FGF signals are required for proper heart looping and show cooperativity between FGF and Nodal in this process. We present evidence FGF may promote heart looping through addition of the secondary heart field. Finally, we demonstrate that loss of FGF signaling affects proper development of the atrioventricular canal (AVC), which likely contributes to abnormal chamber morphologies in FGF-deficient hearts. Together, our data shed insight into how the spatiotemporal dynamics of signaling cues regulate the cellular behaviors underlying organ morphogenesis.
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Affiliation(s)
- Vanessa Gonzalez
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA, 08544
| | - Meagan G. Grant
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA, 08544
| | - Makoto Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan, 739-8526
| | - Briana Christophers
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA, 08544
| | - Jessica Rowland Williams
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA, 08544
- Current affiliation: National Institute for Student Success, at Georgia State University, Atlanta, GA 30303
| | - Rebecca D. Burdine
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA, 08544
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25
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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26
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Feng R, Tong C, Lin T, Liu H, Shao C, Li Y, Sticht C, Kan K, Li X, Liu R, Wang S, Wang S, Munker S, Niess H, Meyer C, Liebe R, Ebert MP, Dooley S, Wang H, Ding H, Weng HL. Insulin Determines Transforming Growth Factor β Effects on Hepatocyte Nuclear Factor 4α Transcription in Hepatocytes. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:52-70. [PMID: 37820926 DOI: 10.1016/j.ajpath.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Loss of hepatocyte nuclear factor 4α (HNF4α) expression is frequently observed in end-stage liver disease and associated with loss of vital liver functions, thus increasing mortality. Loss of HNF4α expression is mediated by inflammatory cytokines, such as transforming growth factor (TGF)-β. However, details of how HNF4α is suppressed are largely unknown to date. Herein, TGF-β did not directly inhibit HNF4α but contributed to its transcriptional regulation by SMAD2/3 recruiting acetyltransferase CREB-binding protein/p300 to the HNF4α promoter. The recruitment of CREB-binding protein/p300 is indispensable for CCAAT/enhancer-binding protein α (C/EBPα) binding, another essential requirement for constitutive HNF4α expression in hepatocytes. Consistent with the in vitro observation, 67 of 98 patients with hepatic HNF4α expressed both phospho-SMAD2 and C/EBPα, whereas 22 patients without HNF4α expression lacked either phospho-SMAD2 or C/EBPα. In contrast to the observed induction of HNF4α, SMAD2/3 inhibited C/EBPα transcription. Long-term TGF-β incubation resulted in C/EBPα depletion, which abrogated HNF4α expression. Intriguingly, SMAD2/3 inhibitory binding to the C/EBPα promoter was abolished by insulin. Two-thirds of patients without C/EBPα lacked membrane glucose transporter type 2 expression in hepatocytes, indicating insulin resistance. Taken together, these data indicate that hepatic insulin sensitivity is essential for hepatic HNF4α expression in the condition of inflammation.
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Affiliation(s)
- Rilu Feng
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chenhao Tong
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tao Lin
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hui Liu
- Department of Pathology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Chen Shao
- Department of Pathology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yujia Li
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kejia Kan
- Department of Surgery, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiaofeng Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Rui Liu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Sai Wang
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shanshan Wang
- Beijing Institute of Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Stefan Munker
- Department of Medicine II, Liver Centre Munich, University Hospital, Campus Großhadern, Ludwig-Maximilians-University Munich, Munich, Germany; Liver Centre Munich, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Hanno Niess
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany; Biobank of the Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christoph Meyer
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Roman Liebe
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Clinical Cooperation Unit Healthy Metabolism, Center of Preventive Medicine and Digital Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Steven Dooley
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hua Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huiguo Ding
- Department of Gastroenterology and Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Hong-Lei Weng
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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von Schalburg KR, Gowen BE, Christensen KA, Ignatz EH, Hall JR, Rise ML. The late-evolving salmon and trout join the GnRH1 club. Histochem Cell Biol 2023; 160:517-539. [PMID: 37566258 DOI: 10.1007/s00418-023-02227-z] [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] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Although it is known that the whitefish, an ancient salmonid, expresses three distinct gonadotropin-releasing hormone (GnRH) forms in the brain, it has been thought that the later-evolving salmonids (salmon and trout) had only two types of GnRH: GnRH2 and GnRH3. We now provide evidence for the expression of GnRH1 in the gonads of Atlantic salmon by rapid amplification of cDNA ends, real-time quantitative PCR and immunohistochemistry. We examined six different salmonid genomes and found that each assembly has one gene that likely encodes a viable GnRH1 prepropeptide. In contrast to both functional GnRH2 and GnRH3 paralogs, the GnRH1 homeolog can no longer express the hormone. Furthermore, the viable salmonid GnRH1 mRNA is composed of only three exons, rather than the four exons that build the GnRH2 and GnRH3 mRNAs. Transcribed gnrh1 is broadly expressed (in 17/18 tissues examined), with relative abundance highest in the ovaries. Expression of the gnrh2 and gnrh3 mRNAs is more restricted, primarily to the brain, and not in the gonads. The GnRH1 proximal promoter presents composite binding elements that predict interactions with complexes that contain diverse cell fate and differentiation transcription factors. We provide immunological evidence for GnRH1 peptide in the nucleus of 1-year-old type A spermatogonia and cortical alveoli oocytes. GnRH1 peptide was not detected during other germ cell or reproductive stages. GnRH1 activity in the salmonid gonad may occur only during early stages of development and play a key role in a regulatory network that controls mitotic and/or meiotic processes within the germ cell.
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Affiliation(s)
- Kristian R von Schalburg
- Department of Biology, Electron Microscopy Laboratory, University of Victoria, Victoria, BC, V8W 3N5, Canada.
| | - Brent E Gowen
- Department of Biology, Electron Microscopy Laboratory, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Eric H Ignatz
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
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28
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Richardson L, Wilcockson SG, Guglielmi L, Hill CS. Context-dependent TGFβ family signalling in cell fate regulation. Nat Rev Mol Cell Biol 2023; 24:876-894. [PMID: 37596501 DOI: 10.1038/s41580-023-00638-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/20/2023]
Abstract
The transforming growth factor-β (TGFβ) family are a large group of evolutionarily conserved cytokines whose signalling modulates cell fate decision-making across varying cellular contexts at different stages of life. Here we discuss new findings in early embryos that reveal how, in contrast to our original understanding of morphogen interpretation, robust cell fate specification can originate from a noisy combination of signalling inputs and a broad range of signalling levels. We compare this evidence with novel findings on the roles of TGFβ family signalling in tissue maintenance and homeostasis during juvenile and adult life, spanning the skeletal, haemopoietic and immune systems. From these comparisons, it emerges that in contrast to robust developing systems, relatively small perturbations in TGFβ family signalling have detrimental effects at later stages in life, leading to aberrant cell fate specification and disease, for example in cancer or congenital disorders. Finally, we highlight novel strategies to target and amend dysfunction in signalling and discuss how gleaning knowledge from different fields of biology can help in the development of therapeutics for aberrant TGFβ family signalling in disease.
