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Golestan A, Tahmasebi A, Maghsoodi N, Faraji SN, Irajie C, Ramezani A. Unveiling promising breast cancer biomarkers: an integrative approach combining bioinformatics analysis and experimental verification. BMC Cancer 2024; 24:155. [PMID: 38291367 PMCID: PMC10829368 DOI: 10.1186/s12885-024-11913-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Breast cancer remains a significant health challenge worldwide, necessitating the identification of reliable biomarkers for early detection, accurate prognosis, and targeted therapy. MATERIALS AND METHODS Breast cancer RNA expression data from the TCGA database were analyzed to identify differentially expressed genes (DEGs). The top 500 up-regulated DEGs were selected for further investigation using random forest analysis to identify important genes. These genes were evaluated based on their potential as diagnostic biomarkers, their overexpression in breast cancer tissues, and their low median expression in normal female tissues. Various validation methods, including online tools and quantitative Real-Time PCR (qRT-PCR), were used to confirm the potential of the identified genes as breast cancer biomarkers. RESULTS The study identified four overexpressed genes (CACNG4, PKMYT1, EPYC, and CHRNA6) among 100 genes with higher importance scores. qRT-PCR analysis confirmed the significant upregulation of these genes in breast cancer patients compared to normal samples. CONCLUSIONS These findings suggest that CACNG4, PKMYT1, EPYC, and CHRNA6 may serve as valuable biomarkers for breast cancer diagnosis, and PKMYT1 may also have prognostic significance. Furthermore, CACNG4, CHRNA6, and PKMYT1 show promise as potential therapeutic targets. These findings have the potential to advance diagnostic methods and therapeutic approaches for breast cancer.
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Affiliation(s)
- Ali Golestan
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Nafiseh Maghsoodi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Nooreddin Faraji
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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Yang Z, Li H, Hao J, Mei H, Qiu M, Wang H, Gao M. EPYC functions as a novel prognostic biomarker for pancreatic cancer. Sci Rep 2024; 14:719. [PMID: 38184732 PMCID: PMC10771449 DOI: 10.1038/s41598-024-51478-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: 10/30/2023] [Accepted: 01/05/2024] [Indexed: 01/08/2024] Open
Abstract
Pancreatic cancer (PC) has become a worldwide challenge attributed to its difficult early diagnosis and rapid progression. Treatments continue to be limited besides surgical resection. Hence, we aimed to discover novel biological signatures as clinically effective therapeutic targets for PC via the mining of public tumor databases. We found that epiphycan (EPYC) could function as an independent risk factor to predict the poor prognosis in PC based on integrated bioinformatics analysis. We downloaded associated PC data profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) online websites, then applied the software Rstudio to filter out genes under the strict criteria. After the batch survival analysis using Log-rank test and univariate cox regression, we obtained 39 candidate genes. Subsequently, we narrowed the scope to 8 genes by establishing a Lasso regression model. Eventually, we focused on 2 genes (EPYC and MET) by further building a multivariate cox regression model. Given that the role of EPYC in PC remains obscure, we then performed a series of molecular functional experiments, including RT-qPCR, CCK8, EdU, colony formation, Transwell, western blot, cell live-dead staining, subcutaneous tumor formation, to enhance our insight into its underlying molecular mechanisms. The above results demonstrated that EPYC was highly expressed in PC cell lines and could promote the proliferation of PCs via PI3K-AKT signaling pathway in vivo and in vitro. We arrived at a conclusion that EPYC was expected to be a biological neo-biomarker for PC followed by being a potential therapeutic target.
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Affiliation(s)
- Zhen Yang
- Department of Clinical Laboratory, Tianjin Union Medical Center of Nankai University, Tianjin, China.
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China.
| | - Honglin Li
- Department of Clinical Laboratory, Dachuan District People's Hospital, Sichuan, China
| | - Jie Hao
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center of Nankai University, Tianjin, China
| | - Hanwei Mei
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China
- Department of Oncology, Tianjin Union Medical Center of Nankai University, Tianjin, China
| | - Minghan Qiu
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China
- Department of Oncology, Tianjin Union Medical Center of Nankai University, Tianjin, China
| | - Huaqing Wang
- The Institute of Translational Medicine, Tianjin Union Medical Center of Nankai University, Tianjin, China.
