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Yang J, Li Y, Tang Y, Yang L, Guo C, Peng C. Spatial transcriptome reveals the region-specific genes and pathways regulated by Satb2 in neocortical development. BMC Genomics 2024; 25:757. [PMID: 39095712 PMCID: PMC11297773 DOI: 10.1186/s12864-024-10672-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: 04/15/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND It is known that the neurodevelopmental disorder associated gene, Satb2, plays important roles in determining the upper layer neuron specification. However, it is not well known how this gene regulates other neocortical regions during the development. It is also lack of comprehensive delineation of its spatially regulatory pathways in neocortical development. RESULTS In this work, we utilized spatial transcriptomics and immuno-staining to systematically investigate the region-specific gene regulation of Satb2 by comparing the Satb2+/+ and Satb2-/- mice at embryonic stages, including the ventricle zone (VZ) or subventricle zone (SVZ), intermediate zone (IZ) and cortical plate (CP) respectively. The staining result reveals that these three regions become moderately or significantly thinner in the Satb2-/- mice. In the cellular level, the cell number increases in the VZ/SVZ, whereas the cell number decreases in the CP. The spatial transcriptomics data show that many important genes and relevant pathways are dysregulated in Satb2-/- mice in a region-specific manner. In the VZ/SVZ, the key genes involved in neural precursor cell proliferation, including the intermediate progenitor marker Tbr2 and the lactate production related gene Ldha, are up-regulated in Satb2-/- mice. In the IZ, the key genes in regulating neuronal differentiation and migration, such as Rnd2, exhibit ectopic expressions in the Satb2-/- mice. In the CP, the lineage-specific genes, Tbr1 and Bcl11b, are abnormally expressed. The neuropeptide related gene Npy is down-regulated in Satb2-/- mice. Finally, we validated the abnormal expressions of key regulators by using immunofluorescence or qPCR. CONCLUSIONS In summary, our work provides insights on the region-specific genes and pathways which are regulated by Satb2 in neocortical development.
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Affiliation(s)
- Jianfen Yang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Yu Li
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Yiyuli Tang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Ling Yang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Chunming Guo
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China
| | - Cheng Peng
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650500, China.
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Li Z, Chen F, Chen L, Liu J, Tseng D, Hadi F, Omarjee S, Kishore K, Kent J, Kirkpatrick J, D’Santos C, Lawson M, Gertz J, Sikora MJ, McDonnell DP, Carroll JS, Polyak K, Oesterreich S, Lee AV. EstroGene2.0: A multi-omic database of response to estrogens, ER-modulators, and resistance to endocrine therapies in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601163. [PMID: 39005294 PMCID: PMC11244912 DOI: 10.1101/2024.06.28.601163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Endocrine therapies targeting the estrogen receptor (ER/ESR1) are the cornerstone to treat ER-positive breast cancers patients, but resistance often limits their effectiveness. Understanding the molecular mechanisms is thus key to optimize the existing drugs and to develop new ER-modulators. Notable progress has been made although the fragmented way data is reported has reduced their potential impact. Here, we introduce EstroGene2.0, an expanded database of its precursor 1.0 version. EstroGene2.0 focusses on response and resistance to endocrine therapies in breast cancer models. Incorporating multi-omic profiling of 361 experiments from 212 studies across 28 cell lines, a user-friendly browser offers comprehensive data visualization and metadata mining capabilities (https://estrogeneii.web.app/). Taking advantage of the harmonized data collection, our follow-up meta-analysis revealed substantial diversity in response to different classes of ER-modulators including SERMs, SERDs, SERCA and LDD/PROTAC. Notably, endocrine resistant models exhibit a spectrum of transcriptomic alterations including a contra-directional shift in ER and interferon signaling, which is recapitulated clinically. Furthermore, dissecting multiple ESR1-mutant cell models revealed the different clinical relevance of genome-edited versus ectopic overexpression model engineering and identified high-confidence mutant-ER targets, such as NPY1R. These examples demonstrate how EstroGene2.0 helps investigate breast cancer's response to endocrine therapies and explore resistance mechanisms.
