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Fu Y, Li G, Feng Z, Liu J, Wang X, Wang T, Liu J. Methyl Cinnamate (MC) Alleviates Free Fatty Acids (FFAs) Induced Lipid Accumulation Through the AMPK Pathway in HepG2 Cells. Diabetes Metab Syndr Obes 2024; 17:1183-1197. [PMID: 38469107 PMCID: PMC10926926 DOI: 10.2147/dmso.s449300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Background AMP-activated protein kinase (AMPK) plays a critical role in energy metabolism. Its activation leads to the phosphorylation of downstream proteins such as acetyl-CoA carboxylase (ACC) and sterol regulatory element-binding protein-1 (SREBP1), subsequently inhibiting de novo fatty acid synthesis, thereby reducing intracellular triglyceride accumulation. MC is a compound found in extracts from Zanthoxylum armatum DC plants. Research has shown that MC can inhibit the differentiation of 3T3-L1 adipocytes through the CAMKK2-AMPK pathway. However, the biological effect of MC in HepG2 cells remains unknown. Methods In this study, we utilized HepG2 cells to establish a model of MAFLD through FFAs stimulation. We investigated the biological effects of MC on HepG2 cells and studied its impact on lipid metabolism. Small interfering RNA was employed to explore the mechanism by which MC activates AMPK. Finally, molecular docking was conducted, establishing a model of the interaction between AMPK and MC. Results We observed that MC can alleviate triglyceride accumulation in HepG2 cells. We observed the elevated p-AMPK/AMPK, P-ACC/ ACC, and elevated CPT1a after treatment of MC in HepG2 cells. The interference of CAMKK2 mRNA did not impact the ability of MC to phosphorylate AMPK. Compound C attenuates the ability of MC to increase p-AMPK. Molecular docking results led us to hypothesize that MC directly interacts with AMPK, resulting in AMPK phosphorylation and improved lipid accumulation in HepG2 cells.
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Affiliation(s)
- Yingda Fu
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Guangbing Li
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
| | - Zichen Feng
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Jun Liu
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
| | - Xiaoyu Wang
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Tao Wang
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
| | - Jun Liu
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
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152
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Tucureanu MM, Ciortan L, Macarie RD, Mihaila AC, Droc I, Butoi E, Manduteanu I. The Specific Molecular Changes Induced by Diabetic Conditions in Valvular Endothelial Cells and upon Their Interactions with Monocytes Contribute to Endothelial Dysfunction. Int J Mol Sci 2024; 25:3048. [PMID: 38474293 DOI: 10.3390/ijms25053048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 03/02/2024] [Indexed: 03/14/2024] Open
Abstract
Aortic valve disease (AVD) represents a global public health challenge. Research indicates a higher prevalence of diabetes in AVD patients, accelerating disease advancement. Although the specific mechanisms linking diabetes to valve dysfunction remain unclear, alterations of valvular endothelial cells (VECs) homeostasis due to high glucose (HG) or their crosstalk with monocytes play pivotal roles. The aim of this study was to determine the molecular signatures of VECs in HG and upon their interaction with monocytes in normal (NG) or high glucose conditions and to propose novel mechanisms underlying valvular dysfunction in diabetes. VECs and THP-1 monocytes cultured in NG/HG conditions were used. The RNAseq analysis revealed transcriptomic changes in VECs, in processes related to cytoskeleton regulation, focal adhesions, cellular junctions, and cell adhesion. Key molecules were validated by qPCR, Western blot, and immunofluorescence assays. The alterations in cytoskeleton and intercellular junctions impacted VEC function, leading to changes in VECs adherence to extracellular matrix, endothelial permeability, monocyte adhesion, and transmigration. The findings uncover new molecular mechanisms of VEC dysfunction in HG conditions and upon their interaction with monocytes in NG/HG conditions and may help to understand mechanisms of valvular dysfunction in diabetes and to develop novel therapeutic strategies in AVD.
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Affiliation(s)
- Monica Madalina Tucureanu
- Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology "Nicolae Simionescu", 050568 Bucharest, Romania
| | - Letitia Ciortan
- Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology "Nicolae Simionescu", 050568 Bucharest, Romania
| | - Razvan Daniel Macarie
- Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology "Nicolae Simionescu", 050568 Bucharest, Romania
| | - Andreea Cristina Mihaila
- Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology "Nicolae Simionescu", 050568 Bucharest, Romania
| | - Ionel Droc
- Cardiovascular Surgery Department, Central Military Hospital, 010825 Bucharest, Romania
| | - Elena Butoi
- Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology "Nicolae Simionescu", 050568 Bucharest, Romania
| | - Ileana Manduteanu
- Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology "Nicolae Simionescu", 050568 Bucharest, Romania
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153
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Sidoryk-Węgrzynowicz M, Adamiak K, Strużyńska L. Astrocyte-Neuron Interaction via the Glutamate-Glutamine Cycle and Its Dysfunction in Tau-Dependent Neurodegeneration. Int J Mol Sci 2024; 25:3050. [PMID: 38474295 DOI: 10.3390/ijms25053050] [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: 02/14/2024] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Astroglia constitute the largest group of glial cells and are involved in numerous actions that are critical to neuronal development and functioning, such as maintaining the blood-brain barrier, forming synapses, supporting neurons with nutrients and trophic factors, and protecting them from injury. These properties are deeply affected in the course of many neurodegenerative diseases, including tauopathies, often before the onset of the disease. In this respect, the transfer of essential amino acids such as glutamate and glutamine between neurons and astrocytes in the glutamate-glutamine cycle (GGC) is one example. In this review, we focus on the GGC and the disruption of this cycle in tau-dependent neurodegeneration. A profound understanding of the complex functions of the GGC and, in the broader context, searching for dysfunctions in communication pathways between astrocytes and neurons via GGC in health and disease, is of critical significance for the development of novel mechanism-based therapies for neurodegenerative disorders.
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Affiliation(s)
- Marta Sidoryk-Węgrzynowicz
- Laboratory of Pathoneurochemistry, Department of Neurochemistry, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Str., 02-106 Warsaw, Poland
| | - Kamil Adamiak
- Laboratory of Pathoneurochemistry, Department of Neurochemistry, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Str., 02-106 Warsaw, Poland
| | - Lidia Strużyńska
- Laboratory of Pathoneurochemistry, Department of Neurochemistry, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawińskiego Str., 02-106 Warsaw, Poland
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154
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Kim T, James BT, Kahn MC, Blanco-Duque C, Abdurrob F, Islam MR, Lavoie NS, Kellis M, Tsai LH. Gamma entrainment using audiovisual stimuli alleviates chemobrain pathology and cognitive impairment induced by chemotherapy in mice. Sci Transl Med 2024; 16:eadf4601. [PMID: 38446899 DOI: 10.1126/scitranslmed.adf4601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/15/2024] [Indexed: 03/08/2024]
Abstract
Patients with cancer undergoing chemotherapy frequently experience a neurological condition known as chemotherapy-related cognitive impairment, or "chemobrain," which can persist for the remainder of their lives. Despite the growing prevalence of chemobrain, both its underlying mechanisms and treatment strategies remain poorly understood. Recent findings suggest that chemobrain shares several characteristics with neurodegenerative diseases, including chronic neuroinflammation, DNA damage, and synaptic loss. We investigated whether a noninvasive sensory stimulation treatment we term gamma entrainment using sensory stimuli (GENUS), which has been shown to alleviate aberrant immune and synaptic pathologies in mouse models of neurodegeneration, could also mitigate chemobrain phenotypes in mice administered a chemotherapeutic drug. When administered concurrently with the chemotherapeutic agent cisplatin, GENUS alleviated cisplatin-induced brain pathology, promoted oligodendrocyte survival, and improved cognitive function in a mouse model of chemobrain. These effects persisted for up to 105 days after GENUS treatment, suggesting the potential for long-lasting benefits. However, when administered to mice 90 days after chemotherapy, GENUS treatment only provided limited benefits, indicating that it was most effective when used to prevent the progression of chemobrain pathology. Furthermore, we demonstrated that the effects of GENUS in mice were not limited to cisplatin-induced chemobrain but also extended to methotrexate-induced chemobrain. Collectively, these findings suggest that GENUS may represent a versatile approach for treating chemobrain induced by different chemotherapy agents.