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Affiliation(s)
- Louise Richardson
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Scott G Wilcockson
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK.
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29
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Nogueras Pérez R, Heredia-Nicolás N, de Lara-Peña L, López de Andrés J, Marchal JA, Jiménez G, Griñán-Lisón C. Unraveling the Potential of miRNAs from CSCs as an Emerging Clinical Tool for Breast Cancer Diagnosis and Prognosis. Int J Mol Sci 2023; 24:16010. [PMID: 37958993 PMCID: PMC10647353 DOI: 10.3390/ijms242116010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Breast cancer (BC) is the most diagnosed cancer in women and the second most common cancer globally. Significant advances in BC research have led to improved early detection and effective therapies. One of the key challenges in BC is the presence of BC stem cells (BCSCs). This small subpopulation within the tumor possesses unique characteristics, including tumor-initiating capabilities, contributes to treatment resistance, and plays a role in cancer recurrence and metastasis. In recent years, microRNAs (miRNAs) have emerged as potential regulators of BCSCs, which can modulate gene expression and influence cellular processes like BCSCs' self-renewal, differentiation, and tumor-promoting pathways. Understanding the miRNA signatures of BCSCs holds great promise for improving BC diagnosis and prognosis. By targeting BCSCs and their associated miRNAs, researchers aim to develop more effective and personalized treatment strategies that may offer better outcomes for BC patients, minimizing tumor recurrence and metastasis. In conclusion, the investigation of miRNAs as regulators of BCSCs opens new directions for advancing BC research through the use of bioinformatics and the development of innovative therapeutic approaches. This review summarizes the most recent and innovative studies and clinical trials on the role of BCSCs miRNAs as potential tools for early diagnosis, prognosis, and resistance.
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Affiliation(s)
- Raquel Nogueras Pérez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
| | - Noelia Heredia-Nicolás
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
| | - Laura de Lara-Peña
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Julia López de Andrés
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Juan Antonio Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
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30
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Sadakane H, Matsumura M, Murakami M, Itoyama E, Shimokawa F, Sakota S, Yoshioka H, Kawabata H, Matsui T, Funaba M. Weak response of bovine hepcidin induction to iron through decreased expression of Smad4. FASEB J 2023; 37:e23243. [PMID: 37800888 DOI: 10.1096/fj.202301186rr] [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: 06/14/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Hepcidin negatively regulates systemic iron levels by inhibiting iron entry into the circulation. Hepcidin production is increased in response to an increase in systemic iron via the activation of the bone morphogenetic protein (BMP) pathway. Regulation of hepcidin expression by iron status has been proposed on the basis of evidence mainly from rodents and humans. We evaluated the effect of iron administration on plasma hepcidin concentrations in calves and the expression of bovine hepcidin by the BMP pathway in a cell culture study. Hematocrit as well as levels of blood hemoglobin and plasma iron were lower than the reference level in calves aged 1-4 weeks. Although intramuscular administration of iron increased iron-related parameters, plasma hepcidin concentrations were unaffected. Treatment with BMP6 increased hepcidin expression in human liver-derived cells but not in bovine liver-derived cells. A luciferase-based reporter assay revealed that Smad4 was required for hepcidin reporter transcription induced by Smad1. The reporter activity of hepcidin was lower in the cells transfected with bovine Smad4 than in those transfected with murine Smad4. The lower expression levels of bovine Smad4 were responsible for the lower activity of the hepcidin reporter, which might be due to the instability of bovine Smad4 mRNA. In fact, the endogenous Smad4 protein levels were lower in bovine cells than in human and murine cells. Smad4 also confers TGF-β/activin-mediated signaling. Induction of TGF-β-responsive genes was also lower after treatment with TGF-β1 in bovine hepatocytes than in human hepatoma cells. We revealed the unique regulation of bovine hepcidin expression and the characteristic TGF-β family signaling mediated by bovine Smad4. The present study suggests that knowledge of the regulatory expression of hepcidin as well as TGF-β family signaling obtained in murine and human cells is not always applicable to bovine cells.
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Affiliation(s)
- Hiroyuki Sadakane
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Manami Matsumura
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masaru Murakami
- Laboratory of Molecular Biology, Azabu University School of Veterinary Medicine, Sagamihara, Japan
| | | | - Fumie Shimokawa
- Laboratory of Molecular Biology, Azabu University School of Veterinary Medicine, Sagamihara, Japan
| | - Shotaro Sakota
- Laboratory of Molecular Biology, Azabu University School of Veterinary Medicine, Sagamihara, Japan
| | | | - Hiroshi Kawabata
- National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Tohru Matsui
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masayuki Funaba
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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31
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Taghehchian N, Maharati A, Akhlaghipour I, Zangouei AS, Moghbeli M. PRC2 mediated KLF2 down regulation: a therapeutic and diagnostic axis during tumor progression. Cancer Cell Int 2023; 23:233. [PMID: 37807067 PMCID: PMC10561470 DOI: 10.1186/s12935-023-03086-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023] Open
Abstract
Surgery and chemo-radiotherapy are used as the common first-line treatment options in many cancers. However, tumor relapse is observed in many cancer patients following such first-line treatments. Therefore, targeted therapy according to the molecular cancer biology can be very important in reducing tumor recurrence. In this regard, a wide range of monoclonal antibodies against the growth factors and their receptors can offer more targeted treatment in cancer patients. However, due to the importance of growth factors in the normal biology of body cells, side effects can also be observed following the application of growth factor inhibitors. Therefore, more specific factors should be introduced as therapeutic targets with less side effects. Krüppel-like factors 2 (KLF2) belongs to the KLF family of transcription factors that are involved in the regulation of many cellular processes. KLF2 deregulations have been also reported during the progression of many tumors. In the present review we discussed the molecular mechanisms of KLF2 during tumor growth and invasion. It has been shown that the KLF2 as a tumor suppressor is mainly inhibited by the non-coding RNAs (ncRNAs) through the polycomb repressive complex 2 (PRC2) recruitment. This review is an effective step towards introducing the KLF2 as a suitable diagnostic and therapeutic target in cancer patients.
