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Ouyang X, Matt A, Wang F, Gracheva E, Migunova E, Rajamani S, Dubrovsky EB, Zhou C. Attention LSTM U-Net model for Drosophila melanogaster heart tube segmentation in optical coherence microscopy images. BIOMEDICAL OPTICS EXPRESS 2024; 15:3639-3653. [PMID: 38867790 PMCID: PMC11166423 DOI: 10.1364/boe.523364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/22/2024] [Accepted: 04/28/2024] [Indexed: 06/14/2024]
Abstract
Optical coherence microscopy (OCM) imaging of the Drosophila melanogaster (fruit fly) heart tube has enabled the non-invasive characterization of fly heart physiology in vivo. OCM generates large volumes of data, making it necessary to automate image analysis. Deep-learning-based neural network models have been developed to improve the efficiency of fly heart image segmentation. However, image artifacts caused by sample motion or reflections reduce the accuracy of the analysis. To improve the precision and efficiency of image data analysis, we developed an Attention LSTM U-Net model (FlyNet3.0), which incorporates an attention learning mechanism to track the beating fly heart in OCM images. The new model has improved the intersection over union (IOU) compared to FlyNet2.0 + with reflection artifacts from 86% to 89% and with movement from 81% to 89%. We also extended the capabilities of OCM analysis through the introduction of an automated, in vivo heart wall thickness measurement method, which has been validated on a Drosophila model of cardiac hypertrophy. This work will enable the comprehensive, non-invasive characterization of fly heart physiology in a high-throughput manner.
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Affiliation(s)
- Xiangping Ouyang
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Abigail Matt
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fei Wang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Elena Gracheva
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ekaterina Migunova
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | - Saathvika Rajamani
- Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA
| | | | - Chao Zhou
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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Held JP, Dbouk NH, Strozak AM, Grub LK, Ryou H, Schaffner SH, Patel MR. Germline status and micronutrient availability regulate a somatic mitochondrial quality control pathway via short-chain fatty acid metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.594820. [PMID: 38826313 PMCID: PMC11142046 DOI: 10.1101/2024.05.20.594820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Reproductive status, such as pregnancy and menopause in women, profoundly influences metabolism of the body. Mitochondria likely orchestrate many of these metabolic changes. However, the influence of reproductive status on somatic mitochondria and the underlying mechanisms remain largely unexplored. We demonstrate that reproductive signals modulate mitochondria in the Caenorhabditis elegans soma. We show that the germline acts via an RNA endonuclease, HOE-1, which despite its housekeeping role in tRNA maturation, selectively regulates the mitochondrial unfolded protein response (UPRmt). Mechanistically, we uncover a fatty acid metabolism pathway acting upstream of HOE-1 to convey germline status. Furthermore, we link vitamin B12's dietary intake to the germline's regulatory impact on HOE-1-driven UPRmt. Combined, our study uncovers a germline-somatic mitochondrial connection, reveals the underlying mechanism, and highlights the importance of micronutrients in modulating this connection. Our findings provide insights into the interplay between reproductive biology and metabolic regulation.
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Affiliation(s)
- James P. Held
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Nadir H. Dbouk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Adrianna M. Strozak
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lantana K. Grub
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Hayeon Ryou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Maulik R. Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Evolutionary Studies, Vanderbilt University, VU Box #34-1634, Nashville, TN, USA
- Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Quantitative Systems Biology Center, Vanderbilt University, Nashville, TN, USA
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Migunova E, Rajamani S, Bonanni S, Wang F, Zhou C, Dubrovsky EB. Cardiac RNase Z edited via CRISPR-Cas9 drives heart hypertrophy in Drosophila. PLoS One 2023; 18:e0286214. [PMID: 37228086 PMCID: PMC10212119 DOI: 10.1371/journal.pone.0286214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Cardiomyopathy (CM) is a group of diseases distinguished by morphological and functional abnormalities in the myocardium. It is etiologically heterogeneous and may develop via cell autonomous and/or non-autonomous mechanisms. One of the most severe forms of CM has been linked to the deficiency of the ubiquitously expressed RNase Z endoribonuclease. RNase Z cleaves off the 3'-trailer of both nuclear and mitochondrial primary tRNA (pre-tRNA) transcripts. Cells mutant for RNase Z accumulate unprocessed pre-tRNA molecules. Patients carrying RNase Z variants with reduced enzymatic activity display a plethora of symptoms including muscular hypotonia, microcephaly and severe heart hypertrophy; still, they die primarily due to acute heart decompensation. Determining whether the underlying mechanism of heart malfunction is cell autonomous or not will provide an opportunity to develop novel strategies of more efficient treatments for these patients. In this study, we used CRISPR-TRiM technology to create Drosophila models that carry cardiomyopathy-linked alleles of RNase Z only in the cardiomyocytes. We found that this modification is sufficient for flies to develop heart hypertrophy and systolic dysfunction. These observations support the idea that the RNase Z linked CM is driven by cell autonomous mechanisms.