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Affiliation(s)
- TaeHyun Kim
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin T James
- Computer Science and Artificial intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin C Kahn
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cristina Blanco-Duque
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fatema Abdurrob
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Md Rezaul Islam
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicolas S Lavoie
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Computer Science and Artificial intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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155
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Koparir A, Lekszas C, Keseroglu K, Rose T, Rappl L, Rad A, Maroofian R, Narendran N, Hasanzadeh A, Karimiani EG, Boschann F, Kornak U, Klopocki E, Özbudak EM, Vona B, Haaf T, Liedtke D. Zebrafish as a model to investigate a biallelic gain-of-function variant in MSGN1, associated with a novel skeletal dysplasia syndrome. Hum Genomics 2024; 18:23. [PMID: 38448978 PMCID: PMC10916241 DOI: 10.1186/s40246-024-00593-w] [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: 01/26/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND/OBJECTIVES Rare genetic disorders causing specific congenital developmental abnormalities often manifest in single families. Investigation of disease-causing molecular features are most times lacking, although these investigations may open novel therapeutic options for patients. In this study, we aimed to identify the genetic cause in an Iranian patient with severe skeletal dysplasia and to model its molecular function in zebrafish embryos. RESULTS The proband displays short stature and multiple skeletal abnormalities, including mesomelic dysplasia of the arms with complete humero-radio-ulna synostosis, arched clavicles, pelvic dysplasia, short and thin fibulae, proportionally short vertebrae, hyperlordosis and mild kyphosis. Exome sequencing of the patient revealed a novel homozygous c.374G > T, p.(Arg125Leu) missense variant in MSGN1 (NM_001105569). MSGN1, a basic-Helix-Loop-Helix transcription factor, plays a crucial role in formation of presomitic mesoderm progenitor cells/mesodermal stem cells during early developmental processes in vertebrates. Initial in vitro experiments show protein stability and correct intracellular localization of the novel variant in the nucleus and imply retained transcription factor function. To test the pathogenicity of the detected variant, we overexpressed wild-type and mutant msgn1 mRNA in zebrafish embryos and analyzed tbxta (T/brachyury/ntl). Overexpression of wild-type or mutant msgn1 mRNA significantly reduces tbxta expression in the tailbud compared to control embryos. Mutant msgn1 mRNA injected embryos depict a more severe effect, implying a gain-of-function mechanism. In vivo analysis on embryonic development was performed by clonal msgn1 overexpression in zebrafish embryos further demonstrated altered cell compartments in the presomitic mesoderm, notochord and pectoral fin buds. Detection of ectopic tbx6 and bmp2 expression in these embryos hint to affected downstream signals due to Msgn1 gain-of-function. CONCLUSION In contrast to loss-of-function effects described in animal knockdown models, gain-of-function of MSGN1 explains the only mildly affected axial skeleton of the proband and rather normal vertebrae. In this context we observed notochord bending and potentially disruption of pectoral fin buds/upper extremity after overexpression of msgn1 in zebrafish embryos. The latter might result from Msgn1 function on mesenchymal stem cells or on chondrogenesis in these regions. In addition, we detected ectopic tbx6 and bmp2a expression after gain of Msgn1 function in zebrafish, which are interconnected to short stature, congenital scoliosis, limb shortening and prominent skeletal malformations in patients. Our findings highlight a rare, so far undescribed skeletal dysplasia syndrome associated with a gain-of-function mutation in MSGN1 and hint to its molecular downstream effectors.
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Affiliation(s)
- Asuman Koparir
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Caroline Lekszas
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Kemal Keseroglu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thalia Rose
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Lena Rappl
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Aboulfazl Rad
- Cellular and Molecular Research Centre, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Nakul Narendran
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Atefeh Hasanzadeh
- Cellular and Molecular Research Centre, Sabzevar University of Medical Sciences, Sabzevar, 009851, Iran
| | | | - Felix Boschann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Klopocki
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Daniel Liedtke
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany.
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156
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly. Genome Biol Evol 2024; 16:evae018. [PMID: 38319079 PMCID: PMC10950046 DOI: 10.1093/gbe/evae018] [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: 06/15/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, USA
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157
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Kimura A, Go AC, Markow T, Ranz JM. Evidence of Nonrandom Patterns of Functional Chromosome Organization in Danaus plexippus. Genome Biol Evol 2024; 16:evae054. [PMID: 38488057 PMCID: PMC10972686 DOI: 10.1093/gbe/evae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/01/2024] Open
Abstract
Our understanding on the interplay between gene functionality and gene arrangement at different chromosome scales relies on a few Diptera and the honeybee, species with quality reference genome assemblies, accurate gene annotations, and abundant transcriptome data. Using recently generated 'omic resources in the monarch butterfly Danaus plexippus, a species with many more and smaller chromosomes relative to Drosophila species and the honeybee, we examined the organization of genes preferentially expressed at broadly defined developmental stages (larva, pupa, adult males, and adult females) at both fine and whole-chromosome scales. We found that developmental stage-regulated genes do not form more clusters, but do form larger clusters, than expected by chance, a pattern consistent across the gene categories examined. Notably, out of the 30 chromosomes in the monarch genome, 12 of them, plus the fraction of the chromosome Z that corresponds to the ancestral Z in other Lepidoptera, were found enriched for developmental stage-regulated genes. These two levels of nonrandom gene organization are not independent as enriched chromosomes for developmental stage-regulated genes tend to harbor disproportionately large clusters of these genes. Further, although paralogous genes were overrepresented in gene clusters, their presence is not enough to explain two-thirds of the documented cases of whole-chromosome enrichment. The composition of the largest clusters often included paralogs from more than one multigene family as well as unrelated single-copy genes. Our results reveal intriguing patterns at the whole-chromosome scale in D. plexippus while shedding light on the interplay between gene expression and chromosome organization beyond Diptera and Hymenoptera.
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Affiliation(s)
- Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92647, USA
| | - Alwyn C Go
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - Therese Markow
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato, GTO 36824, México
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92647, USA
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158
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Yan S, Zheng D. A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer. Interdiscip Sci 2024; 16:218-230. [PMID: 38183569 DOI: 10.1007/s12539-023-00596-6] [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: 08/13/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 01/08/2024]
Abstract
The exploration of drug combinations presents an opportunity to amplify therapeutic effectiveness while alleviating undesirable side effects. Nevertheless, the extensive array of potential combinations poses challenges in terms of cost and time constraints for experimental screening. Thus, it is crucial to narrow down the search space. Deep learning approaches have gained widespread popularity in predicting synergistic drug combinations tailored for specific cell lines in vitro settings. In the present study, we introduce a novel method termed GTextSyn, which utilizes the integration of gene expression data and chemical structure information for the prediction of synergistic effects in drug combinations. GTextSyn employs a sentence classification model within the domain of Natural Language Processing (NLP), wherein drugs and cell lines are regarded as entities possessing biochemical relevance. Meanwhile, combinations of drug pairs and cell lines are construed as sentences with biochemical relational significance. To assess the efficacy of GTextSyn, we conduct a comparative analysis with alternative deep learning approaches using a standard benchmark dataset. The results from a five-fold cross-validation demonstrate a 49.5% reduction in Mean Square Error (MSE) achieved by GTextSyn, surpassing the performance of the next best method in the regression task. Furthermore, we conduct a comprehensive literature survey on the predicted novel drug combinations and find substantial support from prior experimental studies for many of the combinations identified by GTextSyn.
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Affiliation(s)
- Shiyu Yan
- School of Computer, University of South China, West Changsheng Road, Hengyang, 421001, Hunan, China.
| | - Ding Zheng
- School of Computer, University of South China, West Changsheng Road, Hengyang, 421001, Hunan, China
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159
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Hosseini SM, Borys B, Karimi-Abdolrezaee S. Neural stem cell therapies for spinal cord injury repair: an update on recent preclinical and clinical advances. Brain 2024; 147:766-793. [PMID: 37975820 DOI: 10.1093/brain/awad392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Traumatic spinal cord injury (SCI) is a leading cause of lifelong disabilities. Permanent sensory, motor and autonomic impairments after SCI are substantially attributed to degeneration of spinal cord neurons and axons, and disintegration of neural network. To date, minimal regenerative treatments are available for SCI with an unmet need for new therapies to reconstruct the damaged spinal cord neuron-glia network and restore connectivity with the supraspinal pathways. Multipotent neural precursor cells (NPCs) have a unique capacity to generate neurons, oligodendrocytes and astrocytes. Due to this capacity, NPCs have been an attractive cell source for cellular therapies for SCI. Transplantation of NPCs has been extensively tested in preclinical models of SCI in the past two decades. These studies have identified opportunities and challenges associated with NPC therapies. While NPCs have the potential to promote neuroregeneration through various mechanisms, their low long-term survival and integration within the host injured spinal cord limit the functional benefits of NPC-based therapies for SCI. To address this challenge, combinatorial strategies have been developed to optimize the outcomes of NPC therapies by enriching SCI microenvironment through biomaterials, genetic and pharmacological therapies. In this review, we will provide an in-depth discussion on recent advances in preclinical NPC-based therapies for SCI. We will discuss modes of actions and mechanism by which engrafted NPCs contribute to the repair process and functional recovery. We will also provide an update on current clinical trials and new technologies that have facilitated preparation of medical-grade human NPCs suitable for transplantation in clinical studies.
