1
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Guo L, Yuan H, Zhu H, Zhou J, Wan Z, Zhou Y. SPAG5 deficiency activates autophagy to reduce atherosclerotic plaque formation in ApoE -/- mice. BMC Cardiovasc Disord 2024; 24:275. [PMID: 38807081 DOI: 10.1186/s12872-024-03945-5] [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: 11/28/2023] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Autophagy, as a regulator of cell survival, plays an important role in atherosclerosis (AS). Sperm associated antigen 5 (SPAG5) is closely associated with the classical autophagy pathway, PI3K/Akt/mTOR signaling pathway. This work attempted to investigate whether SPAG5 can affect AS development by regulating autophagy. METHODS Human umbilical vein endothelial cells (HUVECs) were treated with oxidized-low density lipoprotein (ox-LDL) to induce cell damage. ApoE-/- mice were fed a Western diet to establish an AS mouse model. Haematoxylin and eosin (H&E) staining and Oil Red O staining evaluated the pathological changes and in lipid deposition in aortic tissues. CCK-8 and flow cytometry detected cell proliferation and apoptosis. Immunohistochemistry, Enzyme linked immunosorbent assay, qRT-PCR and western blotting assessed the levels of mRNA and proteins. RESULTS Ox-LDL treatment elevated SPAG5 expression and the expression of autophagy-related proteins, LC3-I, LC3-II, Beclin-1, and p62, in HUVECs. GFP-LC3 dots were increased in ox-LDL-treated HUVECs and LPS-treated HUVECs. SPAG5 knockdown reversed both ox-LDL and LPS treatment-mediated inhibition of cell proliferation and promotion of apoptosis in HUVECs. SPAG5 silencing further elevated autophagy and repressed the expression of PI3K, p-Akt/Akt, and p-mTOR/mTOR in ox-LDL-treated HUVECs. 3-MA (autophagy inhibitor) treatment reversed SPAG5 silencing-mediated increase of cell proliferation and decrease of apoptosis in ox-LDL-treated HUVECs. In vivo, SPAG5 knockdown reduced atherosclerotic plaques in AS mice through activating autophagy and inhibiting PI3K/Akt/mTOR signaling pathway. CONCLUSION This work demonstrated that SPAG5 knockdown alleviated AS development through activating autophagy. Thus, SPAG5 may be a potential target for AS therapy.
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Affiliation(s)
- Liangyun Guo
- Department of Ultrasound, The Second Affiliated Hospital of Nanchang University, No.1, Minde Road, Nanchang, Jiangxi, 330006, China
| | - Huijing Yuan
- Department of Obstetrics, Jiangxi Maternal and Child Health Hospital, No. 318 Bayi avenue, Nanchang, Jiangxi, 330006, China
| | - Huayao Zhu
- Department of ICU, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, Jiangxi, 330006, China
| | - Jie Zhou
- Department of ICU, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, Jiangxi, 330006, China
| | - Zixin Wan
- Department of ICU, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, Jiangxi, 330006, China
| | - Yihua Zhou
- Department of ICU, The Second Affiliated Hospital of Nanchang University, No.1 Minde Road, Nanchang, Jiangxi, 330006, China.
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2
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Tourigny DS, Altieri B, Secener KA, Sbiera S, Schauer MP, Arampatzi P, Herterich S, Sauer S, Fassnacht M, Ronchi CL. Cellular landscape of adrenocortical carcinoma at single-nuclei resolution. Mol Cell Endocrinol 2024; 590:112272. [PMID: 38759836 DOI: 10.1016/j.mce.2024.112272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Adrenocortical carcinoma (ACC) is a rare yet devastating tumour of the adrenal gland with a molecular pathology that remains incompletely understood. To gain novel insights into the cellular landscape of ACC, we generated single-nuclei RNA sequencing (snRNA-seq) data sets from twelve ACC tumour samples and analysed these alongside snRNA-seq data sets from normal adrenal glands (NAGs). We find the ACC tumour microenvironment to be relatively devoid of immune cells compared to NAG tissues, consistent with known high tumour purity values for ACC as an immunologically "cold" tumour. Our analysis identifies three separate groups of ACC samples that are characterised by different relative compositions of adrenocortical cell types. These include cell populations that are specifically enriched in the most clinically aggressive and hormonally active tumours, displaying hallmarks of reorganised cell mechanobiology and dysregulated steroidogenesis, respectively. We also identified and validated a population of mitotically active adrenocortical cells that strongly overexpress genes POLQ, DIAPH3 and EZH2 to support tumour expansion alongside an LGR4+ progenitor-like or cell-of-origin candidate for adrenocortical carcinogenesis. Trajectory inference suggests the fate adopted by malignant adrenocortical cells upon differentiation is associated with the copy number or allelic balance state of the imprinted DLK1/MEG3 genomic locus, which we verified by assessing bulk tumour DNA methylation status. In conclusion, our results therefore provide new insights into the clinical and cellular heterogeneity of ACC, revealing how genetic perturbations to healthy adrenocortical renewal and zonation provide a molecular basis for disease pathogenesis.
