1
|
Polesskaya O, Boussaty E, Cheng R, Lamonte O, Zhou T, Du E, Sanches TM, Nguyen KM, Okamoto M, Palmer AA, Friedman R. Genome-wide association study for age-related hearing loss in CFW mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598304. [PMID: 38915500 PMCID: PMC11195089 DOI: 10.1101/2024.06.10.598304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Age-related hearing impairment is the most common cause of hearing loss and is one of the most prevalent conditions affecting the elderly globally. It is influenced by a combination of environmental and genetic factors. The mouse and human inner ears are functionally and genetically homologous. Investigating the genetic basis of age-related hearing loss (ARHL) in an outbred mouse model may lead to a better understanding of the molecular mechanisms of this condition. We used Carworth Farms White (CFW) outbred mice, because they are genetically diverse and exhibit variation in the onset and severity of ARHL. The goal of this study was to identify genetic loci involved in regulating ARHL. Hearing at a range of frequencies was measured using Auditory Brainstem Response (ABR) thresholds in 946 male and female CFW mice at the age of 1, 6, and 10 months. We obtained genotypes at 4.18 million single nucleotide polymorphisms (SNP) using low-coverage (mean coverage 0.27x) whole-genome sequencing followed by imputation using STITCH. To determine the accuracy of the genotypes we sequenced 8 samples at >30x coverage and used calls from those samples to estimate the discordance rate, which was 0.45%. We performed genetic analysis for the ABR thresholds for each frequency at each age, and for the time of onset of deafness for each frequency. The SNP heritability ranged from 0 to 42% for different traits. Genome-wide association analysis identified several regions associated with ARHL that contained potential candidate genes, including Dnah11, Rapgef5, Cpne4, Prkag2, and Nek11. We confirmed, using functional study, that Prkag2 deficiency causes age-related hearing loss at high frequency in mice; this makes Prkag2 a candidate gene for further studies. This work helps to identify genetic risk factors for ARHL and to define novel therapeutic targets for the treatment and prevention of ARHL.
Collapse
Affiliation(s)
- Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ely Boussaty
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivia Lamonte
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Thomas Zhou
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Eric Du
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mika Okamoto
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rick Friedman
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
2
|
Sheng B, Zhao B, Dong Y, Zhang J, Wu S, Ji H, Zhu X. Copine 1 predicts poor clinical outcomes by promoting M2 macrophage activation in ovarian cancer. Carcinogenesis 2023; 44:748-759. [PMID: 37747823 PMCID: PMC10773812 DOI: 10.1093/carcin/bgad067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/05/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023] Open
Abstract
OBJECTIVE Copine 1 (CPNE1), a membrane-binding protein, influences the prognosis of various cancers. According to cBioPortal, CPNE1 amplification is a prevalent genetic mutation in ovarian cancer but with unknown oncogenic mechanism. METHODS This study analysed the CPNE1 expression in ovarian cancer using online datasets, as validated by immunohistochemistry (IHC), quantitative polymerase chain reaction (qPCR) and western blotting. Concurrently, the prognostic value of CPNE1 was accessed. Cell Counting Kit-8, colony formation, transwells and xenograft experiments were performed to evaluate the functions of CPNE1 during ovarian cancer carcinogenesis. CPNE1 and its related genes were analysed by g:Profiler and Tumour Immune Estimation Resource. Furthermore, human monocytic THP-1 cells were co-cultured with ES2 cells to investigate the effect of CPNE1 on macrophage polarization. RESULTS The results of bioinformatic analysis, IHC, qPCR and western blotting indicated a higher CPNE1 in ovarian cancer. CPNE1 overexpression demonstrated an association with a poor prognosis of ovarian cancer. Functionally, CPNE1 overexpression increased ES2 and SKOV3 cell proliferation, invasion and migration in vitro and promoted ovarian tumour xenograft growth in vivo, while CPNE1 knockdown led to opposite effects. Additionally, CPNE1 expression demonstrated an association with immune cell infiltration in ovarian cancer, especially macrophage. CPNE1 promoted protumour M2 macrophage polarization by upregulating cluster of differentiation 163 (CD163), CD206 and interleukin-10. CONCLUSIONS Our study revealed that CPNE1 mediated M2 macrophage polarization and provided a therapeutic target for ovarian cancer.
Collapse
Affiliation(s)
- Bo Sheng
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Bo Zhao
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yue Dong
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Jiamin Zhang
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Suni Wu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Huihui Ji
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Xueqiong Zhu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| |
Collapse
|
3
|
Goel M, Aponte AM, Wistow G, Badea TC. Molecular studies into cell biological role of Copine-4 in Retinal Ganglion Cells. PLoS One 2021; 16:e0255860. [PMID: 34847148 PMCID: PMC8631636 DOI: 10.1371/journal.pone.0255860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/12/2021] [Indexed: 11/19/2022] Open
Abstract
The molecular mechanisms underlying morphological diversity in retinal cell types are poorly understood. We have previously reported that several members of the Copine family of Ca-dependent membrane adaptors are expressed in Retinal Ganglion Cells and transcriptionally regulated by Brn3 transcription factors. Several Copines are enriched in the retina and their over-expression leads to morphological changes -formation of elongated processes-, reminiscent of neurites, in HEK293 cells. However, the role of Copines in the retina is largely unknown. We now investigate Cpne4, a Copine whose expression is restricted to Retinal Ganglion Cells. Over-expression of Cpne4 in RGCs in vivo led to formation of large varicosities on the dendrites but did not otherwise visibly affect dendrite or axon formation. Protein interactions studies using yeast two hybrid analysis from whole retina cDNA revealed two Cpne4 interacting proteins-Host Cell Factor 1 and Morn2. Mass Spectrometry analysis of retina lysate pulled down using Cpne4 or its vonWillebrand A domain showed 207 interacting proteins. A Gene Ontology analysis of the discovered proteins suggests that Cpne4 is involved in several metabolic and signaling pathways in the retina.