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Affiliation(s)
- Seyed Mojtaba Hosseini
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Multiple Sclerosis Research Center, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ben Borys
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
| | - Soheila Karimi-Abdolrezaee
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Multiple Sclerosis Research Center, Winnipeg, Manitoba R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
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160
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Baisley K, Kemp TJ, Mugo NR, Whitworth H, Onono MA, Njoroge B, Indangasi J, Bukusi EA, Prabhu PR, Mutani P, Galloway DA, Mwanzalime D, Kapiga S, Lacey CJ, Hayes RJ, Changalucha J, Pinto LA, Barnabas RV, Watson-Jones D. Comparing one dose of HPV vaccine in girls aged 9-14 years in Tanzania (DoRIS) with one dose in young women aged 15-20 years in Kenya (KEN SHE): an immunobridging analysis of randomised controlled trials. Lancet Glob Health 2024; 12:e491-e499. [PMID: 38365419 PMCID: PMC10882205 DOI: 10.1016/s2214-109x(23)00586-7] [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: 08/09/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND The first randomised controlled trial of single-dose human papillomavirus (HPV) vaccine efficacy, the Kenya single-dose HPV-vaccine efficacy (KEN SHE) trial, showed greater than 97% efficacy against persistent HPV16 and HPV18 infection at 36 months among women in Kenya. We compared antibody responses after one dose of HPV vaccine in the Dose Reduction Immunobridging and Safety Study (DoRIS), the first randomised trial of the single- dose regimen in girls aged 9-14 years, the target age range for vaccination, with those after one dose of the same vaccine in KEN SHE. METHODS In the DoRIS trial, 930 girls aged 9-14 years in Tanzania were randomly assigned to one, two, or three doses of the 2-valent vaccine (Cervarix) or the 9-valent vaccine (Gardasil-9). The proportion seroconverting and geometric mean concentrations (GMCs) at month 24 after one dose were compared with those in women aged 15-20 years who were randomly assigned to one dose of the same vaccines at the same timepoint in KEN SHE. Batched samples were tested together by virus-like particle ELISA for HPV16 and HPV18 IgG antibodies. Non-inferiority of GMC ratios (DoRIS trial:KEN SHE) was predefined as a lower bound of the 95% CI less than 0·50. FINDINGS Month 24 HPV16 and HPV18 antibody GMCs in DoRIS were similar or higher than those in KEN SHE. 2-valent GMC ratios were 0·90 (95% CI 0·72-1·14) for HPV16 and 1·02 (0·78-1·33) for HPV18. 9-valent GMC ratios were 1·44 (95% CI 1·14-1·82) and 1·47 (1·13-1·90), respectively. Non-inferiority of antibody GMCs and seropositivity was met for HPV16 and HPV18 for both vaccines. INTERPRETATION HPV16 and HPV18 immune responses in young girls 24 months after a single dose of 2-valent or 9-valent HPV vaccine were comparable to those in young women who were randomly assigned to a single dose of the same vaccines and in whom efficacy had been shown. A single dose of HPV vaccine, when given to girls in the target age range for vaccination, induces immune responses that could be effective against persistent HPV16 and HPV18 infection at least two years after vaccination. FUNDING The UK Department of Health and Social Care, the Foreign, Commonwealth, & Development Office, the Global Challenges Research Fund, the UK Medical Research Council and Wellcome Trust Joint Global Health Trials scheme, the Bill and Melinda Gates Foundation, the US National Cancer Institute; the US National Institutes of Health, and the Francis and Dorothea Reed Endowed Chair in Infectious Diseases. TRANSLATION For the KiSwahili translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Kathy Baisley
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
| | - Troy J Kemp
- HPV Serology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nelly R Mugo
- Department of Global Health, University of Washington, Seattle, WA, USA; Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Hilary Whitworth
- Faculty of Infectious and Tropical Diseases UK, London School of Hygiene & Tropical Medicine, London, UK; Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | - Maricianah A Onono
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Betty Njoroge
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jackton Indangasi
- Faculty of Infectious and Tropical Diseases UK, London School of Hygiene & Tropical Medicine, London, UK; Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | - Elizabeth A Bukusi
- Department of Global Health, University of Washington, Seattle, WA, USA; Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Priya R Prabhu
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paul Mutani
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | - Denise A Galloway
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Mwanzalime
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | - Saidi Kapiga
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | - Charles J Lacey
- York Biomedical Research Institute & Hull York Medical School, University of York, York, UK
| | - Richard J Hayes
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - John Changalucha
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | - Ligia A Pinto
- HPV Serology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ruanne V Barnabas
- Department of Global Health, University of Washington, Seattle, WA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Deborah Watson-Jones
- Faculty of Infectious and Tropical Diseases UK, London School of Hygiene & Tropical Medicine, London, UK; Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
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Höglund A, Henriksen R, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken. PLoS Genet 2024; 20:e1010719. [PMID: 38457441 PMCID: PMC10954189 DOI: 10.1371/journal.pgen.1010719] [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: 03/28/2023] [Revised: 03/20/2024] [Accepted: 01/31/2024] [Indexed: 03/10/2024] Open
Abstract
DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.
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Affiliation(s)
- Andrey Höglund
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M. Guerrero-Bosagna
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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Saint C, Gittings W, Bunda J, Giles C, Sacco SM, Vandenboom R, Ward WE, LeBlanc PJ. Maternal folic acid supplementation does not impact skeletal muscle function and metabolism in male and female CD-1 mouse offspring. Appl Physiol Nutr Metab 2024; 49:306-318. [PMID: 37913528 DOI: 10.1139/apnm-2023-0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Folic acid fortification of all white flour, enriched pasta, and cornmeal products became mandatory in Canada to reduce risk of neural tube defects at birth. Furthermore, Health Canada and the Society of Obstetricians and Gynaecologists of Canada recommend women take daily prenatal folic acid supplements in addition to folic acid fortified foods during pregnancy. However, the influence of maternal folic acid supplementation on offspring development, specifically the highly abundant and metabolically active skeletal muscle, is currently unknown. Thus, the purpose of this study was to determine the effect of supplemental folic acid (four times higher than normal dietary consumption), in utero and throughout suckling on muscle size, function, and metabolism in male and female CD-1 mouse offspring. The major findings were that maternal exposure to supplemental folic acid (i) had no impact on postpartum growth rates or muscle mass in female and male offspring, (ii) had no impact on skeletal muscle contractile kinetics in females and male offspring, and (iii) increased maximal phosphofructokinase activity in extensor digitorum longus of female and male offspring. These findings suggest that exposure to folic acid supplementation in utero and throughout suckling at levels four times higher than recommended had minimal effect on skeletal muscle size, function, and metabolism regardless of sex. Future research is needed explore the underlying biological pathways and mechanisms affected by folic acid supplementation during pregnancy and lactation on offspring skeletal muscle tissue, specifically in humans.
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Affiliation(s)
- Caitlin Saint
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
| | - William Gittings
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
- Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Jordan Bunda
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
- Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Cameron Giles
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
| | - Sandra M Sacco
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
- Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Rene Vandenboom
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
- Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Wendy E Ward
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
- Department of Kinesiology, Brock University, St. Catharines, ON, Canada
| | - Paul J LeBlanc
- Department of Health Sciences, Brock University, St. Catharines, ON, Canada
- Centre for Bone and Muscle Health, Brock University, St. Catharines, ON, Canada
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Maeda T, Shimamori K, Kurita H, Tokuraku K, Kuragano M. Amyloid β interferes with wound healing of brain microvascular endothelial cells by disorganizing the actin cytoskeleton. Exp Cell Res 2024; 436:113958. [PMID: 38325585 DOI: 10.1016/j.yexcr.2024.113958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is a disease in which amyloid β (Aβ) is deposited in the cerebral blood vessels, reducing compliance, tearing and weakening of vessel walls, leading to cerebral hemorrhage. The mechanisms by which Aβ leads to focal wall fragmentation and intimal damage are not well understood. We analyzed the motility of human brain microvascular endothelial cells (hBMECs) in real-time using a wound-healing assay. We observed the suppression of cell migration by visualizing Aβ aggregation using quantum dot (QD) nanoprobes. In addition, using QD nanoprobes and a SiR-actin probe, we simultaneously observed Aβ aggregation and F-actin organization in real-time for the first time. Aβ began to aggregate at the edge of endothelial cells, reducing cell motility. In addition, Aβ aggregation disorganized the actin cytoskeleton and induced abnormal actin aggregation. Aβ aggregated actively in the anterior group, where cell motility was active. Our findings may be a first step toward explaining the mechanism by which Aβ causes vascular wall fragility, bleeding, and rebleeding in CAA.
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Affiliation(s)
- Takuma Maeda
- Graduate School of Engineering, Muroran Institute of Technology, Hokkaido, 050-8585, Japan; Department of Neurosurgery, Ohkawara Neurosurgical Hospital, Hokkaido, 050-0082, Japan; Department of Cerebrovascular Surgery, Saitama Medical University International Medical Center, Saitama, 350-1298, Japan
| | - Keiya Shimamori
- Graduate School of Engineering, Muroran Institute of Technology, Hokkaido, 050-8585, Japan
| | - Hiroki Kurita
- Department of Cerebrovascular Surgery, Saitama Medical University International Medical Center, Saitama, 350-1298, Japan
| | - Kiyotaka Tokuraku
- Graduate School of Engineering, Muroran Institute of Technology, Hokkaido, 050-8585, Japan
| | - Masahiro Kuragano
- Graduate School of Engineering, Muroran Institute of Technology, Hokkaido, 050-8585, Japan.
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164
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Yadav R, Patel B. Insights on effects of Wnt pathway modulation on insulin signaling and glucose homeostasis for the treatment of type 2 diabetes mellitus: Wnt activation or Wnt inhibition? Int J Biol Macromol 2024; 261:129634. [PMID: 38272413 DOI: 10.1016/j.ijbiomac.2024.129634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/27/2023] [Accepted: 01/06/2024] [Indexed: 01/27/2024]
Abstract
Type 2 diabetes mellitus (T2DM) is a major worldwide chronic disease and can lead to serious diabetic complications. Despite the availability of many anti-diabetic agents in the market, they are unable to meet the long-term treatment goals. Also, they cause many side effects which justify the need for novel class of anti-diabetic drugs with newer mechanism of action. Wnt signaling is one of such novel target pathways which can be explored for metabolic disorders. Many key components of the Wnt signaling are involved in the regulation of glucose homeostasis. Polymorphism in the Transcription factor 7-like 2 (TCF7L2) gene, and mutations in the LRP5 (LDL Receptor Related Protein 5) gene lead to disturbed glucose metabolism and obesity. Despite of several years of research in this field, there is no concrete proof of concept available on whether Wnt activation or Wnt inhibition is the beneficial approach for the treatment of T2DM. Here, we have summarized the conclusions of relevant published research studies to give structured insights into possibilities to explore Wnt modulation as a novel target pathway for the treatment of T2DM. The review also highlights the present challenges and future opportunities towards the development of anti-diabetic small molecules targeting the Wnt signaling pathway.
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Affiliation(s)
- Ruchi Yadav
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India
| | - Bhumika Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481, India.