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Affiliation(s)
- David S Tourigny
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Kerim A Secener
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany; Institute of Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, 14195, Germany
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Marc P Schauer
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany; Center for Cellular Immunotherapy, Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, 97080, Germany
| | | | - Sabine Herterich
- Central Laboratory, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Cristina L Ronchi
- Institute of Metabolism and System Research, University of Birmingham, Birmingham, B15 2TT, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, B15 2GW, UK.
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Vial Y, Nardelli J, Bonnard AA, Rousselot J, Souyri M, Gressens P, Cavé H, Drunat S. Mcph1, mutated in primary microcephaly, is also crucial for erythropoiesis. EMBO Rep 2024; 25:2418-2440. [PMID: 38605277 PMCID: PMC11094029 DOI: 10.1038/s44319-024-00123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
Microcephaly is a common feature in inherited bone marrow failure syndromes, prompting investigations into shared pathways between neurogenesis and hematopoiesis. To understand this association, we studied the role of the microcephaly gene Mcph1 in hematological development. Our research revealed that Mcph1-knockout mice exhibited congenital macrocytic anemia due to impaired terminal erythroid differentiation during fetal development. Anemia's cause is a failure to complete cell division, evident from tetraploid erythroid progenitors with DNA content exceeding 4n. Gene expression profiling demonstrated activation of the p53 pathway in Mcph1-deficient erythroid precursors, leading to overexpression of Cdkn1a/p21, a major mediator of p53-dependent cell cycle arrest. Surprisingly, fetal brain analysis revealed hypertrophied binucleated neuroprogenitors overexpressing p21 in Mcph1-knockout mice, indicating a shared pathophysiological mechanism underlying both erythroid and neurological defects. However, inactivating p53 in Mcph1-/- mice failed to reverse anemia and microcephaly, suggesting that p53 activation in Mcph1-deficient cells resulted from their proliferation defect rather than causing it. These findings shed new light on Mcph1's function in fetal hematopoietic development, emphasizing the impact of disrupted cell division on neurogenesis and erythropoiesis - a common limiting pathway.
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Affiliation(s)
- Yoann Vial
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | | | - Adeline A Bonnard
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | - Justine Rousselot
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | - Michèle Souyri
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
| | - Pierre Gressens
- Université Paris Cité, NeuroDiderot, Inserm, F-75019, Paris, France
| | - Hélène Cavé
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | - Séverine Drunat
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France.
- Université Paris Cité, NeuroDiderot, Inserm, F-75019, Paris, France.
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Chehade G, El Hajj N, Aittaleb M, Alkailani MI, Bejaoui Y, Mahdi A, Aldaalis AAH, Verbiest M, Lelotte J, Ruiz-Reig N, Durá I, Raftopoulos C, Tajeddine N, Tissir F. DIAPH3 predicts survival of patients with MGMT-methylated glioblastoma. Front Oncol 2024; 14:1359652. [PMID: 38454929 PMCID: PMC10917989 DOI: 10.3389/fonc.2024.1359652] [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: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
Background Glioblastoma is one of the most aggressive primary brain tumors, with a poor outcome despite multimodal treatment. Methylation of the MGMT promoter, which predicts the response to temozolomide, is a well-established prognostic marker for glioblastoma. However, a difference in survival can still be detected within the MGMT methylated group, with some patients exhibiting a shorter survival than others, emphasizing the need for additional predictive factors. Methods We analyzed DIAPH3 expression in glioblastoma samples from the cancer genome atlas (TCGA). We also retrospectively analyzed one hundred seventeen histological glioblastomas from patients operated on at Saint-Luc University Hospital between May 2013 and August 2019. We analyzed the DIAPH3 expression, explored the relationship between mRNA levels and Patient's survival after the surgical resection. Finally, we assessed the methylation pattern of the DIAPH3 promoter using a targeted deep bisulfite sequencing approach. Results We found that 36% and 1% of the TCGA glioblastoma samples exhibit copy number alterations and mutations in DIAPH3, respectively. We scrutinized the expression of DIAPH3 at single cell level and detected an overlap with MKI67 expression in glioblastoma proliferating cells, including neural progenitor-like, oligodendrocyte progenitor-like and astrocyte-like states. We quantitatively analyzed DIAPH3 expression in our cohort and uncovered a positive correlation between DIAPH3 mRNA level and patient's survival. The effect of DIAPH3 was prominent in MGMT-methylated glioblastoma. Finally, we report that the expression of DIAPH3 is at least partially regulated by the methylation of three CpG sites in the promoter region. Conclusion We propose that combining the DIAPH3 expression with MGMT methylation could offer a better prediction of survival and more adapted postsurgical treatment for patients with MGMT-methylated glioblastoma.