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Affiliation(s)
- Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Iman Akhlaghipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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32
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McCracken IR, Baker AH, Smart N, De Val S. Transcriptional regulators of arterial and venous identity in the developing mammalian embryo. CURRENT OPINION IN PHYSIOLOGY 2023; 35:None. [PMID: 38328689 PMCID: PMC10844100 DOI: 10.1016/j.cophys.2023.100691] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The complex and hierarchical vascular network of arteries, veins, and capillaries features considerable endothelial heterogeneity, yet the regulatory pathways directing arteriovenous specification, differentiation, and identity are still not fully understood. Recent advances in analysis of endothelial-specific gene-regulatory elements, single-cell RNA sequencing, and cell lineage tracing have both emphasized the importance of transcriptional regulation in this process and shed considerable light on the mechanism and regulation of specification within the endothelium. In this review, we discuss recent advances in our understanding of how endothelial cells acquire arterial and venous identity and the role different transcription factors play in this process.
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Affiliation(s)
- Ian R McCracken
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Nicola Smart
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom
| | - Sarah De Val
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom
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33
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Li Y, Xu M, Zhai H, Yang C, Yang J, Ke Z, Chen W, Ou J, Sha Z, Xiao Q. Lipopolysaccharide (LPS) extracted from Bacteroides vulgatus effectively prevents LPS extracted from Escherichia coli from inducing epithelial‑mesenchymal transition. Mol Med Rep 2023; 28:195. [PMID: 37681466 PMCID: PMC10502948 DOI: 10.3892/mmr.2023.13082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Pathological epithelial‑mesenchymal transition (EMT) has been shown to fulfill a key role in the development and progression of a variety of lung diseases. It has been demonstrated that the inflammatory microenvironment is a decisive factor in inducing pathological EMT. Hexacylated lipopolysaccharide (LPS) [or proacylated lipopolysaccharide (P‑LPS), which functions as proinflammatory lipopolysaccharide] is one of the most effective Toll‑like receptor 4 (TLR4) agonists. Furthermore, the pentacylated and tetracylated form of lipopolysaccharide (or A‑LPS, which functions as anti‑inflammatory lipopolysaccharide) has been shown to elicit competitive antagonistic effects against the pro‑inflammatory activity of P‑LPS. At present, it remains unclear whether LPS extracted from Bacteroides vulgatus (BV‑LPS) can prevent LPS extracted from Escherichia coli (EC‑LPS) from inducing pathological EMT. In the present study, A549 cells and C57BL/6 mice lung tissue were both induced by EC‑LPS (P‑LPS) and BV‑LPS (A‑LPS), either alone or in combination. The anticipated anti‑inflammatory effects of BV‑LPS were analyzed by examining the lung coefficient, lung pathology, A549 cell morphology and expression levels both of the inflammatory cytokines, IL‑1β, IL‑6 and TNF‑α and of the EMT signature proteins, epithelial cadherin (E‑cadherin), α‑smooth muscle actin (α‑SMA) and vimentin. In addition, the expression levels of TLR4, bone morphogenic protein and activin membrane‑bound inhibitor (BAMBI) and Snail were detected and the possible mechanism underlying how BV‑LPS may prevent EC‑LPS‑induced EMT was analyzed. The results obtained showed that the morphology of the A549 cells was significantly polarized, the lung index was significantly increased, the alveolar structure was collapsed and the expression levels of IL‑1β, IL‑6, TNF‑α, α‑SMA, vimentin, TLR4 and Snail in both lung tissue and A549 cells were significantly increased, whereas those of E‑cadherin and BAMBI were significantly decreased. Treatment with BV‑LPS in combination with EC‑LPS was found to reverse these changes. In conclusion, the present study demonstrated that BV‑LPS is able to effectively prevent EC‑LPS‑induced EMT in A549 cells and in mouse lung tissue and furthermore, the underlying mechanism may be associated with inhibition of the TLR4/BAMBI/Snail signaling pathway.
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Affiliation(s)
- Yuping Li
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Mengdan Xu
- Shizhen College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550200, P.R. China
| | - Haiying Zhai
- The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550000, P.R. China
| | - Changfu Yang
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Jiaotong Yang
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Zunli Ke
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Wanhao Chen
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Jiangqin Ou
- The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550000, P.R. China
| | - Zongge Sha
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Qiaoqiao Xiao
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
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34
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Liu C, Guo H, Shi C, Sun H. BMP signaling in the development and regeneration of tooth roots: from mechanisms to applications. Front Cell Dev Biol 2023; 11:1272201. [PMID: 37779895 PMCID: PMC10540449 DOI: 10.3389/fcell.2023.1272201] [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: 08/03/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Short root anomaly (SRA), along with caries, periodontitis, and trauma, can cause tooth loss, affecting the physical and mental health of patients. Dental implants have become widely utilized for tooth restoration; however, they exhibit certain limitations compared to natural tooth roots. Tissue engineering-mediated root regeneration offers a strategy to sustain a tooth with a physiologically more natural function by regenerating the bioengineered tooth root (bio-root) based on the bionic principle. While the process of tooth root development has been reported in previous studies, the specific molecular mechanisms remain unclear. The Bone Morphogenetic Proteins (BMPs) family is an essential factor regulating cellular activities and is involved in almost all tissue development. Recent studies have focused on exploring the mechanism of BMP signaling in tooth root development by using transgenic animal models and developing better tissue engineering strategies for bio-root regeneration. This article reviews the unique roles of BMP signaling in tooth root development and regeneration.