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165
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Roggenbuck EC, Hall EA, Hanson IB, Roby AA, Zhang KK, Alkatib KA, Carter JA, Clewner JE, Gelfius AL, Gong S, Gordon FR, Iseler JN, Kotapati S, Li M, Maysun A, McCormick EO, Rastogi G, Sengupta S, Uzoma CU, Wolkov MA, Clowney EJ. Let's talk about sex: Mechanisms of neural sexual differentiation in Bilateria. WIREs Mech Dis 2024; 16:e1636. [PMID: 38185860 DOI: 10.1002/wsbm.1636] [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: 05/09/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
In multicellular organisms, sexed gonads have evolved that facilitate release of sperm versus eggs, and bilaterian animals purposefully combine their gametes via mating behaviors. Distinct neural circuits have evolved that control these physically different mating events for animals producing eggs from ovaries versus sperm from testis. In this review, we will describe the developmental mechanisms that sexually differentiate neural circuits across three major clades of bilaterian animals-Ecdysozoa, Deuterosomia, and Lophotrochozoa. While many of the mechanisms inducing somatic and neuronal sex differentiation across these diverse organisms are clade-specific rather than evolutionarily conserved, we develop a common framework for considering the developmental logic of these events and the types of neuronal differences that produce sex-differentiated behaviors. This article is categorized under: Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development.
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Affiliation(s)
- Emma C Roggenbuck
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elijah A Hall
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Isabel B Hanson
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyssa A Roby
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine K Zhang
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Kyle A Alkatib
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph A Carter
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jarred E Clewner
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna L Gelfius
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Shiyuan Gong
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Finley R Gordon
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jolene N Iseler
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Samhita Kotapati
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Marilyn Li
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Areeba Maysun
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elise O McCormick
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Geetanjali Rastogi
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Srijani Sengupta
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Chantal U Uzoma
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Madison A Wolkov
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, Michigan, USA
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166
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Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X, Chen G. The Molecular Mechanism of the Response of Rice to Arsenic Stress and Effective Strategies to Reduce the Accumulation of Arsenic in Grain. Int J Mol Sci 2024; 25:2861. [PMID: 38474107 DOI: 10.3390/ijms25052861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/18/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Rice (Oryza sativa L.) is the staple food for more than 50% of the world's population. Owing to its growth characteristics, rice has more than 10-fold the ability to enrich the carcinogen arsenic (As) than other crops, which seriously affects world food security. The consumption of rice is one of the primary ways for humans to intake As, and it endangers human health. Effective measures to control As pollution need to be studied and promoted. Currently, there have been many studies on reducing the accumulation of As in rice. They are generally divided into agronomic practices and biotechnological approaches, but simultaneously, the problem of using the same measures to obtain the opposite results may be due to the different species of As or soil environments. There is a lack of systematic discussion on measures to reduce As in rice based on its mechanism of action. Therefore, an in-depth understanding of the molecular mechanism of the accumulation of As in rice could result in accurate measures to reduce the content of As based on local conditions. Different species of As have different toxicity and metabolic pathways. This review comprehensively summarizes and reviews the molecular mechanisms of toxicity, absorption, transport and redistribution of different species of As in rice in recent years, and the agronomic measures to effectively reduce the accumulation of As in rice and the genetic resources that can be used to breed for rice that only accumulates low levels of As. The goal of this review is to provide theoretical support for the prevention and control of As pollution in rice, facilitate the creation of new types of germplasm aiming to develop without arsenic accumulation or within an acceptable limit to prevent the health consequences associated with heavy metal As as described here.
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Affiliation(s)
- Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yihan Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Minghao Liu
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yue Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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167
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Sinaga P, Klichowska E, Nowak A, Nobis M. Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia. PLoS One 2024; 19:e0298760. [PMID: 38412151 PMCID: PMC10898772 DOI: 10.1371/journal.pone.0298760] [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: 10/31/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.
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Affiliation(s)
- Patar Sinaga
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden – Center for Biological Diversity Conservation in Powsin, Warszawa, Poland
- Botanical Garden of the Wrocław University, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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da Silva Filho JLB, Pestana RKN, da Silva Júnior WJ, Coelho Filho MA, Ferreira CF, de Oliveira EJ, Kido EA. Exploiting DNA methylation in cassava under water deficit for crop improvement. PLoS One 2024; 19:e0296254. [PMID: 38386677 PMCID: PMC10883565 DOI: 10.1371/journal.pone.0296254] [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: 09/13/2023] [Accepted: 12/08/2023] [Indexed: 02/24/2024] Open
Abstract
DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.
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Affiliation(s)
| | | | - Wilson José da Silva Júnior
- Laboratório de Genética Molecular de Plantas, Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - Ederson Akio Kido
- Laboratório de Genética Molecular de Plantas, Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
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169
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-y] [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: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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170
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Yang M, Yu L, Jiang D, Deng C, Wang Z, Xu X, Wang J, Wu S, Zhang F, Hu X. Calcium stress reduces the reproductive capacity and pathogenicity of the pine wood nematode (Bursaphelenchus xylophilus) by inhibiting oxidative phosphorylation reaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169531. [PMID: 38145666 DOI: 10.1016/j.scitotenv.2023.169531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
The continuous use of chemical pesticides to control nematodes could result in the developing of pesticide-resistant nematodes. Novel nucleic acid pesticides are becoming the focus of pesticide research due to their strong specificity, high efficiency, and environmental friendliness. However, the limited known biochemical targets restrict the development of target pesticides for nematodes. The calcium stress experiments on pine wood nematodes (PWN) showed that 100 mmol/L Ca2+ resulted in longitudinal depression on the PWN body wall, reduced oviposition, and increased corrected mortality. To enrich the biological targets of nematode pesticides, we further investigated the response mechanism of PWN to calcium stress at the molecular level. Differentially expressed gene analysis showed that genes involved in the oxidative phosphorylation (OXPHOS) pathway were significantly enriched. RNA interference results of 6 key genes belonging to four mitochondrial complex I (BXNDUFA2), III (BXQCR8), IV (BXCOX17), V (BXV-ATPaseB, BXV-ATPaseE, BXV-ATPaseε) in non-stressed nematodes showed reduction in PWN oviposition, population size, feeding ability, and pathogenicity. The BXNDUFA2 gene interference had the highest inhibitory impact by decreasing the oviposition from 31.00 eggs to 6.75 eggs and PWN population size from 8.27 × 103 nematodes to 1.64 × 103 nematodes, respectively. Interestingly, RNA interference of these 6 key genes in calcium-stressed nematodes also led to increased mortality and decreased oviposition of PWN. In summary, calcium stress inhibited the reproductive capacity of PWN by down-regulating key genes BXNDUFA2, BXQCR8, BXV-ATPaseB, BXV-ATPaseE, BXV-ATPaseε, and BXCOX17, thereby reducing the pathogenicity. The current results enrich the RNAi targets in PWN and provide a scientific basis for developing novel nucleic nematicides.
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Affiliation(s)
- Meijiao Yang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lu Yu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Di Jiang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chao Deng
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeguang Wang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuhuizi Xu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinda Wang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Songqing Wu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiping Zhang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xia Hu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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171
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Vergnes L, Wiese CB, Zore T, Riestenberg C, Avetisyan R, Reue K. Gene Regulation and Mitochondrial Activity During White and Brown Adipogenesis Are Modulated by KDM5 Histone Demethylase. J Endocr Soc 2024; 8:bvae029. [PMID: 38425435 PMCID: PMC10904225 DOI: 10.1210/jendso/bvae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 03/02/2024] Open
Abstract
Body fat accumulation differs between males and females and is influenced by both gonadal sex (ovaries vs testes) and chromosomal sex (XX vs XY). We previously showed that an X chromosome gene, Kdm5c, is expressed at higher levels in females compared to males and correlates with adiposity in mice and humans. Kdm5c encodes a KDM5 histone demethylase that regulates gene expression by modulating histone methylation at gene promoters and enhancers. Here, we use chemical inhibition and genetic knockdown to identify a role for KDM5 activity during early stages of white and brown preadipocyte differentiation, with specific effects on white adipocyte clonal expansion, and white and brown adipocyte gene expression and mitochondrial activity. In white adipogenesis, KDM5 activity modulates H3K4 histone methylation at the Dlk1 gene promoter to repress gene expression and promote progression from preadipocytes to mature adipocytes. In brown adipogenesis, KDM5 activity modulates H3K4 methylation and gene expression of Ucp1, which is required for thermogenesis. Unbiased transcriptome analysis revealed that KDM5 activity regulates genes associated with cell cycle regulation and mitochondrial function, and this was confirmed by functional analyses of cell proliferation and cellular bioenergetics. Using genetic knockdown, we demonstrate that KDM5C is the likely KDM5 family member that is responsible for regulation of white and brown preadipocyte programming. Given that KDM5C levels are higher in females compared to males, our findings suggest that sex differences in white and brown preadipocyte gene regulation may contribute to sex differences in adipose tissue function.
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Affiliation(s)
- Laurent Vergnes
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie B Wiese
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Temeka Zore
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Carrie Riestenberg
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Rozeta Avetisyan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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172
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Heinisch JJ, Murra A, Fernández Murillo L, Schmitz HP. The Role of Glucose-6-phosphate Dehydrogenase in the Wine Yeast Hanseniaspora uvarum. Int J Mol Sci 2024; 25:2395. [PMID: 38397078 PMCID: PMC10889316 DOI: 10.3390/ijms25042395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Hanseniaspora uvarum is the predominant yeast species in the majority of wine fermentations, which has only recently become amenable to directed genetic manipulation. The genetics and metabolism of H. uvarum have been poorly studied as compared to other yeasts of biotechnological importance. This work describes the construction and characterization of homozygous deletion mutants in the HuZWF1 gene, encoding glucose-6-phosphate dehydrogenase (G6PDH), which provides the entrance into the oxidative part of the pentose phosphate pathway (PPP) and serves as a major source of NADPH for anabolic reactions and oxidative stress response. Huzwf1 deletion mutants grow more slowly on glucose medium than wild-type and are hypersensitive both to hydrogen peroxide and potassium bisulfite, indicating that G6PDH activity is required to cope with these stresses. The mutant also requires methionine for growth. Enzyme activity can be restored by the expression of heterologous G6PDH genes from other yeasts and humans under the control of a strong endogenous promoter. These findings provide the basis for a better adaptation of H. uvarum to conditions used in wine fermentations, as well as its use for other biotechnological purposes and as an expression organism for studying G6PDH functions in patients with hemolytic anemia.