Collapse
Affiliation(s)
- Manvi Goel
- Retinal Circuit Development & Genetics Unit, Neurobiology Neurodegeneration & Repair Laboratory, NEI, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Angel M. Aponte
- Proteomics Core, NHLBI, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, NEI, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tudor C. Badea
- Retinal Circuit Development & Genetics Unit, Neurobiology Neurodegeneration & Repair Laboratory, NEI, National Institutes of Health, Bethesda, Maryland, United States of America
- Faculty of Medicine, Research and Development Institute, Transilvania University of Brasov, Brasov, Romania
| |
Collapse
|
4
|
Tang H, Pang P, Qin Z, Zhao Z, Wu Q, Song S, Li F. The CPNE Family and Their Role in Cancers. Front Genet 2021; 12:689097. [PMID: 34367247 PMCID: PMC8345009 DOI: 10.3389/fgene.2021.689097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Despite significant advances in cancer research and treatment, the overall prognosis of lung cancer patients remains poor. Therefore, the identification for novel therapeutic targets is critical for the diagnosis and treatment of lung cancer. CPNEs (copines) are a family of membrane-bound proteins that are highly conserved, soluble, ubiquitous, calcium dependent in a variety of eukaryotes. Emerging evidences have also indicated CPNE family members are involved in cancer development and progression as well. However, the expression patterns and clinical roles in cancer have not yet been well understood. In this review, we summarize recent advances concerning CPNE family members and provide insights into new potential mechanism involved in cancer development.
Collapse
Affiliation(s)
- Haicheng Tang
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Pei Pang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhu Qin
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhangyan Zhao
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qingguo Wu
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shu Song
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Feng Li
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|
5
|
Molecular correlates of muscle spindle and Golgi tendon organ afferents. Nat Commun 2021; 12:1451. [PMID: 33649316 PMCID: PMC7977083 DOI: 10.1038/s41467-021-21880-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/18/2021] [Indexed: 12/16/2022] Open
Abstract
Proprioceptive feedback mainly derives from groups Ia and II muscle spindle (MS) afferents and group Ib Golgi tendon organ (GTO) afferents, but the molecular correlates of these three afferent subtypes remain unknown. We performed single cell RNA sequencing of genetically identified adult proprioceptors and uncovered five molecularly distinct neuronal clusters. Validation of cluster-specific transcripts in dorsal root ganglia and skeletal muscle demonstrates that two of these clusters correspond to group Ia MS afferents and group Ib GTO afferent proprioceptors, respectively, and suggest that the remaining clusters could represent group II MS afferents. Lineage analysis between proprioceptor transcriptomes at different developmental stages provides evidence that proprioceptor subtype identities emerge late in development. Together, our data provide comprehensive molecular signatures for groups Ia and II MS afferents and group Ib GTO afferents, enabling genetic interrogation of the role of individual proprioceptor subtypes in regulating motor output. Coordinated movement critically depends on sensory feedback from muscle spindles (MSs) and Golgi tendon organs (GTOs) but the afferents supplying this proprioceptive feedback have remained genetically inseparable. Here the authors use single cell transcriptome analysis to reveal the molecular basis of MS (groups Ia and II) and GTO (group Ib) afferent identities in the mouse.
Collapse
|
6
|
Insights into Potential Targets for Therapeutic Intervention in Epilepsy. Int J Mol Sci 2020; 21:ijms21228573. [PMID: 33202963 PMCID: PMC7697405 DOI: 10.3390/ijms21228573] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Epilepsy is a chronic brain disease that affects approximately 65 million people worldwide. However, despite the continuous development of antiepileptic drugs, over 30% patients with epilepsy progress to drug-resistant epilepsy. For this reason, it is a high priority objective in preclinical research to find novel therapeutic targets and to develop effective drugs that prevent or reverse the molecular mechanisms underlying epilepsy progression. Among these potential therapeutic targets, we highlight currently available information involving signaling pathways (Wnt/β-catenin, Mammalian Target of Rapamycin (mTOR) signaling and zinc signaling), enzymes (carbonic anhydrase), proteins (erythropoietin, copine 6 and complement system), channels (Transient Receptor Potential Vanilloid Type 1 (TRPV1) channel) and receptors (galanin and melatonin receptors). All of them have demonstrated a certain degree of efficacy not only in controlling seizures but also in displaying neuroprotective activity and in modifying the progression of epilepsy. Although some research with these specific targets has been done in relation with epilepsy, they have not been fully explored as potential therapeutic targets that could help address the unsolved issue of drug-resistant epilepsy and develop new antiseizure therapies for the treatment of epilepsy.
Collapse
|