- Department of Oncology, Tianjin Union Medical Center of Nankai University, Tianjin, China.
| | - Ming Gao
- Department of Thyroid and Breast Surgery, Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center of Nankai University, Tianjin, China.
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). Front Cell Neurosci 2023; 17:1256619. [PMID: 38094513 PMCID: PMC10716316 DOI: 10.3389/fncel.2023.1256619] [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: 07/11/2023] [Accepted: 10/11/2023] [Indexed: 12/20/2023] Open
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types, and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach-first by linking to expression of known marker genes, then using the NSForest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website, and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes within the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
- Ely Cheikh Boussaty
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Neil Tedeschi
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Mark Novotny
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Uri Manor
- Department of Cell and Developmental Biology, University of California San Diego, Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528661. [PMID: 36824745 PMCID: PMC9948975 DOI: 10.1101/2023.02.15.528661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach - first by linking to expression of known marker genes, then using the NS-Forest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website (https://umgear.org/), and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
| | | | | | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, CA
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, CA
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, CA
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA
| | - Uri Manor
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA
- Department of Pathology, University of California, San Diego, CA
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, CA
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Identification of Biomarkers Associated with Diagnosis of Osteoarthritis Patients Based on Bioinformatics and Machine Learning. J Immunol Res 2022; 2022:5600190. [PMID: 35733917 PMCID: PMC9208923 DOI: 10.1155/2022/5600190] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Osteoarthritis (OA) is thought to be the most prevalent chronic joint disease. The incidence of OA is rising because of the ageing population and the epidemic of obesity. This research was designed for the identification of novel diagnostic biomarkers for OA and analyzing the possible association between critical genes and infiltrated immune cells. 10 OA samples from patients with spinal OA and 10 normal samples were collected. GSE55235 and GSE55457 datasets including human OA and normal samples were downloaded from the GEO datasets. Differentially expressed genes (DEGs) were identified between 20 OA and 20 controls. SVM-RFE analysis and LASSO regression model were carried out to screen possible markers. The compositional patterns of the 22 types of immune cell fraction in OA were determined by the use of CIBERSORT. The expression level of the biomarkers in OA was examined by the use of RT-PCR. In this study, an overall 44 DEGs were identified: 18 genes were remarkably upregulated and 26 genes were distinctly downregulated. KEGG pathway analyses revealed that pathways were significantly enriched including IL-17 signal path, rheumatoid arthritis, TNF signal path, and lipid and atherosclerosis. Based on the results of machine learning, we identified APOLD1 and EPYC as critical diagnostic genes in OA, which were further confirmed using ROC assays. Immune cell infiltration analysis revealed that APOLD1 was correlated with mastocytes stimulated, NK cells resting, T cells CD4 memory resting, DCs stimulated, T cells gamma delta, macrophages M0, NK cells stimulated, and mastocytes resting. Moreover, we found that EPYC was correlated with mastocytes stimulated, NK cells resting, T cells CD4 memory resting, DCs stimulated, T cells gamma delta, macrophages M0, NK cells stimulated, and mastocytes resting. Overall, our findings might provide some novel clue for the exploration of novel markers for OA diagnosis. The critical genes and their associations with immune infiltration may offer new insight into understanding OA developments.