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Affiliation(s)
- Jürgen J. Heinisch
- AG Genetik, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, D-49076 Osnabrück, Germany; (A.M.); (L.F.M.); (H.-P.S.)
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173
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Pajic P, Landau L, Gokcumen O, Ruhl S. Emergence of saliva protein genes in the secretory calcium-binding phosphoprotein (SCPP) locus and accelerated evolution in primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580359. [PMID: 38405690 PMCID: PMC10888740 DOI: 10.1101/2024.02.14.580359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genes within the secretory calcium-binding phosphoprotein (SCPP) family evolved in conjunction with major evolutionary milestones: the formation of a calcified skeleton in vertebrates, the emergence of tooth enamel in fish, and the introduction of lactation in mammals. The SCPP gene family also contains genes expressed primarily and abundantly in human saliva. Here, we explored the evolution of the saliva-related SCPP genes by harnessing currently available genomic and transcriptomic resources. Our findings provide insights into the expansion and diversification of SCPP genes, notably identifying previously undocumented convergent gene duplications. In primate genomes, we found additional duplication and diversification events that affected genes coding for proteins secreted in saliva. These saliva-related SCPP genes exhibit signatures of positive selection in the primate lineage while the other genes in the same locus remain conserved. We found that regulatory shifts and gene turnover events facilitated the accelerated gain of salivary expression. Collectively, our results position the SCPP gene family as a hotbed of evolutionary innovation, suggesting the potential role of dietary and pathogenic pressures in the adaptive diversification of the saliva composition in primates, including humans.
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Affiliation(s)
- Petar Pajic
- Department of Biological Sciences, University at Buffalo, The State University of New York, NY 14260, USA
| | - Luane Landau
- Department of Biological Sciences, University at Buffalo, The State University of New York, NY 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, NY 14260, USA
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, NY 14214, USA
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174
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [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: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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175
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Grüning NM, Ralser M. Monogenic Disorders of ROS Production and the Primary Anti-Oxidative Defense. Biomolecules 2024; 14:206. [PMID: 38397443 PMCID: PMC10887155 DOI: 10.3390/biom14020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Oxidative stress, characterized by an imbalance between the production of reactive oxygen species (ROS) and the cellular anti-oxidant defense mechanisms, plays a critical role in the pathogenesis of various human diseases. Redox metabolism, comprising a network of enzymes and genes, serves as a crucial regulator of ROS levels and maintains cellular homeostasis. This review provides an overview of the most important human genes encoding for proteins involved in ROS generation, ROS detoxification, and production of reduced nicotinamide adenine dinucleotide phosphate (NADPH), and the genetic disorders that lead to dysregulation of these vital processes. Insights gained from studies on inherited monogenic metabolic diseases provide valuable basic understanding of redox metabolism and signaling, and they also help to unravel the underlying pathomechanisms that contribute to prevalent chronic disorders like cardiovascular disease, neurodegeneration, and cancer.
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Affiliation(s)
- Nana-Maria Grüning
- Department of Biochemistry, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany;
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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176
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Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Microb Cell Fact 2024; 23:43. [PMID: 38331812 PMCID: PMC10851509 DOI: 10.1186/s12934-024-02314-3] [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: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions. RESULTS By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival. CONCLUSIONS In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
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Affiliation(s)
- Corinna Rebnegger
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Benjamin L Coltman
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - David A Peña
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Axel Mentler
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Harald Schöny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria.
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Fu L, Wang W, Lin L, Gao F, Yang J, Lv Y, Ge R, Wu M, Chen L, Liu A, Xin E, Yu J, Cheng J, Wang Y. Multitask prediction models for serous ovarian cancer by preoperative CT image assessments based on radiomics. Front Med (Lausanne) 2024; 11:1334062. [PMID: 38384418 PMCID: PMC10880444 DOI: 10.3389/fmed.2024.1334062] [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] [Received: 11/06/2023] [Accepted: 01/11/2024] [Indexed: 02/23/2024] Open
Abstract
Objective High-grade serous ovarian cancer (HGSOC) has the highest mortality rate among female reproductive system tumors. Accurate preoperative assessment is crucial for treatment planning. This study aims to develop multitask prediction models for HGSOC using radiomics analysis based on preoperative CT images. Methods This study enrolled 112 patients diagnosed with HGSOC. Laboratory findings, including serum levels of CA125, HE-4, and NLR, were collected. Radiomic features were extracted from manually delineated ROI on CT images by two radiologists. Classification models were developed using selected optimal feature sets to predict R0 resection, lymph node invasion, and distant metastasis status. Model evaluation was conducted by quantifying receiver operating curves (ROC), calculating the area under the curve (AUC), De Long's test. Results The radiomics models applied to CT images demonstrated superior performance in the testing set compared to the clinical models. The area under the curve (AUC) values for the combined model in predicting R0 resection were 0.913 and 0.881 in the training and testing datasets, respectively. De Long's test indicated significant differences between the combined and clinical models in the testing set (p = 0.003). For predicting lymph node invasion, the AUCs of the combined model were 0.868 and 0.800 in the training and testing datasets, respectively. The results also revealed significant differences between the combined and clinical models in the testing set (p = 0.002). The combined model for predicting distant metastasis achieved AUCs of 0.872 and 0.796 in the training and test datasets, respectively. The combined model displayed excellent agreement between observed and predicted results in predicting R0 resection, while the radiomics model demonstrated better calibration than both the clinical model and combined model in predicting lymph node invasion and distant metastasis. The decision curve analysis (DCA) for predicting R0 resection favored the combined model over both the clinical and radiomics models, whereas for predicting lymph node invasion and distant metastasis, DCA favored the radiomics model over both the clinical model and combined model. Conclusion The identified radiomics signature holds potential value in preoperatively evaluating the R0, lymph node invasion and distant metastasis in patients with HGSC. The radiomics nomogram demonstrated the incremental value of clinical predictors for surgical outcome and metastasis estimation.
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Affiliation(s)
- Le Fu
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenjing Wang
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lingling Lin
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Feng Gao
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiani Yang
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yunyun Lv
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ruiqiu Ge
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Meixuan Wu
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lei Chen
- Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Aie Liu
- Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Enhui Xin
- Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China
| | - Jianli Yu
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiejun Cheng
- Department of Radiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yu Wang
- Department of Obstetrics and Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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Hu AJ, Li W, Dinh C, Zhang Y, Hu JK, Daniele SG, Hou X, Yang Z, Asara JM, Hu GF, Farmer SR, Hu MG. CDK6 inhibits de novo lipogenesis in white adipose tissues but not in the liver. Nat Commun 2024; 15:1091. [PMID: 38316780 PMCID: PMC10844593 DOI: 10.1038/s41467-024-45294-z] [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: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Increased de novo lipogenesis (DNL) in white adipose tissue is associated with insulin sensitivity. Under both Normal-Chow-Diet and High-Fat-Diet, mice expressing a kinase inactive Cyclin-dependent kinase 6 (Cdk6) allele (K43M) display an increase in DNL in visceral white adipose tissues (VAT) as compared to wild type mice (WT), accompanied by markedly increased lipogenic transcriptional factor Carbohydrate-responsive element-binding proteins (CHREBP) and lipogenic enzymes in VAT but not in the liver. Treatment of WT mice under HFD with a CDK6 inhibitor recapitulates the phenotypes observed in K43M mice. Mechanistically, CDK6 phosphorylates AMP-activated protein kinase, leading to phosphorylation and inactivation of acetyl-CoA carboxylase, a key enzyme in DNL. CDK6 also phosphorylates CHREBP thus preventing its entry into the nucleus. Ablation of runt related transcription factor 1 in K43M mature adipocytes reverses most of the phenotypes observed in K43M mice. These results demonstrate a role of CDK6 in DNL and a strategy to alleviate metabolic syndromes.
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Affiliation(s)
- Alexander J Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Wei Li
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, PR China
| | - Calvin Dinh
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
| | - Yongzhao Zhang
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
| | - Jamie K Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- University of Miami Miller School of Medicine, Dermatology. 1295 NW 14th St. University of Miami Hospital South Bldg. Suites K-M, Miami, FL, USA
| | - Stefano G Daniele
- Yale School of Medicine, MD-PhD program, 333 Cedar St, New Haven, CT, USA
| | - Xiaoli Hou
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- Zhejiang Chinese Medical University, Center for Analysis and Testing, 548 Bin-Wen Road, Hangzhou, PR China
| | - Zixuan Yang
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
- TUFTS University Friedman School of Nutrition Science and Policy, TUFTS University, 150 Harrison Avenue, MA, Boston, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guo-Fu Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA
| | - Stephen R Farmer
- Boston University School of Medicine, Department of Biochemistry, 72E Concord St, Boston, MA, USA
| | - Miaofen G Hu
- Department of Medicine, Division of Hematology and Oncology, Tufts Medical Center, Boston, MA, USA.