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Affiliation(s)
- Georges Chehade
- Université Catholique de Louvain, Institute of Neuroscience, Cellular and Molecular Division, Brussels, Belgium
| | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Mohamed Aittaleb
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Maisa I. Alkailani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Yosra Bejaoui
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Asma Mahdi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Arwa A. H. Aldaalis
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Michael Verbiest
- Laboratory of Population Genomics, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Julie Lelotte
- Department of Neuropathology, Saint-Luc University Hospital, Brussels, Belgium
| | - Nuria Ruiz-Reig
- Université Catholique de Louvain, Institute of Neuroscience, Cellular and Molecular Division, Brussels, Belgium
| | - Irene Durá
- Université Catholique de Louvain, Institute of Neuroscience, Cellular and Molecular Division, Brussels, Belgium
| | | | - Nicolas Tajeddine
- Université Catholique de Louvain, Institute of Neuroscience, Cellular and Molecular Division, Brussels, Belgium
| | - Fadel Tissir
- Université Catholique de Louvain, Institute of Neuroscience, Cellular and Molecular Division, Brussels, Belgium
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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5
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Li S, Zhang P, Chen W, Ye L, Brannan KW, Le NT, Abe JI, Cooke JP, Wang G. A relay velocity model infers cell-dependent RNA velocity. Nat Biotechnol 2024; 42:99-108. [PMID: 37012448 PMCID: PMC10545816 DOI: 10.1038/s41587-023-01728-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023]
Abstract
RNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal kinetics from all cells in an scRNA-seq experiment, resulting in unpredictable performance in experiments with multi-stage and/or multi-lineage transition of cell states where the assumption of the same kinetic rates for all cells no longer holds. Here we present cellDancer, a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. In the simulation benchmark, cellDancer shows robust performance in multiple kinetic regimes, high dropout ratio datasets and sparse datasets. We show that cellDancer overcomes the limitations of existing RNA velocity models in modeling erythroid maturation and hippocampus development. Moreover, cellDancer provides cell-specific predictions of transcription, splicing and degradation rates, which we identify as potential indicators of cell fate in the mouse pancreas.
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Affiliation(s)
- Shengyu Li
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pengzhi Zhang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Weiqing Chen
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, Cornell University, Ithaca, NY, USA
| | - Lingqun Ye
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
| | - Kristopher W Brannan
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Nhat-Tu Le
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jun-Ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA
| | - Guangyu Wang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA.
- Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX, USA.
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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6
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Hao M, Qin Y, Li Y, Tang Y, Ma Z, Tan J, Jin L, Wang F, Gong X. Metabolome subtyping reveals multi-omics characteristics and biological heterogeneity in major psychiatric disorders. Psychiatry Res 2023; 330:115605. [PMID: 38006718 DOI: 10.1016/j.psychres.2023.115605] [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: 08/26/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023]
Abstract
Growing evidence suggests that major psychiatric disorders (MPDs) share common etiologies and pathological processes. However, the diagnosis is currently based on descriptive symptoms, which ignores the underlying pathogenesis and hinders the development of clinical treatments. This highlights the urgency of characterizing molecular biomarkers and establishing objective diagnoses of MPDs. Here, we collected untargeted metabolomics, proteomics and DNA methylation data of 327 patients with MPDs, 131 individuals with genetic high risk and 146 healthy controls to explore the multi-omics characteristics of MPDs. First, differential metabolites (DMs) were identified and we classified MPD patients into 3 subtypes based on DMs. The subtypes showed distinct metabolomics, proteomics and DNA methylation signatures. Specifically, one subtype showed dysregulation of complement and coagulation proteins, while the DNA methylation showed abnormalities in chemical synapses and autophagy. Integrative analysis in metabolic pathways identified the important roles of the citrate cycle, sphingolipid metabolism and amino acid metabolism. Finally, we constructed prediction models based on the metabolites and proteomics that successfully captured the risks of MPD patients. Our study established molecular subtypes of MPDs and elucidated their biological heterogeneity through a multi-omics investigation. These results facilitate the understanding of pathological mechanisms and promote the diagnosis and prevention of MPDs.