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Deng L, Wang D, Chen S, Hu W, Zhang R. Epiphycan Predicts Poor Outcomes and Promotes Metastasis in Ovarian Cancer. Front Oncol 2021; 11:653782. [PMID: 34888227 PMCID: PMC8650094 DOI: 10.3389/fonc.2021.653782] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
The small leucine-rich proteoglycan (SLRP) family is widely expressed in extracellular matrix and aggravates tumor progression. However, epiphycan (EPYC), as a member of the SLRPs family, its biological function in cancer has not been confirmed. Thus, we aimed to clarify the role of EPYC in progression of ovarian cancer (OC), and further analyze the molecular mechanisms implicated in tumorigenesis. Here, we analyzed the differential expression genes of GSE38734, including 4 matched primary OC and metastatic tissues. We obtained OC RNAseqs data from the Cancer Genome Atlas (TCGA) and analyzed the correlation between EPYC expression and OC staging, pathological grading, etc. The expression of EPYC in OC and normal ovarian tissues was compared in Oncomine website. We used siRNAs to interfere the expression of EPYC in ovarian cancer cell line SKOV3. Scratch test, transwell-matrigel chamber, CCK8 assay were used to detect the changes of SKOV3 migration, invasion and proliferation ability after EPYC was interfered. We used R software to make GO and KEGG analysis of related genes of EPYC. We used the Hitpredict website to predict interacting proteins. The results showed that the expression of EPYC in metastatic ovarian cancer was higher than primary ovarian cancer, and that in primary cancer was higher than normal ovaries. After siRNA interferes with EPYC expression, the migration, invasion and proliferation of SKOV3 cells were weakened. EPYC mainly played a role in ECM organization, and involved in PI3K/Akt, focal adhesion signaling pathways. EPYC might interact with PLCG2 and CRK, and be involved in signal transduction.
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Affiliation(s)
- Lu Deng
- Department of Gynaecology, The Hospital of Obstetrics & Gynaecology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Bio-Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Dandan Wang
- Department of Gynecology and Obstetrics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Shouzhen Chen
- Department of Gynaecology, The Hospital of Obstetrics & Gynaecology, Fudan University, Shanghai, China
| | - Weiguo Hu
- Department of Gynaecology, The Hospital of Obstetrics & Gynaecology, Fudan University, Shanghai, China
| | - Ru Zhang
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Bio-Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, China
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Daple deficiency causes hearing loss in adult mice by inducing defects in cochlear stereocilia and apical microtubules. Sci Rep 2021; 11:20224. [PMID: 34642354 PMCID: PMC8511111 DOI: 10.1038/s41598-021-96232-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/20/2021] [Indexed: 12/29/2022] Open
Abstract
The V-shaped arrangement of hair bundles on cochlear hair cells is critical for auditory sensing. However, regulation of hair bundle arrangements has not been fully understood. Recently, defects in hair bundle arrangement were reported in postnatal Dishevelled-associating protein (ccdc88c, alias Daple)-deficient mice. In the present study, we found that adult Daple−/− mice exhibited hearing disturbances over a broad frequency range through auditory brainstem response testing. Consistently, distorted patterns of hair bundles were detected in almost all regions, more typically in the basal region of the cochlear duct. In adult Daple−/− mice, apical microtubules were irregularly aggregated, and the number of microtubules attached to plasma membranes was decreased. Similar phenotypes were manifested upon nocodazole treatment in a wild type cochlea culture without affecting the microtubule structure of the kinocilium. These results indicate critical role of Daple in hair bundle arrangement through the orchestration of apical microtubule distribution, and thereby in hearing, especially at high frequencies.
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Hayes AJ, Melrose J. Neural Tissue Homeostasis and Repair Is Regulated via CS and DS Proteoglycan Motifs. Front Cell Dev Biol 2021; 9:696640. [PMID: 34409033 PMCID: PMC8365427 DOI: 10.3389/fcell.2021.696640] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
Chondroitin sulfate (CS) is the most abundant and widely distributed glycosaminoglycan (GAG) in the human body. As a component of proteoglycans (PGs) it has numerous roles in matrix stabilization and cellular regulation. This chapter highlights the roles of CS and CS-PGs in the central and peripheral nervous systems (CNS/PNS). CS has specific cell regulatory roles that control tissue function and homeostasis. The CNS/PNS contains a diverse range of CS-PGs which direct the development of embryonic neural axonal networks, and the responses of neural cell populations in mature tissues to traumatic injury. Following brain trauma and spinal cord injury, a stabilizing CS-PG-rich scar tissue is laid down at the defect site to protect neural tissues, which are amongst the softest tissues of the human body. Unfortunately, the CS concentrated in gliotic scars also inhibits neural outgrowth and functional recovery. CS has well known inhibitory properties over neural behavior, and animal models of CNS/PNS injury have demonstrated that selective degradation of CS using chondroitinase improves neuronal functional recovery. CS-PGs are present diffusely in the CNS but also form denser regions of extracellular matrix termed perineuronal nets which surround neurons. Hyaluronan is immobilized in hyalectan CS-PG aggregates in these perineural structures, which provide neural protection, synapse, and neural plasticity, and have roles in memory and cognitive learning. Despite the generally inhibitory cues delivered by CS-A and CS-C, some CS-PGs containing highly charged CS disaccharides (CS-D, CS-E) or dermatan sulfate (DS) disaccharides that promote neural outgrowth and functional recovery. CS/DS thus has varied cell regulatory properties and structural ECM supportive roles in the CNS/PNS depending on the glycoform present and its location in tissue niches and specific cellular contexts. Studies on the fruit fly, Drosophila melanogaster and the nematode Caenorhabditis elegans have provided insightful information on neural interconnectivity and the role of the ECM and its PGs in neural development and in tissue morphogenesis in a whole organism environment.