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179
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Yun HM, Hyun B, Song X, Hyun S. Piwi expressed in Drosophila adipose tissues regulates systemic IGF signaling and growth via IGF-binding protein. Biochem Biophys Res Commun 2024; 695:149495. [PMID: 38211532 DOI: 10.1016/j.bbrc.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
Piwi and its partner, Piwi-interacting RNA (piRNA), are pivotal in suppressing the harmful effects of transposable elements (TEs) linked to genomic insertional mutagenesis. While primarily active in Drosophila's adult gonadal tissues, causing sterility in its absence, Piwi's role in post-embryonic development remains unclear. Our study reveals Piwi's functional presence in the larval fat body, where it governs developmental growth through systemic insulin/insulin-like growth factor (IGF) signaling (IIS). Piwi knockdown in the fat body resulted in dysregulated TE expression, reduced developmental rate and body growth, and diminished systemic IIS activity. Notably, Piwi knockdown increased Imaginal Morphogenic Protein Late 2 (Imp-L2) expression, akin to insulin-like growth factor-binding protein 7 (IGFBP7), reducing systemic IIS and inhibiting body growth. This unveils a novel role for Piwi in larval adipose tissues, emphasizing its importance in regulating systemic IIS and overall organismal growth.
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Affiliation(s)
- Hyun Myoung Yun
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Bom Hyun
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Xinge Song
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seogang Hyun
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
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180
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Shobade SO, Zabotina OA, Nilsen-Hamilton M. Plant root associated chitinases: structures and functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1344142. [PMID: 38362446 PMCID: PMC10867124 DOI: 10.3389/fpls.2024.1344142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5-7 and 30-40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50-60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.
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Affiliation(s)
- Samuel O. Shobade
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A. Zabotina
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Marit Nilsen-Hamilton
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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181
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Silva RCMC, Gomes FM. Evolution of the Major Components of Innate Immunity in Animals. J Mol Evol 2024; 92:3-20. [PMID: 38281163 DOI: 10.1007/s00239-024-10155-2] [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: 10/28/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
Innate immunity is present in all animals. In this review, we explore the main conserved mechanisms of recognition and innate immune responses among animals. In this sense, we discuss the receptors, critical for binding to pathogen-associated molecular patterns (PAMPs) or danger-associated molecular patterns (DAMPs); the downstream signaling proteins; and transcription factors that govern immune responses. We also highlight conserved inflammatory mediators that are induced after the recognition of DAMPs and PAMPs. At last, we discuss the mechanisms that are involved in the regulation and/or generation of reactive oxygen species (ROS), influencing immune responses, like heme-oxygenases (HOs).
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Affiliation(s)
- Rafael Cardoso Maciel Costa Silva
- Laboratory of Immunoreceptors and Signaling, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fábio Mendonça Gomes
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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182
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Bavuso M, Miller N, Sill JM, Dobrian A, Colunga Biancatelli RML. Extracellular vesicles in acute respiratory distress syndrome: Understanding protective and harmful signaling for the development of new therapeutics. Histol Histopathol 2024; 39:131-144. [PMID: 37712224 DOI: 10.14670/hh-18-659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is a severe respiratory condition characterized by increased lung permeability, hyper-inflammatory state, and fluid leak into the alveolar spaces. ARDS is a heterogeneous disease, with multiple direct and indirect causes that result in a mortality of up to 40%. Due to the ongoing Covid-19 pandemic, its incidence has increased up to ten-fold. Extracellular vesicles (EVs) are small liposome-like particles that mediate intercellular communication and play a major role in ARDS pathophysiology. Indeed, they participate in endothelial barrier dysfunction and permeability, neutrophil, and macrophage activation, and also in the development of a hypercoagulable state. A more thorough understanding of the variegated and cell-specific functions of EVs may lead to the development of safe and effective therapeutics. In this review, we have collected evidence of EVs role in ARDS, revise the main mechanisms of production and internalization and summarize the current therapeutical approaches that have shown the ability to modulate EV signaling.
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Affiliation(s)
- Matthew Bavuso
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Noel Miller
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Joshua M Sill
- Division of Pulmonary and Critical Care, Department of Internal Medicine, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Anca Dobrian
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Ruben M L Colunga Biancatelli
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA
- Division of Pulmonary and Critical Care, Department of Internal Medicine, Eastern Virginia Medical School, Norfolk, Virginia, USA
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, USA.
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183
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Rattan SIS. Seven knowledge gaps in modern biogerontology. Biogerontology 2024; 25:1-8. [PMID: 38206540 DOI: 10.1007/s10522-023-10089-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
About a year ago, members of the editorial board of Biogerontology were requested to respond to a query by the editor-in-chief of the journal as to what one question within their field of ageing research still needs to be asked and answered. This editorial is inspired by the wide range and variety of questions, ideas, comments and suggestions received in response to that query. The seven knowledge gaps identified in this article are arranged into three main categories: evolutionary aspects of longevity, biological survival and death aspects, and heterogeneity in the progression and phenotype of ageing. This is not an exhaustive and exclusive list, and may be modified and expanded. Implications of these knowledge gaps, especially in the context of ongoing attempts to develop effective interventions in ageing and longevity are also discussed.
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Affiliation(s)
- Suresh I S Rattan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.
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184
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Ali MA, Gioscia-Ryan R, Yang D, Sutton NR, Tyrrell DJ. Cardiovascular aging: spotlight on mitochondria. Am J Physiol Heart Circ Physiol 2024; 326:H317-H333. [PMID: 38038719 PMCID: PMC11219063 DOI: 10.1152/ajpheart.00632.2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
Mitochondria are cellular organelles critical for ATP production and are particularly relevant to cardiovascular diseases including heart failure, atherosclerosis, ischemia-reperfusion injury, and cardiomyopathies. With advancing age, even in the absence of clinical disease, mitochondrial homeostasis becomes disrupted (e.g., redox balance, mitochondrial DNA damage, oxidative metabolism, and mitochondrial quality control). Mitochondrial dysregulation leads to the accumulation of damaged and dysfunctional mitochondria, producing excessive reactive oxygen species and perpetuating mitochondrial dysfunction. In addition, mitochondrial DNA, cardiolipin, and N-formyl peptides are potent activators of cell-intrinsic and -extrinsic inflammatory pathways. These age-related mitochondrial changes contribute to the development of cardiovascular diseases. This review covers the impact of aging on mitochondria and links these mechanisms to therapeutic implications for age-associated cardiovascular diseases.
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Affiliation(s)
- Md Akkas Ali
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Rachel Gioscia-Ryan
- Department of Anesthesiology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States
| | - Dongli Yang
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Nadia R Sutton
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States
| | - Daniel J Tyrrell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
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185
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Nguyen HT, Wiederkehr A, Wollheim CB, Park KS. Regulation of autophagy by perilysosomal calcium: a new player in β-cell lipotoxicity. Exp Mol Med 2024; 56:273-288. [PMID: 38297165 PMCID: PMC10907728 DOI: 10.1038/s12276-024-01161-x] [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: 05/03/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 02/02/2024] Open
Abstract
Autophagy is an essential quality control mechanism for maintaining organellar functions in eukaryotic cells. Defective autophagy in pancreatic beta cells has been shown to be involved in the progression of diabetes through impaired insulin secretion under glucolipotoxic stress. The underlying mechanism reveals the pathologic role of the hyperactivation of mechanistic target of rapamycin (mTOR), which inhibits lysosomal biogenesis and autophagic processes. Moreover, accumulating evidence suggests that oxidative stress induces Ca2+ depletion in the endoplasmic reticulum (ER) and cytosolic Ca2+ overload, which may contribute to mTOR activation in perilysosomal microdomains, leading to autophagic defects and β-cell failure due to lipotoxicity. This review delineates the antagonistic regulation of autophagic flux by mTOR and AMP-dependent protein kinase (AMPK) at the lysosomal membrane, and both of these molecules could be activated by perilysosomal calcium signaling. However, aberrant and persistent Ca2+ elevation upon lipotoxic stress increases mTOR activity and suppresses autophagy. Therefore, normalization of autophagy is an attractive therapeutic strategy for patients with β-cell failure and diabetes.
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Affiliation(s)
- Ha Thu Nguyen
- Department of Physiology, Yonsei University Wonju College of Medicine, Wonju, Korea
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Korea
| | | | - Claes B Wollheim
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.
- Department of Clinical Sciences, Lund University, Malmö, Sweden.
| | - Kyu-Sang Park
- Department of Physiology, Yonsei University Wonju College of Medicine, Wonju, Korea.
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Korea.
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186
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Chakraborty S, Schuster S. How Plant Toxins Cause Early Larval Mortality in Herbivorous Insects: An Explanation by Modeling the Net Energy Curve. Toxins (Basel) 2024; 16:72. [PMID: 38393150 PMCID: PMC10892588 DOI: 10.3390/toxins16020072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Plants store chemical defenses that act as toxins against herbivores, such as toxic isothiocyanates (ITCs) in Brassica plants, hydrolyzed from glucosinolate (GLS) precursors. The fitness of herbivorous larvae can be strongly affected by these toxins, causing immature death. We modeled this phenomenon using a set of ordinary differential equations and established a direct relationship between feeding, toxin exposure, and the net energy of a larva, where the fitness of an organism is proportional to its net energy according to optimal foraging theory. Optimal foraging theory is widely used in ecology to model the feeding and searching behavior of organisms. Although feeding provides energy gain, plant toxins and foraging cause energy loss for the larvae. Our equations explain that toxin exposure and foraging can sharply reduce larval net energy to zero at an instar. Since herbivory needs energy, the only choice left for a larva is to stop feeding at that time point. If that is significantly earlier than the end of the last instar stage, the larva dies without food. Thus, we show that plant toxins can cause immature death in larvae from the perspective of optimal foraging theory.