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Affiliation(s)
- Ekaterina Migunova
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Saathvika Rajamani
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Stefania Bonanni
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
| | - Fei Wang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Chao Zhou
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Edward B. Dubrovsky
- Department of Biological Sciences, Fordham University, Bronx, NY, United States of America
- Center for Cancer, Genetic Diseases, and Gene Regulation, Fordham University, Bronx, NY, United States of America
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Huang Y, Zhou B. Mitochondrial Dysfunction in Cardiac Diseases and Therapeutic Strategies. Biomedicines 2023; 11:biomedicines11051500. [PMID: 37239170 DOI: 10.3390/biomedicines11051500] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondria are the main site of intracellular synthesis of ATP, which provides energy for various physiological activities of the cell. Cardiomyocytes have a high density of mitochondria and mitochondrial damage is present in a variety of cardiovascular diseases. In this paper, we describe mitochondrial damage in mitochondrial cardiomyopathy, congenital heart disease, coronary heart disease, myocardial ischemia-reperfusion injury, heart failure, and drug-induced cardiotoxicity, in the context of the key roles of mitochondria in cardiac development and homeostasis. Finally, we discuss the main current therapeutic strategies aimed at alleviating mitochondrial impairment-related cardiac dysfunction, including pharmacological strategies, gene therapy, mitochondrial replacement therapy, and mitochondrial transplantation. It is hoped that this will provide new ideas for the treatment of cardiovascular diseases.
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Affiliation(s)
- Yafei Huang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical College, 167 North Lishi Road, Xicheng District, Beijing 100037, China
| | - Bingying Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Science and Peking Union Medical College, 167 North Lishi Road, Xicheng District, Beijing 100037, China
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Zhao Y, van de Leemput J, Han Z. The opportunities and challenges of using Drosophila to model human cardiac diseases. Front Physiol 2023; 14:1182610. [PMID: 37123266 PMCID: PMC10130661 DOI: 10.3389/fphys.2023.1182610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
The Drosophila heart tube seems simple, yet it has notable anatomic complexity and contains highly specialized structures. In fact, the development of the fly heart tube much resembles that of the earliest stages of mammalian heart development, and the molecular-genetic mechanisms driving these processes are highly conserved between flies and humans. Combined with the fly's unmatched genetic tools and a wide variety of techniques to assay both structure and function in the living fly heart, these attributes have made Drosophila a valuable model system for studying human heart development and disease. This perspective focuses on the functional and physiological similarities between fly and human hearts. Further, it discusses current limitations in using the fly, as well as promising prospects to expand the capabilities of Drosophila as a research model for studying human cardiac diseases.