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Affiliation(s)
- Anthony J. Hayes
- Bioimaging Research Hub, Cardiff School of Biosciences, Cardiff University, Wales, United Kingdom
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, Australia
- Raymond Purves Bone and Joint Research Laboratories, Kolling Institute of Medical Research, Royal North Shore Hospital and The Faculty of Medicine and Health, The University of Sydney, St. Leonard’s, NSW, Australia
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Stabenau KA, Zimmermann MT, Mathison A, Zeighami A, Samuels TL, Chun RH, Papsin BC, McCormick ME, Johnston N, Kerschner JE. RNA Sequencing and Pathways Analyses of Middle Ear Epithelia From Patients With Otitis Media. Laryngoscope 2021; 131:2590-2597. [PMID: 33844317 DOI: 10.1002/lary.29551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 01/24/2023]
Abstract
OBJECTIVES Otitis media (OM) is the most common pediatric diagnosis in the United States. However, our understanding of the molecular pathogenesis of OM remains relatively poor. Investigation of molecular pathways involved in OM may improve the understanding of this disease process and elucidate novel therapeutic targets. In this study, RNA sequencing (RNA-Seq) was used to discern cellular changes associated with OME compared to healthy middle ear epithelium (MEE). STUDY DESIGN Ex vivo case-control translational. METHODS Middle ear epithelia was collected from five pediatric patients diagnosed with OME undergoing tympanostomy tube placement and five otherwise healthy pediatric patients undergoing cochlear implantation. Specimens underwent RNA-Seq and pathways analyses. RESULTS A total of 1,292 genes exhibited differential expression in MEE from OME patients compared to controls including genes involved in inflammation, immune response to bacterial OM pathogens, mucociliary clearance, regulation of proliferation and transformation, and auditory cell differentiation. Top networks identified in OME were organismal injury and abnormalities, cell morphology, and auditory disease. Top Ingenuity canonical pathways identified were axonal guidance signaling, which contains genes associated with auditory development and disease and nicotine degradation II and III pathways. Associated upstream regulators included β-estradiol, dexamethasone, and G-protein-coupled estrogen receptor-1 (GPER1), which are associated with otoprotection or inflammation during insult. CONCLUSIONS RNA-Seq demonstrates differential gene expression in MEE from patients with OME compared to healthy controls with important implications for infection susceptibility, hearing loss, and a role for tobacco exposure in the development and/or severity of OME in pediatric patients. LEVEL OF EVIDENCE 4 Laryngoscope, 2021.