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Affiliation(s)
- Suman Chakraborty
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany;
- International Max Planck Research School “Chemical Communication in Ecological Systems”, 07745 Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany;
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187
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Adeosun WB, Loots DT. Medicinal Plants against Viral Infections: A Review of Metabolomics Evidence for the Antiviral Properties and Potentials in Plant Sources. Viruses 2024; 16:218. [PMID: 38399995 PMCID: PMC10892737 DOI: 10.3390/v16020218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Most plants have developed unique mechanisms to cope with harsh environmental conditions to compensate for their lack of mobility. A key part of their coping mechanisms is the synthesis of secondary metabolites. In addition to their role in plants' defense against pathogens, they also possess therapeutic properties against diseases, and their use by humans predates written history. Viruses are a unique class of submicroscopic agents, incapable of independent existence outside a living host. Pathogenic viruses continue to pose a significant threat to global health, leading to innumerable fatalities on a yearly basis. The use of medicinal plants as a natural source of antiviral agents has been widely reported in literature in the past decades. Metabolomics is a powerful research tool for the identification of plant metabolites with antiviral potentials. It can be used to isolate compounds with antiviral capacities in plants and study the biosynthetic pathways involved in viral disease progression. This review discusses the use of medicinal plants as antiviral agents, with a special focus on the metabolomics evidence supporting their efficacy. Suggestions are made for the optimization of various metabolomics methods of characterizing the bioactive compounds in plants and subsequently understanding the mechanisms of their operation.
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Affiliation(s)
- Wilson Bamise Adeosun
- Human Metabolomics, North-West University, Private Bag X6001, Box 269, Potchefstroom 2531, South Africa;
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188
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Bhattacharya S, Sadhukhan D, Saraswathy R. Role of sex in immune response and epigenetic mechanisms. Epigenetics Chromatin 2024; 17:1. [PMID: 38247002 PMCID: PMC10802034 DOI: 10.1186/s13072-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The functioning of the human immune system is highly dependent on the sex of the individual, which comes by virtue of sex chromosomes and hormonal differences. Epigenetic mechanisms such as X chromosome inactivation, mosaicism, skewing, and dimorphism in X chromosome genes and Y chromosome regulatory genes create a sex-based variance in the immune response between males and females. This leads to differential susceptibility in immune-related disorders like infections, autoimmunity, and malignancies. Various naturally available immunomodulators are also available which target immune pathways containing X chromosome genes.
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Affiliation(s)
- Sombodhi Bhattacharya
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Debasmita Sadhukhan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Radha Saraswathy
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
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189
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Qian W, Chen CC, Huang Y, Zhu X. Exposure concentration ratios and biological responses play a critical role in determining the joint toxicity of TiO 2 nanoparticles and As(V) to the organism: The case study in marine algae Phaeodactylum tricornutum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168508. [PMID: 37977401 DOI: 10.1016/j.scitotenv.2023.168508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Environmental risks of manufactured nanomaterials (MNMs) have been widely investigated while the understanding for joint toxicity mechanism of MNMs with other contaminants is still limited. This limitation may be attributed to variations in the concentration ratios of MNMs and co-existing contaminants in the real environment. To better assess the joint toxicity and clarify its underlying mechanisms, this study exposed Phaeodactylum tricornutum to different concentration combinations of nano-sized titanium dioxide (nTiO2) and As(V) at toxic unit (TU) ratios of 1:4,1:1, and 4:1. The results demonstrated that the joint toxicity modes of nTiO2 and As(V) varied with the TU ratios exhibiting synergism for 1:4, partially addition for 1:1, and antagonism for 4:1. Specifically, at low TU ratio of 1:4, the adsorption of As(V) by nTiO2 together with the subsequent internalization of nTiO2 promoted a significant enrichment of As in algae. Simultaneously, the up-regulation of pst (phosphate transporter) genes in charge of the As(V) transport molecular further exacerbated the enrichment of inorganic As in algae, while the down-regulation of ArsM (arsenite S-adenosylmethionine methyltransferases) genes in charge of the As metabolism inhibited As biotransformation from toxic inorganic to nontoxic organic, causing the aggravated accumulation of toxic inorganic As in algae. At higher TU ratios of 1:1 and 4:1, the accumulation of As decreased in algae due to the higher sedimentation of nTiO2 and thus the lower internalization of As-adsorbed nTiO2, as well as the down-regulation of pst genes restricting the transportation of As(V) into algal cells, which jointly accelerated the As biotransformation from toxic inorganic to nontoxic organic. Our results suggest that more attention should be paid to exposure concentration ratios of MNMs and co-existing contaminants and biological responses including bioavailability, bioaccumulation, biotransformation, which would play a critical role in determining the joint toxicity to the organism.
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Affiliation(s)
- Wei Qian
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; School of Ecology and Environment, Hainan University, Haikou 570208, China; Shenzhen International Graduate school, Tsinghua University, Shenzhen 518055, China
| | - Ciara Chun Chen
- College of Chemistry and Chemical Engineering, Shantou University, Shantou 515063, China
| | - Yuxiong Huang
- Shenzhen International Graduate school, Tsinghua University, Shenzhen 518055, China
| | - Xiaoshan Zhu
- School of Ecology and Environment, Hainan University, Haikou 570208, China; Shenzhen International Graduate school, Tsinghua University, Shenzhen 518055, China.
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190
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Danov A, Segev O, Bograd A, Ben Eliyahu Y, Dotan N, Kaplan T, Levy A. Toxinome-the bacterial protein toxin database. mBio 2024; 15:e0191123. [PMID: 38117054 PMCID: PMC10790787 DOI: 10.1128/mbio.01911-23] [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: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Microbes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas "Toxin Islands." The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins.
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Affiliation(s)
- Aleks Danov
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Segev
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avi Bograd
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yedidya Ben Eliyahu
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Dotan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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191
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Zeng Y, Chen H, Liu X, Song Z, Yao Y, Lei X, Lv X, Cheng L, Chen Z, Bai C, Yin Z, Lv Y, Lu J, Li J, Land KC, Yashin A, O'Rand AM, Sun L, Yang Z, Tao W, Gu J, Gottschalk W, Tan Q, Christensen K, Hesketh T, Tian XL, Yang H, Egidi V, Caselli G, Robine JM, Wang H, Shi X, Vaupel JW, Lutz MW, Nie C, Min J. Genetic associations with longevity are on average stronger in females than in males. Heliyon 2024; 10:e23691. [PMID: 38192771 PMCID: PMC10772631 DOI: 10.1016/j.heliyon.2023.e23691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 01/10/2024] Open
Abstract
It is long observed that females tend to live longer than males in nearly every country. However, the underlying mechanism remains elusive. In this study, we discovered that genetic associations with longevity are on average stronger in females than in males through bio-demographic analyses of genome-wide association studies (GWAS) dataset of 2178 centenarians and 2299 middle-age controls of Chinese Longitudinal Healthy Longevity Study (CLHLS). This discovery is replicated across North and South regions of China, and is further confirmed by North-South discovery/replication analyses of different and independent datasets of Chinese healthy aging candidate genes with CLHLS participants who are not in CLHLS GWAS, including 2972 centenarians and 1992 middle-age controls. Our polygenic risk score analyses of eight exclusive groups of sex-specific genes, analyses of sex-specific and not-sex-specific individual genes, and Genome-wide Complex Trait Analysis using all SNPs all reconfirm that genetic associations with longevity are on average stronger in females than in males. Our discovery/replication analyses are based on genetic datasets of in total 5150 centenarians and compatible middle-age controls, which comprises the worldwide largest sample of centenarians. The present study's findings may partially explain the well-known male-female health-survival paradox and suggest that genetic variants may be associated with different reactions between males and females to the same vaccine, drug treatment and/or nutritional intervention. Thus, our findings provide evidence to steer away from traditional view that "one-size-fits-all" for clinical interventions, and to consider sex differences for improving healthcare efficiency. We suggest future investigations focusing on effects of interactions between sex-specific genetic variants and environment on longevity as well as biological function.
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Affiliation(s)
- Yi Zeng
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, 100871, China
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Huashuai Chen
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, 100871, China
- Business School of Xiangtan University, Xiangtan, 411105, China
| | | | - Zijun Song
- The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yao Yao
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Xiaoyan Lei
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Xiaozhen Lv
- French National Institute of Health and Medical Research (INSERM) and Ecole Pratique des Hautes Etudes (EPHE) FR, Italy
| | - Lingguo Cheng
- School of Business, Nanjing University, Nanjing, 210093, China
| | | | - Chen Bai
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Zhaoxue Yin
- Division of Non-Communicable Disease Control and Community Health, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuebin Lv
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Jiehua Lu
- Department of Sociology, Peking University, Beijing, 100871, China
| | - Jianxin Li
- Department of Sociology, Peking University, Beijing, 100871, China
| | - Kenneth C. Land
- Duke Population Research Institute's Center for Population Health and Aging, Duke University, Durham, NC, USA, 27710
| | - Anatoliy Yashin
- Duke Population Research Institute's Center for Population Health and Aging, Duke University, Durham, NC, USA, 27710
| | - Angela M. O'Rand
- Duke Population Research Institute's Center for Population Health and Aging, Duke University, Durham, NC, USA, 27710
| | - Liang Sun
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
| | - Ze Yang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC, USA, 27710
| | - Qihua Tan
- University of Southern Denmark, Odense, DK-5000, Denmark
| | | | - Therese Hesketh
- Institute for Global Health, University College London, London, UK
- Institute for Global Health, School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Li Tian
- Human Aging Research Institute and School of Life Science, Nanchang University, Jiangxi, 330031, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310008, China310058
| | - Viviana Egidi
- Department of Statistical Sciences, University of Rome La Sapienza, Roma, 00161, Italy
| | - Graziella Caselli
- Department of Statistical Sciences, University of Rome La Sapienza, Roma, 00161, Italy
| | - Jean-Marie Robine
- French National Institute of Health and Medical Research (INSERM) and Ecole Pratique des Hautes Etudes (EPHE) FR, Italy
| | - Huali Wang
- The Third Affiliated Hospital of Health Science Center, Peking University, Italy
| | - Xiaoming Shi
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | | | - Michael W. Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC, USA, 27710
| | - Chao Nie
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
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192
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Zhang W, Chen X, Eleftherianos I, Mohamed A, Bastin A, Keyhani NO. Cross-talk between immunity and behavior: insights from entomopathogenic fungi and their insect hosts. FEMS Microbiol Rev 2024; 48:fuae003. [PMID: 38341280 PMCID: PMC10883697 DOI: 10.1093/femsre/fuae003] [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: 06/23/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/12/2024] Open
Abstract
Insects are one of the most successful animals in nature, and entomopathogenic fungi play a significant role in the natural epizootic control of insect populations in many ecosystems. The interaction between insects and entomopathogenic fungi has continuously coevolved over hundreds of millions of years. Many components of the insect innate immune responses against fungal infection are conserved across phyla. Additionally, behavioral responses, which include avoidance, grooming, and/or modulation of body temperature, have been recognized as important mechanisms for opposing fungal pathogens. In an effort to investigate possible cross-talk and mediating mechanisms between these fundamental biological processes, recent studies have integrated and/or explored immune and behavioral responses. Current information indicates that during discrete stages of fungal infection, several insect behavioral and immune responses are altered simultaneously, suggesting important connections between the two systems. This review synthesizes recent advances in our understanding of the physiological and molecular aspects influencing cross-talk between behavioral and innate immune antifungal reactions, including chemical perception and olfactory pathways.