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Affiliation(s)
- Meng Hao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China
| | - Yue Qin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China; International Human Phenome Institutes, Shanghai, China
| | - Yanqing Tang
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Zehan Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Zhangjiang Fudan International Innovation Center, Fudan Zhangjiang Institute, Obstetrics and Gynecology Hospital, Human Phenome Institute, Fudan University, China; International Human Phenome Institutes, Shanghai, China
| | - Fei Wang
- Early Intervention Unit, Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China; Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China.
| | - Xiaohong Gong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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7
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Innocenti M. Investigating Mammalian Formins with SMIFH2 Fifteen Years in: Novel Targets and Unexpected Biology. Int J Mol Sci 2023; 24:ijms24109058. [PMID: 37240404 DOI: 10.3390/ijms24109058] [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: 04/06/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The mammalian formin family comprises fifteen multi-domain proteins that regulate actin dynamics and microtubules in vitro and in cells. Evolutionarily conserved formin homology (FH) 1 and 2 domains allow formins to locally modulate the cell cytoskeleton. Formins are involved in several developmental and homeostatic processes, as well as human diseases. However, functional redundancy has long hampered studies of individual formins with genetic loss-of-function approaches and prevents the rapid inhibition of formin activities in cells. The discovery of small molecule inhibitor of formin homology 2 domains (SMIFH2) in 2009 was a disruptive change that provided a powerful chemical tool to explore formins' functions across biological scales. Here, I critically discuss the characterization of SMIFH2 as a pan-formin inhibitor, as well as growing evidence of unexpected off-target effects. By collating the literature and information hidden in public repositories, outstanding controversies and fundamental open questions about the substrates and mechanism of action of SMIFH2 emerge. Whenever possible, I propose explanations for these discrepancies and roadmaps to address the paramount open questions. Furthermore, I suggest that SMIFH2 be reclassified as a multi-target inhibitor for its appealing activities on proteins involved in pathological formin-dependent processes. Notwithstanding all drawbacks and limitations, SMIFH2 will continue to prove useful in studying formins in health and disease in the years to come.
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Affiliation(s)
- Metello Innocenti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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8
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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Hein JI, Scholz J, Körber S, Kaufmann T, Faix J. Unleashed Actin Assembly in Capping Protein-Deficient B16-F1 Cells Enables Identification of Multiple Factors Contributing to Filopodium Formation. Cells 2023; 12:cells12060890. [PMID: 36980231 PMCID: PMC10047565 DOI: 10.3390/cells12060890] [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: 12/02/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
Background: Filopodia are dynamic, finger-like actin-filament bundles that overcome membrane tension by forces generated through actin polymerization at their tips to allow extension of these structures a few microns beyond the cell periphery. Actin assembly of these protrusions is regulated by accessory proteins including heterodimeric capping protein (CP) or Ena/VASP actin polymerases to either terminate or promote filament growth. Accordingly, the depletion of CP in B16-F1 melanoma cells was previously shown to cause an explosive formation of filopodia. In Ena/VASP-deficient cells, CP depletion appeared to result in ruffling instead of inducing filopodia, implying that Ena/VASP proteins are absolutely essential for filopodia formation. However, this hypothesis was not yet experimentally confirmed. Methods: Here, we used B16-F1 cells and CRISPR/Cas9 technology to eliminate CP either alone or in combination with Ena/VASP or other factors residing at filopodia tips, followed by quantifications of filopodia length and number. Results: Unexpectedly, we find massive formations of filopodia even in the absence of CP and Ena/VASP proteins. Notably, combined inactivation of Ena/VASP, unconventional myosin-X and the formin FMNL3 was required to markedly impair filopodia formation in CP-deficient cells. Conclusions: Taken together, our results reveal that, besides Ena/VASP proteins, numerous other factors contribute to filopodia formation.