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Affiliation(s)
- Cangwei Liu
- Department of Oral Pathology, Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, China
| | - Hao Guo
- Department of Oral Pathology, Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, China
| | - Ce Shi
- Department of Oral Pathology, Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, China
| | - Hongchen Sun
- Department of Oral Pathology, Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, China
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35
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Jatzlau J, Mendez PL, Altay A, Raaz L, Zhang Y, Mähr S, Sesver A, Reichenbach M, Mundlos S, Vingron M, Knaus P. Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription. iScience 2023; 26:107405. [PMID: 37680470 PMCID: PMC10481294 DOI: 10.1016/j.isci.2023.107405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 09/09/2023] Open
Abstract
Bone morphogenetic protein (BMP) signaling and fluid shear stress (FSS) mediate complementary functions in vascular homeostasis and disease development. It remains to be shown whether altered chromatin accessibility downstream of BMP and FSS offers a crosstalk level to explain changes in SMAD-dependent transcription. Here, we employed ATAC-seq to analyze arterial endothelial cells stimulated with BMP9 and/or FSS. We found that BMP9-sensitive regions harbor non-palindromic GC-rich SMAD-binding elements (GGCTCC) and 69.7% of these regions become BMP-insensitive in the presence of FSS. While GATA and KLF transcription factor (TF) motifs are unique to BMP9- and FSS-sensitive regions, respectively, SOX motifs are common to both. Finally, we show that both SOX(13/18) and GATA(2/3/6) family members are directly upregulated by SMAD1/5. These findings highlight the mechano-dependency of SMAD-signaling by a sequential mechanism of first elevated pioneer TF expression, allowing subsequent chromatin opening to eventually providing accessibility to novel SMAD binding sites.
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Affiliation(s)
- Jerome Jatzlau
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Paul-Lennard Mendez
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
| | - Aybuge Altay
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lion Raaz
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin, 13353 Berlin, Germany
| | - Yufei Zhang
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sophia Mähr
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Akin Sesver
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Maria Reichenbach
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin, 13353 Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
| | - Petra Knaus
- Institute of Chemistry and Biochemistry - Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany
- International Max-Planck Research School for Biology AND Computation (IMPRS-BAC), 14195 Berlin, Germany
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36
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Mostufi-Zadeh-Haghighi G, Veratti P, Zodel K, Greve G, Waterhouse M, Zeiser R, Cleary ML, Lübbert M, Duque-Afonso J. Functional Characterization of Transforming Growth Factor-β Signaling in Dasatinib Resistance and Pre-BCR + Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:4328. [PMID: 37686604 PMCID: PMC10486903 DOI: 10.3390/cancers15174328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The multi-kinase inhibitor dasatinib has been implicated to be effective in pre-B-cell receptor (pre-BCR)-positive acute lymphoblastic leukemia (ALL) expressing the E2A-PBX1 fusion oncoprotein. The TGFβ signaling pathway is involved in a wide variety of cellular processes, including embryonic development and cell homeostasis, and it can have dual roles in cancer: suppressing tumor growth at early stages and mediating tumor progression at later stages. In this study, we identified the upregulation of the TGFβ signaling pathway in our previously generated human dasatinib-resistant pre-BCR+/E2A-PBX1+ ALL cells using global transcriptomic analysis. We confirm the upregulation of the TGFβ pathway member SMAD3 at the transcriptional and translational levels in dasatinib-resistant pre-BCR+/E2A-PBX1+ ALL cells. Hence, dasatinib blocks, at least partially, TGFβ-induced SMAD3 phosphorylation in several B-cell precursor (BCP) ALL cell lines as well as in dasatinib-resistant pre-BCR+/E2A-PBX1+ ALL cells. Activation of the TGFβ signaling pathway by TGF-β1 leads to growth inhibition by cell cycle arrest at the G0/G1 stage, increase in apoptosis and transcriptional changes of SMAD-targeted genes, e.g. c-MYC downregulation, in pre-BCR+/E2A-PBX1+ ALL cells. These results provide a better understanding about the role that the TGFβ signaling pathway plays in leukemogenesis of BCP-ALL as well as in secondary drug resistance to dasatinib.
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Affiliation(s)
- Gila Mostufi-Zadeh-Haghighi
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
| | - Pia Veratti
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106 Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kyra Zodel
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
| | - Gabriele Greve
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
| | - Miguel Waterhouse
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
| | - Robert Zeiser
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
| | - Michael L. Cleary
- Department of Pathology, Stanford University, Stanford, CA 94305, USA;
| | - Michael Lübbert
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Jesús Duque-Afonso
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (G.M.-Z.-H.); (P.V.); (K.Z.); (G.G.); (M.W.); (R.Z.); (M.L.)
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37
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Pan L, Vlahopoulos S, Tanner L, Bergwik J, Bacsi A, Radak Z, Egesten A, Ba X, Brasier AR, Boldogh I. Substrate-specific binding of 8-oxoguanine DNA glycosylase 1 (OGG1) reprograms mucosal adaptations to chronic airway injury. Front Immunol 2023; 14:1186369. [PMID: 37614238 PMCID: PMC10442650 DOI: 10.3389/fimmu.2023.1186369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/24/2023] [Indexed: 08/25/2023] Open
Abstract
Recent advances have uncovered the non-random distribution of 7, 8-dihydro-8-oxoguanine (8-oxoGua) induced by reactive oxygen species, which is believed to have epigenetic effects. Its cognate repair protein, 8-oxoguanine DNA glycosylase 1 (OGG1), reads oxidative substrates and participates in transcriptional initiation. When redox signaling is activated in small airway epithelial cells, the DNA repair function of OGG1 is repurposed to transmit acute inflammatory signals accompanied by cell state transitions and modification of the extracellular matrix. Epithelial-mesenchymal and epithelial-immune interactions act cooperatively to establish a local niche that instructs the mucosal immune landscape. If the transitional cell state governed by OGG1 remains responsive to inflammatory mediators instead of differentiation, the collateral damage provides positive feedback to inflammation, ascribing inflammatory remodeling to one of the drivers in chronic pathologies. In this review, we discuss the substrate-specific read through OGG1 has evolved in regulating the innate immune response, controlling adaptations of the airway to environmental and inflammatory injury, with a focus on the reader function of OGG1 in initiation and progression of epithelial to mesenchymal transitions in chronic pulmonary disease.
