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Yadav SS, Nair RR, Singh K. Editorial: Cause or effect: role of inflammation in metabolic disorder. Front Endocrinol (Lausanne) 2024; 15:1359605. [PMID: 38344663 PMCID: PMC10853463 DOI: 10.3389/fendo.2024.1359605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 02/15/2024] Open
Affiliation(s)
- Suresh Singh Yadav
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Rohini R. Nair
- Department of Medical Biotechnology Gujarat Biotechnology University, Gandhinagar, India
| | - Kanahiya Singh
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States
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2
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Tisi A, Palaniappan S, Maccarrone M. Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease. Biomolecules 2023; 13:1534. [PMID: 37892216 PMCID: PMC10605747 DOI: 10.3390/biom13101534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.
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Affiliation(s)
- Annamaria Tisi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Sakthimala Palaniappan
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Laboratory of Lipid Neurochemistry, European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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3
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Gordillo GM, Guda PR, Singh K, Biswas A, Abouhashem AS, Rustagi Y, Sen A, Kumar M, Das A, Ghatak S, Khanna S, Sen CK, Roy S. Tissue nanotransfection causes tumor regression by its effect on nanovesicle cargo that alters microenvironmental macrophage state. Mol Ther 2023; 31:1402-1417. [PMID: 36380587 PMCID: PMC10188642 DOI: 10.1016/j.ymthe.2022.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Extracellular vesicles (EVs) are nanovesicles released by all eukaryotic cells. This work reports the first nanoscale fluorescent visualization of tumor-originating vesicles bearing an angiogenic microRNA (miR)-126 cargo. In a validated experimental model of lethal murine vascular neoplasm, tumor-originating EV delivered its miR-126 cargo to tumor-associated macrophages (TAMs). Such delivery resulted in an angiogenic (LYVE+) change of state in TAM that supported tumor formation. Study of the trafficking of tumor-originating fluorescently tagged EV revealed colocalization with TAM demonstrating uptake by these cells. Ex vivo treatment of macrophages with tumor-derived EVs led to gain of tumorigenicity in these isolated cells. Single-cell RNA sequencing of macrophages revealed that EV-borne miR-126 characterized the angiogenic change of state. Unique gene expression signatures of specific macrophage clusters responsive to miR-126-enriched tumor-derived EVs were revealed. Topical tissue nanotransfection (TNT) delivery of an oligonucleotide comprising an anti-miR against miR-126 resulted in significant knockdown of miR-126 in the tumor tissue. miR-126 knockdown resulted in complete involution of the tumor and improved survival rate of tumor-affected mice. This work identifies a novel tumorigenic mechanism that relies on tumorigenic state change of TAM caused by tumor-originating EV-borne angiomiR. This disease process can be effectively targeted by topical TNT of superficial tumors.
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Affiliation(s)
- Gayle M Gordillo
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA.
| | - Poornachander Reddy Guda
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Kanhaiya Singh
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Ayan Biswas
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Ahmed S Abouhashem
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Yashika Rustagi
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Abhishek Sen
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Manishekhar Kumar
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Amitava Das
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Savita Khanna
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Chandan K Sen
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA.
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4
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Ya D, Zhang Y, Cui Q, Jiang Y, Yang J, Tian N, Xiang W, Lin X, Li Q, Liao R. Application of spatial transcriptome technologies to neurological diseases. Front Cell Dev Biol 2023; 11:1142923. [PMID: 36936681 PMCID: PMC10020196 DOI: 10.3389/fcell.2023.1142923] [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: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function, and cellular interactions, spatial transcriptome technology can deeply explore the pathogenic mechanisms of cell-type-specific responses and spatial localization in neurological diseases. The present article overviews spatial transcriptome technologies based on microdissection, in situ hybridization, in situ sequencing, in situ capture, and live cell labeling. Each technology is described along with its methods, detection throughput, spatial resolution, benefits, and drawbacks. Furthermore, their applications in neurodegenerative disease, neuropsychiatric illness, stroke and epilepsy are outlined. This information can be used to understand disease mechanisms, pick therapeutic targets, and establish biomarkers.