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Affiliation(s)
| | | | | | | | - Jan Faix
- Correspondence: ; Tel.: +49-511-532-2928
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10
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Zhang B, Hu Q, Li Y, Xu C, Xie X, Liu P, Xu M, Gong S, Wu H. Diaphanous-related formin subfamily: Novel prognostic biomarkers and tumor microenvironment regulators for pancreatic adenocarcinoma. Front Mol Biosci 2022; 9:910950. [PMID: 36589226 PMCID: PMC9797685 DOI: 10.3389/fmolb.2022.910950] [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: 04/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
The diaphanous-related formin subfamily includes diaphanous homolog 1 (DIAPH1), DIAPH2, and DIAPH3. DIAPHs play a role in the regulation of actin nucleation and polymerization and in microtubule stability. DIAPH3 also regulates the assembly and bipolarity of mitotic spindles. Accumulating evidence has shown that DIAPHs are anomalously regulated during malignancy. In this study, we reviewed The Cancer Genome Atlas database and found that DIAPHs are abundantly expressed in pancreatic adenocarcinoma (PAAD). Furthermore, we analyzed the gene alteration profiles, protein expression, prognosis, and immune reactivity of DIAPHs in PAAD using data from several well-established databases. In addition, we conducted gene set enrichment analysis to investigate the potential mechanisms underlying the roles of DIAPHs in the carcinogenesis of PAAD. Finally, we performed the experimental validation of DIAPHs expression in several pancreatic cancer cell lines and tissues of patients. This study demonstrated significant correlations between DIAPHs expression and clinical prognosis, oncogenic signature gene sets, T helper 2 cell infiltration, plasmacytoid dendritic cell infiltration, myeloid-derived suppressor cell infiltration, ImmunoScore, and immune checkpoints in PAAD. These data may provide important information regarding the role and mechanisms of DIAPHs in tumorigenesis and PAAD immunotherapy.
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Affiliation(s)
- Bixi Zhang
- Department of Pathology, Hunan Provincial People’s Hospital, Hunan Normal University, Changsha, China
| | - Qing Hu
- Department of Pathology, Hunan Provincial People’s Hospital, Hunan Normal University, Changsha, China
| | - Yanchun Li
- Department of Pathology, Hunan Provincial People’s Hospital, Hunan Normal University, Changsha, China
| | - Canxia Xu
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoran Xie
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Peng Liu
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Meihua Xu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Siming Gong
- Institute of Anatomy, University of Leipzig, Leipzig, Germany
| | - Hao Wu
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, China,Center for Precision Medicine, University of Missouri School of Medicine, Columbia, MO, United States,*Correspondence: Hao Wu,
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11
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Chiereghin C, Robusto M, Massa V, Castorina P, Ambrosetti U, Asselta R, Soldà G. Role of Cytoskeletal Diaphanous-Related Formins in Hearing Loss. Cells 2022; 11:cells11111726. [PMID: 35681420 PMCID: PMC9179844 DOI: 10.3390/cells11111726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
Hearing relies on the proper functioning of auditory hair cells and on actin-based cytoskeletal structures. Diaphanous-related formins (DRFs) are evolutionarily conserved cytoskeletal proteins that regulate the nucleation of linear unbranched actin filaments. They play key roles during metazoan development, and they seem particularly pivotal for the correct physiology of the reproductive and auditory systems. Indeed, in Drosophila melanogaster, a single diaphanous (dia) gene is present, and mutants show sterility and impaired response to sound. Vertebrates, instead, have three orthologs of the diaphanous gene: DIAPH1, DIAPH2, and DIAPH3. In humans, defects in DIAPH1 and DIAPH3 have been associated with different types of hearing loss. In particular, heterozygous mutations in DIAPH1 are responsible for autosomal dominant deafness with or without thrombocytopenia (DFNA1, MIM #124900), whereas regulatory mutations inducing the overexpression of DIAPH3 cause autosomal dominant auditory neuropathy 1 (AUNA1, MIM #609129). Here, we provide an overview of the expression and function of DRFs in normal hearing and deafness.