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Affiliation(s)
- Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Spiros Vlahopoulos
- Horemeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Lloyd Tanner
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Jesper Bergwik
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Attila Bacsi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Hungary, Debrecen, Hungary
| | - Zsolt Radak
- Research Institute of Sport Science, University of Physical Education, Budapest, Hungary
| | - Arne Egesten
- Respiratory Medicine, Allergology & Palliative Medicine, Department of Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
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Gu Y, Becker MA, Müller L, Reuss K, Umlauf F, Tang T, Menger MD, Laschke MW. MicroRNAs in Tumor Endothelial Cells: Regulation, Function and Therapeutic Applications. Cells 2023; 12:1692. [PMID: 37443725 PMCID: PMC10340284 DOI: 10.3390/cells12131692] [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: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Tumor endothelial cells (TECs) are key stromal components of the tumor microenvironment, and are essential for tumor angiogenesis, growth and metastasis. Accumulating evidence has shown that small single-stranded non-coding microRNAs (miRNAs) act as powerful endogenous regulators of TEC function and blood vessel formation. This systematic review provides an up-to-date overview of these endothelial miRNAs. Their expression is mainly regulated by hypoxia, pro-angiogenic factors, gap junctions and extracellular vesicles, as well as long non-coding RNAs and circular RNAs. In preclinical studies, they have been shown to modulate diverse fundamental angiogenesis-related signaling pathways and proteins, including the vascular endothelial growth factor (VEGF)/VEGF receptor (VEGFR) pathway; the rat sarcoma virus (Ras)/rapidly accelerated fibrosarcoma (Raf)/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway; the phosphoinositide 3-kinase (PI3K)/AKT pathway; and the transforming growth factor (TGF)-β/TGF-β receptor (TGFBR) pathway, as well as krüppel-like factors (KLFs), suppressor of cytokine signaling (SOCS) and metalloproteinases (MMPs). Accordingly, endothelial miRNAs represent promising targets for future anti-angiogenic cancer therapy. To achieve this, it will be necessary to further unravel the regulatory and functional networks of endothelial miRNAs and to develop safe and efficient TEC-specific miRNA delivery technologies.
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Affiliation(s)
- Yuan Gu
- Institute for Clinical & Experimental Surgery, Saarland University, 66421 Saar, Germany; (M.A.B.); (L.M.); (K.R.); (F.U.); (T.T.); (M.D.M.); (M.W.L.)
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Hussain S, Sadouni N, van Essen D, Dao LTM, Ferré Q, Charbonnier G, Torres M, Gallardo F, Lecellier CH, Sexton T, Saccani S, Spicuglia S. Short tandem repeats are important contributors to silencer elements in T cells. Nucleic Acids Res 2023; 51:4845-4866. [PMID: 36929452 PMCID: PMC10250210 DOI: 10.1093/nar/gkad187] [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: 05/09/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
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Affiliation(s)
- Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Dominic van Essen
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Quentin Ferré
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Charles-Henri Lecellier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Tom Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire – IGBMC (CNRS UMR 7104, INSERM U1258, Université de Strasbourg), 67404 Illkirch, France
| | - Simona Saccani
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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Hye T, Hossain MR, Saha D, Foyez T, Ahsan F. Emerging biologics for the treatment of pulmonary arterial hypertension. J Drug Target 2023; 31:1-15. [PMID: 37026714 PMCID: PMC10228297 DOI: 10.1080/1061186x.2023.2199351] [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: 08/26/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 04/08/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a rare pulmonary vascular disorder, wherein mean systemic arterial pressure (mPAP) becomes abnormally high because of aberrant changes in various proliferative and inflammatory signalling pathways of pulmonary arterial cells. Currently used anti-PAH drugs chiefly target the vasodilatory and vasoconstrictive pathways. However, an imbalance between bone morphogenetic protein receptor type II (BMPRII) and transforming growth factor beta (TGF-β) pathways is also implicated in PAH predisposition and pathogenesis. Compared to currently used PAH drugs, various biologics have shown promise as PAH therapeutics that elicit their therapeutic actions akin to endogenous proteins. Biologics that have thus far been explored as PAH therapeutics include monoclonal antibodies, recombinant proteins, engineered cells, and nucleic acids. Because of their similarity with naturally occurring proteins and high binding affinity, biologics are more potent and effective and produce fewer side effects when compared with small molecule drugs. However, biologics also suffer from the limitations of producing immunogenic adverse effects. This review describes various emerging and promising biologics targeting the proliferative/apoptotic and vasodilatory pathways involved in PAH pathogenesis. Here, we have discussed sotatercept, a TGF-β ligand trap, which is reported to reverse vascular remodelling and reduce PVR with an improved 6-minute walk distance (6-MWDT). We also elaborated on other biologics including BMP9 ligand and anti-gremlin1 antibody, anti-OPG antibody, and getagozumab monoclonal antibody and cell-based therapies. Overall, recent literature suggests that biologics hold excellent promise as a safe and effective alternative to currently used PAH therapeutics.
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Affiliation(s)
- Tanvirul Hye
- Department of Foundational Medical Studies, Oakland University William Beaumont School of Medicine, Rochester, Michigan
| | - Md Riajul Hossain
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Dipongkor Saha
- Department of Pharmaceutical and Biomedical Sciences, California Northstate College of Pharmacy, Elk Grove, California
| | - Tahmina Foyez
- Department of Hematology Blood Research Center School of Medicine, The University of North Carolina at Chapel Hill, North Carolina
| | - Fakhrul Ahsan
- Department of Pharmaceutical and Biomedical Sciences, California Northstate College of Pharmacy, Elk Grove, California
- MedLuidics LLC, Elk Grove, California, USA
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Mazi FA, Cakiroglu E, Uysal M, Kalyoncu M, Demirci D, Sozeri PYG, Yilmaz GO, Ozhan SE, Senturk S. The paracaspase MALT1 is a downstream target of Smad3 and potentiates the crosstalk between TGF-β and NF-kB signaling pathways in cancer cells. Cell Signal 2023; 105:110611. [PMID: 36708753 DOI: 10.1016/j.cellsig.2023.110611] [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: 07/21/2022] [Revised: 12/30/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
TGF-β signaling mediates its biological effects by engaging canonical Smad proteins and crosstalking extensively with other signaling networks, including the NF-kB pathway. The paracaspase MALT1 is an intracellular signaling molecule essential for NF-kB activation downstream of several key cell surface receptors. Despite intensive research on TGF-β and NF-kB interactions, the significance of MALT1 in this context remains undecoded. Here we provide experimental evidence supporting that MALT1 functions to converge these pathways. Using A549 and Huh7 cancer cell line models, we report that TGF-β stimulation enhances MALT1 protein and transcript levels in a time- and dose-dependent manner. Systematic and selective perturbation of TGF-β signaling components identifies MALT1 as a downstream target of Smad3. Rescue experiments in SMAD3 knockout cells confirm that C-terminal phosphorylation of Smad3 is central to MALT1 induction. Corroborating these data, we document that the expression of SMAD3 and MALT1 genes are positively correlated in TCGA cohorts, and we trace the molecular basis of MALT1 elevation to promoter activation. Functional studies in parental as well as NF-kB p65 signaling reporter engineered cells conclusively reveal that MALT1 is paramount for TGF-β-stimulated nuclear translocation and transcriptional activation of NF-kB p65. Furthermore, we find that BCL10 is also implicated in TGF-β activation of NF-kB target genes, potentially coupling the TGF-β-MALT1-NF-kB signaling axis to the CARMA-BCL10-MALT1 (CBM) signalosome. The novel findings of this study indicate that MALT1 is a downstream target of the canonical TGF-β/Smad3 pathway and plays a critical role in modulating TGF-β and NF-kB crosstalk in cancer.