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Affiliation(s)
- Kaleigh A Stabenau
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A.,Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Angela Mathison
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Atefeh Zeighami
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Tina L Samuels
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Robert H Chun
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Blake C Papsin
- Archie's Cochlear Implant Laboratory, Department of Otolaryngology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael E McCormick
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Nikki Johnston
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
| | - Joseph E Kerschner
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A
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Gu S, Olszewski R, Taukulis I, Wei Z, Martin D, Morell RJ, Hoa M. Characterization of rare spindle and root cell transcriptional profiles in the stria vascularis of the adult mouse cochlea. Sci Rep 2020; 10:18100. [PMID: 33093630 PMCID: PMC7581811 DOI: 10.1038/s41598-020-75238-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
The stria vascularis (SV) in the cochlea generates and maintains the endocochlear potential, thereby playing a pivotal role in normal hearing. Knowing transcriptional profiles and gene regulatory networks of SV cell types establishes a basis for studying the mechanism underlying SV-related hearing loss. While we have previously characterized the expression profiles of major SV cell types in the adult mouse, transcriptional profiles of rare SV cell types remained elusive due to the limitation of cell capture in single-cell RNA-Seq. The role of these rare cell types in the homeostatic function of the adult SV remain largely undefined. In this study, we performed single-nucleus RNA-Seq on the adult mouse SV in conjunction with sample preservation treatments during the isolation steps. We distinguish rare SV cell types, including spindle cells and root cells, from other cell types, and characterize their transcriptional profiles. Furthermore, we also identify and validate novel specific markers for these rare SV cell types. Finally, we identify homeostatic gene regulatory networks within spindle and root cells, establishing a basis for understanding the functional roles of these cells in hearing. These novel findings will provide new insights for future work in SV-related hearing loss and hearing fluctuation.
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Affiliation(s)
- Shoujun Gu
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Ian Taukulis
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Zheng Wei
- Biomedical Research Informatics Office, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Daniel Martin
- Biomedical Research Informatics Office, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Robert J Morell
- Computational Biology and Genomics Core, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA.
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Yang LM, Stout L, Rauchman M, Ornitz DM. Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification. Dev Dyn 2020; 249:1217-1242. [PMID: 32492250 DOI: 10.1002/dvdy.211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Understanding the mechanisms that regulate hair cell (HC) differentiation in the organ of Corti (OC) is essential to designing genetic therapies for hearing loss due to HC loss or damage. We have previously identified Fibroblast Growth Factor 20 (FGF20) as having a key role in HC and supporting cell differentiation in the mouse OC. To investigate the genetic landscape regulated by FGF20 signaling in OC progenitors, we employ Translating Ribosome Affinity Purification combined with Next Generation RNA Sequencing (TRAPseq) in the Fgf20 lineage. RESULTS We show that TRAPseq targeting OC progenitors effectively enriched for RNA from this rare cell population. TRAPseq identified differentially expressed genes (DEGs) downstream of FGF20, including Etv4, Etv5, Etv1, Dusp6, Hey1, Hey2, Heyl, Tectb, Fat3, Cpxm2, Sall1, Sall3, and cell cycle regulators such as Cdc20. Analysis of Cdc20 conditional-null mice identified decreased cochlea length, while analysis of Sall1-null and Sall1-ΔZn2-10 mice, which harbor a mutation that causes Townes-Brocks syndrome, identified a decrease in outer hair cell number. CONCLUSIONS We present two datasets: genes with enriched expression in OC progenitors, and DEGs downstream of FGF20 in the embryonic day 14.5 cochlea. We validate select DEGs via in situ hybridization and in vivo functional studies in mice.
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Affiliation(s)
- Lu M Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lisa Stout
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael Rauchman
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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Farooq R, Hussain K, Tariq M, Farooq A, Mustafa M. CRISPR/Cas9: targeted genome editing for the treatment of hereditary hearing loss. J Appl Genet 2020; 61:51-65. [PMID: 31912450 DOI: 10.1007/s13353-019-00535-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
Hereditary hearing loss (HHL) is a neurosensory disorder that affects every 1/500 newborns worldwide and nearly 1/3 people over the age of 65. Congenital deafness is inherited as monogenetic or polygenic disorder. The delicacy, tissue heterogeneity, deep location of the inner ear down the brainstem, and minute quantity of cells present in cochlea are the major challenges for current therapeutic approaches to cure deafness. Targeted genome editing is considered a suitable approach to treat HHL since it can target defective molecular components of auditory transduction to restore normal cochlear function. With the advent of CRISPR/Cas9 technique, targeted genome editing and biomedical research have been revolutionized. The robustness and simplicity of this technology lie in its design and delivery methods. It can directly deliver a complex of Cas9 endonuclease and single guide RNA (sgRNA) into zygote using either vector-mediated stable transfection or transient delivery of ribonucleoproteins complexes. This strategy induces DNA double strand breaks (DSBs) at target site followed by endogenous DNA repairing mechanisms of the cell. CRISPR/Cas9 has been successfully used in model animals to edit hearing genes like calcium and integrin-binding protein 2, myosin VIIA, Xin-actin binding repeat containing 2, leucine-zipper and sterile-alpha motif kinase Zak, epiphycan, transmembrane channel-like protein 1, and cadherin 23. This review discusses the utility of lipid-mediated transient delivery of Cas9/sgRNA complexes, an efficient way to restore hearing in humans, suffering from HHL. Notwithstanding, challenges like PAM requirement, HDR efficiency, off-target activity, and optimized delivery systems need to be addressed.