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Affiliation(s)
- Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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Novel ELAC2 Mutations in Individuals Presenting with Variably Severe Neurological Disease in the Presence or Absence of Cardiomyopathy. Life (Basel) 2023; 13:life13020445. [PMID: 36836802 PMCID: PMC9958991 DOI: 10.3390/life13020445] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Transcription of mitochondrial DNA generates long polycistronic precursors whose nucleolytic cleavage yields the individual mtDNA-encoded transcripts. In most cases, this cleavage occurs at the 5'- and 3'-ends of tRNA sequences by the concerted action of RNAseP and RNaseZ/ELAC2 endonucleases, respectively. Variants in the ELAC2 gene have been predominantly linked to severe to mild cardiomyopathy that, in its milder forms, is accompanied by variably severe neurological presentations. Here, we report five patients from three unrelated families. Four of the patients presented mild to moderate cardiomyopathy and one died at 1 year of age, one patient had no evidence of cardiomyopathy. The patients had variable neurological presentations that included intellectual disability, ataxia, refractory epilepsy, neuropathy and deafness. All patients carried previously unreported missense and nonsense variants. Enzymatic analyses showed multiple OXPHOS deficiencies in biopsies from two patients, whereas immunoblot analyses revealed a decreased abundance of ELAC2 in fibroblasts from three patients. Northern blot analysis revealed an accumulation of unprocessed mt-tRNAVal-precursor consistent with the role of ELAC2 in transcript processing. Our study expands the genetic spectrum of ELAC2-linked disease and suggests that cardiomyopathy is not an invariably present clinical hallmark of this pathology.
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Hooper K, Hmeljak J. Disease Models & Mechanisms helps move heart failure to heart success. Dis Model Mech 2022; 15:275488. [PMID: 35593431 PMCID: PMC9150112 DOI: 10.1242/dmm.049634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Heart failure affects ∼64 million people worldwide, resulting in high morbidity, mortality and societal cost. Current treatment strategies are primarily geared at slowing the progression to an advanced disease state, but do not reverse or cure heart failure. A more comprehensive understanding of the underlying biology and development of preclinical models of this heterogeneous group of disorders will improve diagnosis and treatment. Here, we summarise recent preclinical and translational research in this area published in Disease Models & Mechanisms. We also discuss how our Journal is propelling this field forward by launching a Special Issue and ongoing subject collection, ‘Moving Heart Failure to Heart Success: Mechanisms, Regeneration & Therapy’.
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Affiliation(s)
- Kirsty Hooper
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Julija Hmeljak
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
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Ecovoiu AA, Ratiu AC, Micheu MM, Chifiriuc MC. Inter-Species Rescue of Mutant Phenotype—The Standard for Genetic Analysis of Human Genetic Disorders in Drosophila melanogaster Model. Int J Mol Sci 2022; 23:ijms23052613. [PMID: 35269756 PMCID: PMC8909942 DOI: 10.3390/ijms23052613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
Drosophila melanogaster (the fruit fly) is arguably a superstar of genetics, an astonishing versatile experimental model which fueled no less than six Nobel prizes in medicine. Nowadays, an evolving research endeavor is to simulate and investigate human genetic diseases in the powerful D. melanogaster platform. Such a translational experimental strategy is expected to allow scientists not only to understand the molecular mechanisms of the respective disorders but also to alleviate or even cure them. In this regard, functional gene orthology should be initially confirmed in vivo by transferring human or vertebrate orthologous transgenes in specific mutant backgrounds of D. melanogaster. If such a transgene rescues, at least partially, the mutant phenotype, then it qualifies as a strong candidate for modeling the respective genetic disorder in the fruit fly. Herein, we review various examples of inter-species rescue of relevant mutant phenotypes of the fruit fly and discuss how these results recommend several human genes as candidates to study and validate genetic variants associated with human diseases. We also consider that a wider implementation of this evolutionist exploratory approach as a standard for the medicine of genetic disorders would allow this particular field of human health to advance at a faster pace.
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Affiliation(s)
- Alexandru Al. Ecovoiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
| | - Attila Cristian Ratiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
- Correspondence: ; Tel.: +40-722250366
| | - Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, 014461 Bucharest, Romania;
| | - Mariana Carmen Chifiriuc
- The Research Institute of the University of Bucharest and Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
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First person – Ekaterina Migunova. Dis Model Mech 2021. [DOI: 10.1242/dmm.049235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping early-career researchers promote themselves alongside their papers. Ekaterina Migunova is first author on ‘ ELAC2/RNaseZ-linked cardiac hypertrophy in Drosophila melanogaster’, published in DMM. Ekaterina is a PhD student in the lab of Edward Dubrovsky at Fordham University, Bronx, NY, USA, investigating the role of ELAC2 mutations in cardiomyopathy.
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