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Affiliation(s)
- Fatma Aybuke Mazi
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Ece Cakiroglu
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Merve Uysal
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | | | - Perihan Yagmur Guneri Sozeri
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | | | | | - Serif Senturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey.
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Tsujimura N, Ogino T, Hiraki M, Kai T, Yamamoto H, Hirose H, Yokoyama Y, Sekido Y, Hata T, Miyoshi N, Takahashi H, Uemura M, Mizushima T, Doki Y, Eguchi H, Yamamoto H. Super Carbonate Apatite-miR-497a-5p Complex Is a Promising Therapeutic Option against Inflammatory Bowel Disease. Pharmaceuticals (Basel) 2023; 16:618. [PMID: 37111375 PMCID: PMC10146939 DOI: 10.3390/ph16040618] [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: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The incidence of inflammatory bowel disease (IBD) is increasing worldwide. It is reported that TGF-β/Smad signal pathway is inactivated in patients with Crohn's disease by overexpression of Smad 7. With expectation of multiple molecular targeting by microRNAs (miRNAs), we currently attempted to identify certain miRNAs that activate TGF-β/Smad signal pathway and aimed to prove in vivo therapeutic efficacy in mouse model. Through Smad binding element (SBE) reporter assays, we focused on miR-497a-5p. This miRNA is common between mouse and human species and enhanced the activity of TGF-β/Smad signal pathway, decreased Smad 7 and/or increased phosphorylated Smad 3 expression in non-tumor cell line HEK293, colorectal cancer cell line HCT116 and mouse macrophage J774a.1 cells. MiR-497a-5p also suppressed the production of inflammatory cytokines TNF-α, IL-12p40, a subunit of IL-23, and IL-6 when J774a.1 cells were stimulated by lipopolysaccharides (LPS). In a long-term therapeutic model for mouse dextran sodium sulfate (DSS)-induced colitis, systemic delivery of miR-497a-5p load on super carbonate apatite (sCA) nanoparticle as a vehicle restored epithelial structure of the colonic mucosa and suppressed bowel inflammation compared with negative control miRNA treatment. Our data suggest that sCA-miR-497a-5p may potentially have a therapeutic ability against IBD although further investigation is essential.
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Affiliation(s)
- Naoto Tsujimura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Takayuki Ogino
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Masayuki Hiraki
- Department of Gastroenterological Surgery, Kansai Rosai Hospital, 3-1-69 Inabaso, Amagasaki 660-8511, Japan
| | - Taisei Kai
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| | - Hiroyuki Yamamoto
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yuhki Yokoyama
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
| | - Yuki Sekido
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Osaka Police Hospital, Osaka 543-0035, Japan;
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita City 565-0871, Japan (T.O.); (Y.S.); (T.H.); (N.M.); (H.T.); (M.U.); (Y.D.); (H.E.)
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita City 565-0871, Japan (Y.Y.)
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Watabe T, Takahashi K, Pietras K, Yoshimatsu Y. Roles of TGF-β signals in tumor microenvironment via regulation of the formation and plasticity of vascular system. Semin Cancer Biol 2023; 92:130-138. [PMID: 37068553 DOI: 10.1016/j.semcancer.2023.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/09/2023] [Accepted: 04/13/2023] [Indexed: 04/19/2023]
Abstract
Tumor cells evolve in tumor microenvironment composed of multiple cell types. Among these, endothelial cells (ECs) are the major players in tumor angiogenesis, which is a driver of tumor progression and metastasis. Increasing evidence suggests that ECs also contribute to tumor progression and metastasis as they modify their phenotypes to differentiate into mesenchymal cells through a process known as endothelial-mesenchymal transition (EndoMT). This plasticity of ECs is mediated by various cytokines, including transforming growth factor-β (TGF-β), and modulated by other stimuli depending on the cellular contexts. Recent lines of evidence have shown that EndoMT is involved in various steps of tumor progression, including tumor angiogenesis, intravasation and extravasation of cancer cells, formation of cancer-associated fibroblasts, and cancer therapy resistance. In this review, we summarize current updates on EndoMT, highlight the roles of EndoMT in tumor progression and metastasis, and underline targeting EndoMT as a potential therapeutic strategy.
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Affiliation(s)
- Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Kazuki Takahashi
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.
| | - Kristian Pietras
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University Cancer Centre, Medicon Village, Lund University, 223 81 Lund, Sweden.