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Affiliation(s)
- Chiara Chiereghin
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy; (C.C.); (R.A.)
| | - Michela Robusto
- Experimental Therapeutics Program, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy;
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via Di Rudinì 8, 20146 Milan, Italy;
| | | | - Umberto Ambrosetti
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, UO Audiologia, Via F. Sforza 35, 20122 Milan, Italy;
| | - Rosanna Asselta
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy; (C.C.); (R.A.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy
| | - Giulia Soldà
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy; (C.C.); (R.A.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy
- Correspondence:
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12
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Becker KN, Pettee KM, Sugrue A, Reinard KA, Schroeder JL, Eisenmann KM. The Cytoskeleton Effectors Rho-Kinase (ROCK) and Mammalian Diaphanous-Related (mDia) Formin Have Dynamic Roles in Tumor Microtube Formation in Invasive Glioblastoma Cells. Cells 2022; 11:1559. [PMID: 35563863 PMCID: PMC9103681 DOI: 10.3390/cells11091559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 01/21/2023] Open
Abstract
Glioblastoma (GBM) is a progressive and lethal brain cancer. Malignant control of actin and microtubule cytoskeletal mechanics facilitates two major GBM therapeutic resistance strategies-diffuse invasion and tumor microtube network formation. Actin and microtubule reorganization is controlled by Rho-GTPases, which exert their effects through downstream effector protein activation, including Rho-associated kinases (ROCK) 1 and 2 and mammalian diaphanous-related (mDia) formins (mDia1, 2, and 3). Precise spatial and temporal balancing of the activity between these effectors dictates cell shape, adhesion turnover, and motility. Using small molecules targeting mDia, we demonstrated that global agonism (IMM02) was superior to antagonism (SMIFH2) as anti-invasion strategies in GBM spheroids. Here, we use IDH-wild-type GBM patient-derived cell models and a novel semi-adherent in vitro system to investigate the relationship between ROCK and mDia in invasion and tumor microtube networks. IMM02-mediated mDia agonism disrupts invasion in GBM patient-derived spheroid models, in part by inducing mDia expression loss and tumor microtube network collapse. Pharmacological disruption of ROCK prevented invasive cell-body movement away from GBM spheres, yet induced ultralong, phenotypically abnormal tumor microtube formation. Simultaneously targeting mDia and ROCK did not enhance the anti-invasive/-tumor microtube effects of IMM02. Our data reveal that targeting mDia is a viable GBM anti-invasion/-tumor microtube networking strategy, while ROCK inhibition is contraindicated.
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Affiliation(s)
- Kathryn N. Becker
- Department of Cell and Cancer Biology, University of Toledo Health Science Campus, Toledo, OH 43614, USA; (K.N.B.); (K.M.P.)
| | - Krista M. Pettee
- Department of Cell and Cancer Biology, University of Toledo Health Science Campus, Toledo, OH 43614, USA; (K.N.B.); (K.M.P.)
| | - Amanda Sugrue
- Department of Chemistry and Biochemistry, University of Heidelberg, Tiffin, OH 44883, USA;
| | - Kevin A. Reinard
- Division of Neurosurgery, ProMedica Toledo Hospital, Toledo, OH 43606, USA; (K.A.R.); (J.L.S.)
| | - Jason L. Schroeder
- Division of Neurosurgery, ProMedica Toledo Hospital, Toledo, OH 43606, USA; (K.A.R.); (J.L.S.)
- Department of Surgery, University of Toledo Health Science Campus, Toledo, OH 43614, USA
| | - Kathryn M. Eisenmann
- Department of Cell and Cancer Biology, University of Toledo Health Science Campus, Toledo, OH 43614, USA; (K.N.B.); (K.M.P.)