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Affiliation(s)
- Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Fangyuan Chen
- School of Medicine, Tsinghua University, Beijing, China
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Li Chen
- Computational Biology Department, Carnegie Mellon University, Pittsburgh PA, USA
| | - Jiebin Liu
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Danielle Tseng
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | | | - Soleilmane Omarjee
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joshua Kent
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joanna Kirkpatrick
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Clive D’Santos
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Jiang T, Zheng T, Li R, Sun J, Luan X, Wang M. The role of NPY signaling pathway in diagnosis, prognosis and treatment of stroke. Neuropeptides 2024; 104:102412. [PMID: 38330680 DOI: 10.1016/j.npep.2024.102412] [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: 11/22/2023] [Revised: 01/24/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Neuropeptide Y (NPY), an extensively distributed neurotransmitter within the central nervous system (CNS), was initially detected and isolated from the brain of a pig in 1982. By binding to its G protein-coupled receptors, NPY regulates immune responses and contributes to the pathogenesis of numerous inflammatory diseases. The hippocampus contained the maximum concentration in the CNS, with the cerebral cortex, hypothalamus, thalamus, brainstem, and cerebellum following suit. This arrangement suggests that the substance has a specific function within the CNS. More and more studies have shown that NPY is involved in the physiological and pathological mechanism of stroke, and its serum concentration can be one of the specific biomarkers of stroke and related complications because of its high activity, broad and complex effects. By summarizing relevant literature, this article aims to gain a thorough understanding of the potential clinical applications of NPY in the treatment of stroke, identification of stroke and its related complications, and assessment of prognosis.
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Affiliation(s)
- Taotao Jiang
- Department of Neurology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Ting Zheng
- Department of Neurology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Rundong Li
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Jingjing Sun
- Department of Neurology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Xiaoqing Luan
- Department of Neurology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Manxia Wang
- Department of Neurology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China.
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Viudez-Martínez A, Torregrosa AB, Navarrete F, García-Gutiérrez MS. Understanding the Biological Relationship between Migraine and Depression. Biomolecules 2024; 14:163. [PMID: 38397400 PMCID: PMC10886628 DOI: 10.3390/biom14020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/25/2024] Open
Abstract
Migraine is a highly prevalent neurological disorder. Among the risk factors identified, psychiatric comorbidities, such as depression, seem to play an important role in its onset and clinical course. Patients with migraine are 2.5 times more likely to develop a depressive disorder; this risk becomes even higher in patients suffering from chronic migraine or migraine with aura. This relationship is bidirectional, since depression also predicts an earlier/worse onset of migraine, increasing the risk of migraine chronicity and, consequently, requiring a higher healthcare expenditure compared to migraine alone. All these data suggest that migraine and depression may share overlapping biological mechanisms. Herein, this review explores this topic in further detail: firstly, by introducing the common epidemiological and risk factors for this comorbidity; secondly, by focusing on providing the cumulative evidence of common biological aspects, with a particular emphasis on the serotoninergic system, neuropeptides such as calcitonin-gene-related peptide (CGRP), pituitary adenylate cyclase-activating polypeptide (PACAP), substance P, neuropeptide Y and orexins, sexual hormones, and the immune system; lastly, by remarking on the future challenges required to elucidate the etiopathological mechanisms of migraine and depression and providing updated information regarding new key targets for the pharmacological treatment of these clinical entities.
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Affiliation(s)
- Adrián Viudez-Martínez
- Hospital Pharmacy Service, Hospital General Dr. Balmis de Alicante, 03010 Alicante, Spain;
| | - Abraham B. Torregrosa
- Instituto de Neurociencias, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain; (A.B.T.); (F.N.)
- Research Network on Primary Addictions, Instituto de Salud Carlos III, MICINN and FEDER, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
| | - Francisco Navarrete
- Instituto de Neurociencias, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain; (A.B.T.); (F.N.)
- Research Network on Primary Addictions, Instituto de Salud Carlos III, MICINN and FEDER, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
| | - María Salud García-Gutiérrez
- Instituto de Neurociencias, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain; (A.B.T.); (F.N.)
- Research Network on Primary Addictions, Instituto de Salud Carlos III, MICINN and FEDER, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
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