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Affiliation(s)
- Rimsha Farooq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.,Department of Biological Sciences, Forman Christian College University Lahore, Lahore, Pakistan
| | - Khadim Hussain
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering (NIBGE) College Faisalabad, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Ali Farooq
- Primary and Secondary Healthcare Department, Lahore, Government of Punjab, Pakistan
| | - Muhammad Mustafa
- Department of Biological Sciences, Forman Christian College University Lahore, Lahore, Pakistan
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Listik E, Azevedo Marques Gaschler J, Matias M, Neuppmann Feres MF, Toma L, Raphaelli Nahás-Scocate AC. Proteoglycans and dental biology: the first review. Carbohydr Polym 2019; 225:115199. [DOI: 10.1016/j.carbpol.2019.115199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 01/08/2023]
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14
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Kang W, Sun Z, Zhao X, Wang X, Tao Y, Wu H. Gene editing based hearing impairment research and therapeutics. Neurosci Lett 2019; 709:134326. [PMID: 31195050 DOI: 10.1016/j.neulet.2019.134326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/06/2019] [Accepted: 06/08/2019] [Indexed: 12/26/2022]
Abstract
Hearing impairment affects 1 in 500 newborns worldwide and nearly one out of three people over the age of 65 (WHO, 2019). Hereditary hearing loss is the most common type of congenital deafness; genetic factors also affect deafness susceptibility. Gene therapies may preserve or restore natural sound perception, and have rescued deafness in multiple hereditary murine models. CRISPR-Cas9 and base editors (BEs) are newly developed gene editing technologies that can facilitate gene studies in the inner ear and provide therapeutic approaches for hearing impairment. Here, we present recent applications of gene editing in the inner ear.
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Affiliation(s)
- Wen Kang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, China; Ear Institute, Shanghai Jiaotong University School of Medicine, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, China
| | - Zhuoer Sun
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, China; Ear Institute, Shanghai Jiaotong University School of Medicine, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, China
| | - Xingle Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, China; Ear Institute, Shanghai Jiaotong University School of Medicine, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, China
| | - Xueling Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, China; Ear Institute, Shanghai Jiaotong University School of Medicine, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, China.
| | - Yong Tao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, China; Ear Institute, Shanghai Jiaotong University School of Medicine, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, China.
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, China; Ear Institute, Shanghai Jiaotong University School of Medicine, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, China.
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15
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Fibroblast growth factor 12 is expressed in spiral and vestibular ganglia and necessary for auditory and equilibrium function. Sci Rep 2018; 8:11491. [PMID: 30065296 PMCID: PMC6068167 DOI: 10.1038/s41598-018-28618-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/26/2018] [Indexed: 11/13/2022] Open
Abstract
We investigated fibroblast growth factor 12 (FGF12) as a transcript enriched in the inner ear by searching published cDNA library databases. FGF12 is a fibroblast growth factor homologous factor, a subset of the FGF superfamily. To date, its localisation and function in the inner ear have not been determined. Here, we show that FGF12 mRNA is localised in spiral ganglion neurons (SGNs) and the vestibular ganglion. We also show that FGF12 protein is localised in SGNs, the vestibular ganglion, and nerve fibres extending beneath hair cells. Moreover, we investigated FGF12 function in auditory and vestibular systems using Fgf12-knockout (FGF12-KO) mice generated with CRISPR/Cas9 technology. Our results show that the inner ear morphology of FGF12-KO mice is not significantly different compared with wild-type mice. However, FGF12-KO mice exhibited an increased hearing threshold, as measured by the auditory brainstem response, as well as deficits in rotarod and balance beam performance tests. These results suggest that FGF12 is necessary for normal auditory and equilibrium function.
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