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13
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Stoyanov GS, Lyutfi E, Georgieva R, Georgiev R, Dzhenkov D, Petkova L, Ivanov BD, Kaprelyan A, Ghenev P. Diaph3 underlines tumor cell heterogeneity in glioblastoma with implications for treatment modalities resistance. J Neurooncol 2022; 157:523-531. [PMID: 35380294 DOI: 10.1007/s11060-022-03996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Glioblastoma (GBM) is the most aggressive central nervous system (CNS) tumor with astrocytic differentiation. The growth pattern of GBM mimics that of the precursor cell migration during the fetal development of the brain. Diaphanous homolog (Diaph3) has been established to play a role in both CNS maturation and cancer progression as it is required both for cell migration and division. Furthermore, Diaph3 has been shown to play a role in malignant disease progression through hyperactivation of the EGFR/MEK/ERK in loss of expression and its overexpression correlating to hyperactivity of the mTOR pathway, both of which are with a well-established role in GBM. Herein, we aimed at establishing the diagnostic role of Diaph3 immunohistochemistry expression patterns in GBM and their possible implications for molecular response to different therapies. MATERIALS AND METHODS The study utilized a retrospective nonclinical approach. Results of Diaph3 immunohistochemical expression were compared to healthy controls and reactive gliosis and statistically analyzed for correlation with neuroradiological tumor parameters and patient survival. RESULTS Healthy controls showed individual weakly positive cells, while reactive gliosis controls showed a strong expression in astrocytic projections. GBM samples showed a heterogeneous positive reaction to Diaph3, mean number of positive cells 62.66%, median 61.5, range 12-96%. Areas of migrating cells showed a strong diffuse cytoplasmic reaction. Cells located in the tumor core and those in areas of submeningeal aggregation had no antibody expression. Statistical analysis revealed no correlation with tumor size or patient survival. CONCLUSION The different expression pattern of Diaph3 in healthy controls, reactive gliosis and GBM shows promise as a clinical differentiating marker. Despite Diaph3 expression not correlating with survival and tumor size in GBM, there is an accumulating body of evidence that Diaph3 correlates with mTOR activity and can thus be used as a predictor for response to rapamycin and taxanes, clinical studies of which have shown promising, if mixed results in GBM.
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Affiliation(s)
- George S Stoyanov
- Department of General and Clinical Pathology, Forensic Medicine and Deontology, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Marin Drinov 55 Str, 9002, Varna, Bulgaria.
| | - Emran Lyutfi
- Department of Neurology and Neuroscience, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Varna, Bulgaria
| | - Reneta Georgieva
- Student, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Varna, Bulgaria
| | - Radoslav Georgiev
- Department of Imaging Diagnostics, Interventional Radiology and Radiotherapy, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Varna, Bulgaria
| | - Deyan Dzhenkov
- Department of General and Clinical Pathology, Forensic Medicine and Deontology, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Marin Drinov 55 Str, 9002, Varna, Bulgaria
| | - Lilyana Petkova
- Department of General and Clinical Pathology, Forensic Medicine and Deontology, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Marin Drinov 55 Str, 9002, Varna, Bulgaria
| | - Borislav D Ivanov
- Department of Clinical Medical Sciences, Faculty of Dental Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Varna, Bulgaria
| | - Ara Kaprelyan
- Department of Neurology and Neuroscience, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Varna, Bulgaria
| | - Peter Ghenev
- Department of General and Clinical Pathology, Forensic Medicine and Deontology, Faculty of Medicine, Medical University Varna "Prof. Dr. Paraskev Stoyanov", Marin Drinov 55 Str, 9002, Varna, Bulgaria
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14
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Ossola C, Kalebic N. Roots of the Malformations of Cortical Development in the Cell Biology of Neural Progenitor Cells. Front Neurosci 2022; 15:817218. [PMID: 35069108 PMCID: PMC8766818 DOI: 10.3389/fnins.2021.817218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
The cerebral cortex is a structure that underlies various brain functions, including cognition and language. Mammalian cerebral cortex starts developing during the embryonic period with the neural progenitor cells generating neurons. Newborn neurons migrate along progenitors’ radial processes from the site of their origin in the germinal zones to the cortical plate, where they mature and integrate in the forming circuitry. Cell biological features of neural progenitors, such as the location and timing of their mitoses, together with their characteristic morphologies, can directly or indirectly regulate the abundance and the identity of their neuronal progeny. Alterations in the complex and delicate process of cerebral cortex development can lead to malformations of cortical development (MCDs). They include various structural abnormalities that affect the size, thickness and/or folding pattern of the developing cortex. Their clinical manifestations can entail a neurodevelopmental disorder, such as epilepsy, developmental delay, intellectual disability, or autism spectrum disorder. The recent advancements of molecular and neuroimaging techniques, along with the development of appropriate in vitro and in vivo model systems, have enabled the assessment of the genetic and environmental causes of MCDs. Here we broadly review the cell biological characteristics of neural progenitor cells and focus on those features whose perturbations have been linked to MCDs.