| | - Yasuhiro Yoshimatsu
- Division of Pharmacology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
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44
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Radhakrishnan K, Luu M, Iaria J, Sutherland JM, McLaughlin EA, Zhu HJ, Loveland KL. Activin and BMP Signalling in Human Testicular Cancer Cell Lines, and a Role for the Nucleocytoplasmic Transport Protein Importin-5 in their Crosstalk. Cells 2023; 12:cells12071000. [PMID: 37048077 PMCID: PMC10093041 DOI: 10.3390/cells12071000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Testicular germ cell tumours (TGCTs) are the most common malignancy in young men. Originating from foetal testicular germ cells that fail to differentiate correctly, TGCTs appear after puberty as germ cell neoplasia in situ cells that transform through unknown mechanisms into distinct seminoma and non-seminoma tumour types. A balance between activin and BMP signalling may influence TGCT emergence and progression, and we investigated this using human cell line models of seminoma (TCam-2) and non-seminoma (NT2/D1). Activin A- and BMP4-regulated transcripts measured at 6 h post-treatment by RNA-sequencing revealed fewer altered transcripts in TCam-2 cells but a greater responsiveness to activin A, while BMP4 altered more transcripts in NT2/D1 cells. Activin significantly elevated transcripts linked to pluripotency, cancer, TGF-β, Notch, p53, and Hippo signalling in both lines, whereas BMP4 altered TGF-β, pluripotency, Hippo and Wnt signalling components. Dose-dependent antagonism of BMP4 signalling by activin A in TCam-2 cells demonstrated signalling crosstalk between these two TGF-β superfamily arms. Levels of the nuclear transport protein, IPO5, implicated in BMP4 and WNT signalling, are highly regulated in the foetal mouse germline. IPO5 knockdown in TCam-2 cells using siRNA blunted BMP4-induced transcript changes, indicating that IPO5 levels could determine TGF-β signalling pathway outcomes in TGCTs.
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Affiliation(s)
- Karthika Radhakrishnan
- Centre for Reproductive Health, Hudson Institute of Medical Research, 27-31 Kanooka Grove, Clayton, VIC 3168, Australia
- Correspondence: (K.R.); (K.L.L.)
| | - Michael Luu
- Centre for Reproductive Health, Hudson Institute of Medical Research, 27-31 Kanooka Grove, Clayton, VIC 3168, Australia
| | - Josie Iaria
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3050, Australia
| | - Jessie M. Sutherland
- Priority Research Centre for Reproductive Science, Schools of Biomedical Science & Pharmacy and Environmental & Life Sciences, University of Newcastle, Callaghan, NSW 2305, Australia
- Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW 2305, Australia
| | - Eileen A. McLaughlin
- Priority Research Centre for Reproductive Science, Schools of Biomedical Science & Pharmacy and Environmental & Life Sciences, University of Newcastle, Callaghan, NSW 2305, Australia
- Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW 2305, Australia
- Faculty of Science, Medicine and Health, University of Wollongong, Gwynneville, NSW 2500, Australia
| | - Hong-Jian Zhu
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3050, Australia
| | - Kate L. Loveland
- Centre for Reproductive Health, Hudson Institute of Medical Research, 27-31 Kanooka Grove, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
- Correspondence: (K.R.); (K.L.L.)
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45
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Xie Y, Yue L, Shi Y, Su X, Gan C, Liu H, Xue T, Ye T. Application and Study of ROCK Inhibitors in Pulmonary Fibrosis: Recent Developments and Future Perspectives. J Med Chem 2023; 66:4342-4360. [PMID: 36940432 DOI: 10.1021/acs.jmedchem.2c01753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Rho-associated coiled-coil-containing kinases (ROCKs), serine/threonine protein kinases, were initially identified as downstream targets of the small GTP-binding protein Rho. Pulmonary fibrosis (PF) is a lethal disease with limited therapeutic options and a particularly poor prognosis. Interestingly, ROCK activation has been demonstrated in PF patients and in animal PF models, making it a promising target for PF treatment. Many ROCK inhibitors have been discovered, and four of these have been approved for clinical use; however, no ROCK inhibitors are approved for the treatment of PF patients. In this article, we describe ROCK signaling pathways and the structure-activity relationship, potency, selectivity, binding modes, pharmacokinetics (PKs), biological functions, and recently reported inhibitors of ROCKs in the context of PF. We will also focus our attention on the challenges to be addressed when targeting ROCKs and discuss the strategy of ROCK inhibitor use in the treatment of PF.
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Affiliation(s)
- Yuting Xie
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Yue
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yaojie Shi
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingping Su
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cailing Gan
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongyao Liu
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Taixiong Xue
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Tinghong Ye
- Sichuan University-Oxford University Huaxi Gastrointestinal Cancer Centre, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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46
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Kriseman ML, Tang S, Liao Z, Jiang P, Parks SE, Cope DI, Yuan F, Chen F, Masand RP, Castro PD, Ittmann MM, Creighton CJ, Tan Z, Monsivais D. SMAD2/3 signaling in the uterine epithelium controls endometrial cell homeostasis and regeneration. Commun Biol 2023; 6:261. [PMID: 36906706 PMCID: PMC10008566 DOI: 10.1038/s42003-023-04619-2] [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: 09/23/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
The regenerative potential of the endometrium is attributed to endometrial stem cells; however, the signaling pathways controlling its regenerative potential remain obscure. In this study, genetic mouse models and endometrial organoids are used to demonstrate that SMAD2/3 signaling controls endometrial regeneration and differentiation. Mice with conditional deletion of SMAD2/3 in the uterine epithelium using Lactoferrin-iCre develop endometrial hyperplasia at 12-weeks and metastatic uterine tumors by 9-months of age. Mechanistic studies in endometrial organoids determine that genetic or pharmacological inhibition of SMAD2/3 signaling disrupts organoid morphology, increases the glandular and secretory cell markers, FOXA2 and MUC1, and alters the genome-wide distribution of SMAD4. Transcriptomic profiling of the organoids reveals elevated pathways involved in stem cell regeneration and differentiation such as the bone morphogenetic protein (BMP) and retinoic acid signaling (RA) pathways. Therefore, TGFβ family signaling via SMAD2/3 controls signaling networks which are integral for endometrial cell regeneration and differentiation.
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Affiliation(s)
- Maya L Kriseman
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Division of Reproductive Endocrinology and Infertility, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suni Tang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zian Liao
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Peixin Jiang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sydney E Parks
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dominique I Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fei Yuan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fengju Chen
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ramya P Masand
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Patricia D Castro
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J Creighton
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhi Tan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diana Monsivais
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA.
- Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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Bohn S, Hexemer L, Huang Z, Strohmaier L, Lenhardt S, Legewie S, Loewer A. State- and stimulus-specific dynamics of SMAD signaling determine fate decisions in individual cells. Proc Natl Acad Sci U S A 2023; 120:e2210891120. [PMID: 36857347 PMCID: PMC10013741 DOI: 10.1073/pnas.2210891120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023] Open
Abstract
SMAD-mediated signaling regulates apoptosis, cell cycle arrest, and epithelial-to-mesenchymal transition to safeguard tissue homeostasis. However, it remains elusive how the relatively simple pathway can determine such a broad range of cell fate decisions and how it differentiates between varying ligands. Here, we systematically investigate how SMAD-mediated responses are modulated by various ligands of the transforming growth factor β (TGFβ) family and compare these ligand responses in quiescent and proliferating MCF10A cells. We find that the nature of the phenotypic response is mainly determined by the proliferation status, with migration and cell cycle arrest being dominant in proliferating cells for all tested TGFβ family ligands, whereas cell death is the major outcome in quiescent cells. In both quiescent and proliferating cells, the identity of the ligand modulates the strength of the phenotypic response proportional to the dynamics of induced SMAD nuclear-to-cytoplasmic translocation and, as a consequence, the corresponding gene expression changes. Interestingly, the proliferation state of a cell has little impact on the set of genes induced by SMAD signaling; instead, it modulates the relative cellular sensitivity to TGFβ superfamily members. Taken together, diversity of SMAD-mediated responses is mediated by differing cellular states, which determine ligand sensitivity and phenotypic effects, while the pathway itself merely serves as a quantitative relay from the cell membrane to the nucleus.
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Affiliation(s)
- Stefan Bohn
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Lorenz Hexemer
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
| | - Zixin Huang
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Laura Strohmaier
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
| | - Sonja Lenhardt
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
- Stuttgart Research Center for Systems Biology, University of Stuttgart, 70569Stuttgart, Germany
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
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48
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Birkhoff JC, Korporaal AL, Brouwer RWW, Nowosad K, Milazzo C, Mouratidou L, van den Hout MCGN, van IJcken WFJ, Huylebroeck D, Conidi A. Zeb2 DNA-Binding Sites in Neuroprogenitor Cells Reveal Autoregulation and Affirm Neurodevelopmental Defects, Including in Mowat-Wilson Syndrome. Genes (Basel) 2023; 14:genes14030629. [PMID: 36980900 PMCID: PMC10048071 DOI: 10.3390/genes14030629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs), Zeb2’s mRNA/protein upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce Flag-V5 epitope-tagged Zeb2 protein from one endogenous allele. Using chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we mapped 2432 DNA-binding sites for this tagged Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major binding site maps promoter-proximal to Zeb2 itself. The homozygous deletion of this site demonstrates that autoregulation of Zeb2 is necessary to elicit the appropriate Zeb2-dependent effects in ESC-to-NPC differentiation. We have also cross-referenced all the mapped Zeb2 binding sites with previously obtained transcriptome data from Zeb2 perturbations in ESC-derived NPCs, GABAergic interneurons from the ventral forebrain of mouse embryos, and stem/progenitor cells from the post-natal ventricular-subventricular zone (V-SVZ) in mouse forebrain, respectively. Despite the different characteristics of each of these neurogenic systems, we found interesting target gene overlaps. In addition, our study also contributes to explaining developmental disorders, including Mowat-Wilson syndrome caused by ZEB2 deficiency, and also other monogenic syndromes.
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Affiliation(s)
- Judith C. Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Anne L. Korporaal
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Center for Biomics-Genomics, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Karol Nowosad
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland
- The Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Claudia Milazzo
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Lidia Mouratidou
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | | | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Center for Biomics-Genomics, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-10-7043169
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49
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Akcan TS, Vilov S, Heinig M. Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures. Nucleic Acids Res 2023; 51:1608-1624. [PMID: 36727445 PMCID: PMC9976927 DOI: 10.1093/nar/gkac1272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023] Open
Abstract
Promoter-proximal Polymerase II (Pol II) pausing is a key rate-limiting step for gene expression. DNA and RNA-binding trans-acting factors regulating the extent of pausing have been identified. However, we lack a quantitative model of how interactions of these factors determine pausing, therefore the relative importance of implicated factors is unknown. Moreover, previously unknown regulators might exist. Here we address this gap with a machine learning model that accurately predicts the extent of promoter-proximal Pol II pausing from large-scale genome and transcriptome binding maps and gene annotation and sequence composition features. We demonstrate high accuracy and generalizability of the model by validation on an independent cell line which reveals the model's cell line agnostic character. Model interpretation in light of prior knowledge about molecular functions of regulatory factors confirms the interconnection of pausing with other RNA processing steps. Harnessing underlying feature contributions, we assess the relative importance of each factor, quantify their predictive effects and systematically identify previously unknown regulators of pausing. We additionally identify 16 previously unknown 7SK ncRNA interacting RNA-binding proteins predictive of pausing. Our work provides a framework to further our understanding of the regulation of the critical early steps in transcriptional elongation.
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Affiliation(s)
- Toray S Akcan
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany
| | - Sergey Vilov
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
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50
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Lee H, Aylward AJ, Pearse RV, Hsieh YC, Augur ZM, Benoit CR, Chou V, Knupp A, Pan C, Goberdhan S, Duong DM, Seyfried NT, Bennett DA, Klein HU, De Jager PL, Menon V, Young JE, Young-Pearse TL. Cell-type-specific regulation of APOE levels in human neurons by the Alzheimer's disease risk gene SORL1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530017. [PMID: 36865313 PMCID: PMC9980168 DOI: 10.1101/2023.02.25.530017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
SORL1 is strongly implicated in the pathogenesis of Alzheimer's disease (AD) through human genetic studies that point to an association of reduced SORL1 levels with higher risk for AD. To interrogate the role(s) of SORL1 in human brain cells, SORL1 null iPSCs were generated, followed by differentiation to neuron, astrocyte, microglia, and endothelial cell fates. Loss of SORL1 led to alterations in both overlapping and distinct pathways across cell types, with the greatest effects in neurons and astrocytes. Intriguingly, SORL1 loss led to a dramatic neuron-specific reduction in APOE levels. Further, analyses of iPSCs derived from a human aging cohort revealed a neuron-specific linear correlation between SORL1 and APOE RNA and protein levels, a finding validated in human post-mortem brain. Pathway analysis implicated intracellular transport pathways and TGF- β/SMAD signaling in the function of SORL1 in neurons. In accord, enhancement of retromer-mediated trafficking and autophagy rescued elevated phospho-tau observed in SORL1 null neurons but did not rescue APOE levels, suggesting that these phenotypes are separable. Stimulation and inhibition of SMAD signaling modulated APOE RNA levels in a SORL1-dependent manner. These studies provide a mechanistic link between two of the strongest genetic risk factors for AD.
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