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Affiliation(s)
- Dongshan Ya
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yingmei Zhang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qi Cui
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yanlin Jiang
- Department of Pharmacology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Jiaxin Yang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ning Tian
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Wenjing Xiang
- Department of Neurology ward 2, Guilin People’s Hospital, Guilin, China
| | - Xiaohui Lin
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qinghua Li
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Rujia Liao
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- *Correspondence: Rujia Liao,
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Șerbănescu MS, Bungărdean RM, Georgiu C, Crișan M. Nodular and Micronodular Basal Cell Carcinoma Subtypes Are Different Tumors Based on Their Morphological Architecture and Their Interaction with the Surrounding Stroma. Diagnostics (Basel) 2022; 12:diagnostics12071636. [PMID: 35885545 PMCID: PMC9323345 DOI: 10.3390/diagnostics12071636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/16/2022] Open
Abstract
Basal cell carcinoma (BCC) is the most frequent cancer of the skin and comprises low-risk and high-risk subtypes. We selected a low-risk subtype, namely, nodular (N), and a high-risk subtype, namely, micronodular (MN), with the aim to identify differences between them using a classical morphometric approach through a gray-level co-occurrence matrix and histogram analysis, as well as an approach based on deep learning semantic segmentation. From whole-slide images, pathologists selected 216 N and 201 MN BCC images. The two groups were then manually segmented and compared based on four morphological areas: center of the BCC islands (tumor, T), peripheral palisading of the BCC islands (touching tumor, TT), peritumoral cleft (PC) and surrounding stroma (S). We found that the TT pattern varied the least, while the PC pattern varied the most between the two subtypes. The combination of two distinct analysis approaches yielded fresh insights into the characterization of BCC, and thus, we were able to describe two different morphological patterns for the T component of the two subtypes.
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Affiliation(s)
- Mircea-Sebastian Șerbănescu
- Department of Medical Informatics and Biostatistics, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Raluca Maria Bungărdean
- Department of Pathology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
- Correspondence:
| | - Carmen Georgiu
- Department of Pathology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Maria Crișan
- Department of Histology, Iuliu Haţieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
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Kelley MW. Cochlear Development; New Tools and Approaches. Front Cell Dev Biol 2022; 10:884240. [PMID: 35813214 PMCID: PMC9260282 DOI: 10.3389/fcell.2022.884240] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 12/21/2022] Open
Abstract
The sensory epithelium of the mammalian cochlea, the organ of Corti, is comprised of at least seven unique cell types including two functionally distinct types of mechanosensory hair cells. All of the cell types within the organ of Corti are believed to develop from a population of precursor cells referred to as prosensory cells. Results from previous studies have begun to identify the developmental processes, lineage restrictions and signaling networks that mediate the specification of many of these cell types, however, the small size of the organ and the limited number of each cell type has hampered progress. Recent technical advances, in particular relating to the ability to capture and characterize gene expression at the single cell level, have opened new avenues for understanding cellular specification in the organ of Corti. This review will cover our current understanding of cellular specification in the cochlea, discuss the most commonly used methods for single cell RNA sequencing and describe how results from a recent study using single cell sequencing provided new insights regarding cellular specification.
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Bhamidipati T, Kumar M, Verma SS, Mohanty SK, Kacar S, Reese D, Martinez MM, Kamocka MM, Dunn KW, Sen CK, Singh K. Epigenetic basis of diabetic vasculopathy. Front Endocrinol (Lausanne) 2022; 13:989844. [PMID: 36568089 PMCID: PMC9780391 DOI: 10.3389/fendo.2022.989844] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) causes peripheral vascular disease because of which several blood-borne factors, including vital nutrients fail to reach the affected tissue. Tissue epigenome is sensitive to chronic hyperglycemia and is known to cause pathogenesis of micro- and macrovascular complications. These vascular complications of T2DM may perpetuate the onset of organ dysfunction. The burden of diabetes is primarily because of a wide range of complications of which nonhealing diabetic ulcers represent a major component. Thus, it is imperative that current research help recognize more effective methods for the diagnosis and management of early vascular injuries. This review addresses the significance of epigenetic processes such as DNA methylation and histone modifications in the evolution of macrovascular and microvascular complications of T2DM.
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Affiliation(s)
- Theja Bhamidipati
- Department of Vascular Surgery, Jefferson-Einstein Medical Center, Philadelphia, PA, United States
| | - Manishekhar Kumar
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sumit S. Verma
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sujit K. Mohanty
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sedat Kacar
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Diamond Reese
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Michelle M. Martinez
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Malgorzata M. Kamocka
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kenneth W. Dunn
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chandan K. Sen
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Kanhaiya Singh, ; Chandan K. Sen,
| | - Kanhaiya Singh
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Kanhaiya Singh, ; Chandan K. Sen,
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