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15
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Wilsch-Bräuninger M, Huttner WB. Primary Cilia and Centrosomes in Neocortex Development. Front Neurosci 2021; 15:755867. [PMID: 34744618 PMCID: PMC8566538 DOI: 10.3389/fnins.2021.755867] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/20/2021] [Indexed: 12/26/2022] Open
Abstract
During mammalian brain development, neural stem and progenitor cells generate the neurons for the six-layered neocortex. The proliferative capacity of the different types of progenitor cells within the germinal zones of the developing neocortex is a major determinant for the number of neurons generated. Furthermore, the various modes of progenitor cell divisions, for which the orientation of the mitotic spindle of progenitor cells has a pivotal role, are a key parameter to ensure the appropriate size and proper cytoarchitecture of the neocortex. Here, we review the roles of primary cilia and centrosomes of progenitor cells in these processes during neocortical development. We specifically focus on the apical progenitor cells in the ventricular zone. In particular, we address the alternating, dual role of the mother centriole (i) as a component of one of the spindle poles during mitosis, and (ii) as the basal body of the primary cilium in interphase, which is pivotal for the fate of apical progenitor cells and their proliferative capacity. We also discuss the interactions of these organelles with the microtubule and actin cytoskeleton, and with junctional complexes. Centriolar appendages have a specific role in this interaction with the cell cortex and the plasma membrane. Another topic of this review is the specific molecular composition of the ciliary membrane and the membrane vesicle traffic to the primary cilium of apical progenitors, which underlie the ciliary signaling during neocortical development; this signaling itself, however, is not covered in depth here. We also discuss the recently emerging evidence regarding the composition and roles of primary cilia and centrosomes in basal progenitors, a class of progenitors thought to be of particular importance for neocortex expansion in development and evolution. While the tight interplay between primary cilia and centrosomes makes it difficult to allocate independent roles to either organelle, mutations in genes encoding ciliary and/or centrosome proteins indicate that both are necessary for the formation of a properly sized and functioning neocortex during development. Human neocortical malformations, like microcephaly, underpin the importance of primary cilia/centrosome-related processes in neocortical development and provide fundamental insight into the underlying mechanisms involved.
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Affiliation(s)
| | - Wieland B Huttner
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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16
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Ye W, Duan Y, Zhang W, Cheng Y, Shi M, Xia XQ. Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits. Genomics 2021; 113:4004-4014. [PMID: 34614437 DOI: 10.1016/j.ygeno.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
Abstract
Grass carp (Ctenopharyngodon idella) is the most productive freshwater aquaculture fish in worldwide. However, the molecular mechanism of its growth traits has not been fully elucidated. Whole transcriptome analysis of the brain and hepatopancreas of 29 six-month-old grass carp with different growth rates was performed. Weighted gene co-expression network analysis (WGCNA) was used to construct a weighted gene co-expression network of mRNA, miRNA and lncRNA separately. A total of 35 hub mRNAs, 47 hub lncRNAs and 33 hub miRNAs were identified from the brain, 37 hub mRNAs, 110 hub lncRNAs and 36 hub miRNAs were identified from the hepatopancreas. The ceRNA networks in the brain and hepatopancreas were involved in brain development and nutrient metabolism, respectively. Overall, this is the first investigation of the growth-related transcriptomic characteristics in the brain and hepatopancreas of grass carp, thus will help us to further explore the molecular mechanism of grass carp growth rate.
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Affiliation(s)
- Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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17
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Abstract
Almost 25 years have passed since a mutation of a formin gene, DIAPH1, was identified as being responsible for a human inherited disorder: a form of sensorineural hearing loss. Since then, our knowledge of the links between formins and disease has deepened considerably. Mutations of DIAPH1 and six other formin genes (DAAM2, DIAPH2, DIAPH3, FMN2, INF2 and FHOD3) have been identified as the genetic cause of a variety of inherited human disorders, including intellectual disability, renal disease, peripheral neuropathy, thrombocytopenia, primary ovarian insufficiency, hearing loss and cardiomyopathy. In addition, alterations in formin genes have been associated with a variety of pathological conditions, including developmental defects affecting the heart, nervous system and kidney, aging-related diseases, and cancer. This review summarizes the most recent discoveries about the involvement of formin alterations in monogenic disorders and other human pathological conditions, especially cancer, with which they have been associated. In vitro results and experiments in modified animal models are discussed. Finally, we outline the directions for future research in this field.
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Affiliation(s)
| | - Miguel A. Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
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