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Affiliation(s)
- Wei Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang, Huaxi District 550025, China
| | - Xuanyu Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang, Huaxi District 550025, China
| | - Ioannis Eleftherianos
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, United States
| | - Amr Mohamed
- Department of Entomology, Faculty of Science, Cairo University, Giza 12613, Egypt
- Research fellow, King Saud University Museum of Arthropods, Plant Protection Department, College of Food and Agricultural Sciences, King Saud University, Saudi Arabia
| | - Ashley Bastin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, United States
| | - Nemat O Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL 60607, United States
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193
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Moztarzadeh S, Sepic S, Hamad I, Waschke J, Radeva MY, García-Ponce A. Cortactin is in a complex with VE-cadherin and is required for endothelial adherens junction stability through Rap1/Rac1 activation. Sci Rep 2024; 14:1218. [PMID: 38216638 PMCID: PMC10786853 DOI: 10.1038/s41598-024-51269-3] [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: 06/30/2023] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
Vascular permeability is mediated by Cortactin (Cttn) and regulated by several molecules including cyclic-adenosine-monophosphate, small Rho family GTPases and the actin cytoskeleton. However, it is unclear whether Cttn directly interacts with any of the junctional components or if Cttn intervenes with signaling pathways affecting the intercellular contacts and the cytoskeleton. To address these questions, we employed immortalized microvascular myocardial endothelial cells derived from wild-type and Cttn-knock-out mice. We found that lack of Cttn compromised barrier integrity due to fragmented membrane distribution of different junctional proteins. Moreover, immunoprecipitations revealed that Cttn is within the VE-cadherin-based adherens junction complex. In addition, lack of Cttn slowed-down barrier recovery after Ca2+ repletion. The role of Cttn for cAMP-mediated endothelial barrier regulation was analyzed using Forskolin/Rolipram. In contrast to Cttn-KO, WT cells reacted with increased transendothelial electrical resistance. Absence of Cttn disturbed Rap1 and Rac1 activation in Cttn-depleted cells. Surprisingly, despite the absence of Cttn, direct activation of Rac1/Cdc42/RhoA by CN04 increased barrier resistance and induced well-defined cortical actin and intracellular actin bundles. In summary, our data show that Cttn is required for basal barrier integrity by allowing proper membrane distribution of junctional proteins and for cAMP-mediated activation of the Rap1/Rac1 signaling pathway.
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Affiliation(s)
- Sina Moztarzadeh
- Chair of Vegetative Anatomy, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstraße 11, 80336, Munich, Germany
| | - Sara Sepic
- Chair of Vegetative Anatomy, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstraße 11, 80336, Munich, Germany
| | - Ibrahim Hamad
- Chair of Vegetative Anatomy, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstraße 11, 80336, Munich, Germany
| | - Jens Waschke
- Chair of Vegetative Anatomy, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstraße 11, 80336, Munich, Germany
| | - Mariya Y Radeva
- Chair of Vegetative Anatomy, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstraße 11, 80336, Munich, Germany
| | - Alexander García-Ponce
- Chair of Vegetative Anatomy, Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Pettenkoferstraße 11, 80336, Munich, Germany.
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194
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Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, Carpenter AE, Singh S, Nehme R, Raychaudhuri S. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nat Commun 2024; 15:347. [PMID: 38184653 PMCID: PMC10771466 DOI: 10.1038/s41467-023-44045-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/28/2023] [Indexed: 01/08/2024] Open
Abstract
The morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combine genomic sequencing and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identify novel associations between rare protein altering variants in WASF2, TSPAN15, and PRLR with several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirms their role in cell morphology. Analysis of common variants yields one significant association and nominate over 300 variants with suggestive evidence (P < 10-6) of association with one or more morphology traits. We then use these data to make predictions about sample size requirements for increasing discovery in cellular genetic studies. We conclude that, similar to molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.
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Affiliation(s)
- Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Centre for Gene Therapy and Regenerative Medicine, King's College, London, UK
| | - Jatin Arora
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samira Asgari
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ajay Nadig
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Peirent
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dhara Liyanage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory P Way
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tiffany Amariuta
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California, La Jolla, CA, USA
- Department of Medicine, University of California, La Jolla, CA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Marzieh Haghighi
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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195
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Yuan T, Zeng C, Liu J, Zhao C, Ge F, Li Y, Qian M, Du J, Wang W, Li Y, Liu Y, Dai X, Zhou J, Chen X, Ma S, Zhu H, He Q, Yang B. Josephin domain containing 2 (JOSD2) promotes lung cancer by inhibiting LKB1 (Liver kinase B1) activity. Signal Transduct Target Ther 2024; 9:11. [PMID: 38177135 PMCID: PMC10766984 DOI: 10.1038/s41392-023-01706-y] [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: 01/05/2023] [Revised: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) ranks as one of the leading causes of cancer-related deaths worldwide. Despite the prominence and effectiveness of kinase-target therapies in NSCLC treatment, these drugs are suitable for and beneficial to a mere ~30% of NSCLC patients. Consequently, the need for novel strategies addressing NSCLC remains pressing. Deubiquitinases (DUBs), a group of diverse enzymes with well-defined catalytic sites that are frequently overactivated in cancers and associated with tumorigenesis and regarded as promising therapeutic targets. Nevertheless, the mechanisms by which DUBs promote NSCLC remain poorly understood. Through a global analysis of the 97 DUBs' contribution to NSCLC survival possibilities using The Cancer Genome Atlas (TCGA) database, we found that high expression of Josephin Domain-containing protein 2 (JOSD2) predicted the poor prognosis of patients. Depletion of JOSD2 significantly impeded NSCLC growth in both cell/patient-derived xenografts in vivo. Mechanically, we found that JOSD2 restricts the kinase activity of LKB1, an important tumor suppressor generally inactivated in NSCLC, by removing K6-linked polyubiquitination, an action vital for maintaining the integrity of the LKB1-STRAD-MO25 complex. Notably, we identified the first small-molecule inhibitor of JOSD2, and observed that its pharmacological inhibition significantly arrested NSCLC proliferation in vitro/in vivo. Our findings highlight the vital role of JOSD2 in hindering LKB1 activity, underscoring the therapeutic potential of targeting JOSD2 in NSCLC, especially in those with inactivated LKB1, and presenting its inhibitors as a promising strategy for NSCLC treatment.
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Affiliation(s)
- Tao Yuan
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chenming Zeng
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 311199, China
| | - Jiawei Liu
- Ministry of Education Key Laboratory of Chinese Medicinal Plants Resource from Lingnan, Research Center of Medicinal Plants Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chenxi Zhao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fujing Ge
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuekang Li
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meijia Qian
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiamin Du
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weihua Wang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghao Li
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yue Liu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyang Dai
- Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou, 310058, China
| | - Jianya Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xueqin Chen
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310002, China
| | - Shenglin Ma
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310002, China
| | - Hong Zhu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Cancer Center of Zhejiang University, Hangzhou, China.
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, China.
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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Shimura T, Sunaga K, Yamazaki M, Honoka N, Sasatani M, Kamiya K, Ushiyama A. Nuclear DNA damage-triggered ATM-dependent AMPK activation regulates the mitochondrial radiation response. Int J Radiat Biol 2024; 100:584-594. [PMID: 38166485 DOI: 10.1080/09553002.2023.2295297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/11/2023] [Indexed: 01/04/2024]
Abstract
PURPOSE AMP-activated protein kinase (AMPK) acts as a cellular energy sensor and is essential for controlling mitochondrial homeostasis. Here, we investigated the regulatory mechanisms involved in AMPK activation to elucidate how networks of intracellular signaling pathways respond to stress conditions. MATERIALS AND METHODS Inhibitors of ATM, DNA-PK, and AKT were tested in normal TIG-3 and MRC-5 human fibroblasts to determine which upstream kinases are responsible for AMPK activation. SV40 transformed-human ATM-deficient fibroblasts (AT5BIVA) and their ATM-complemented cells (i.e., AT5BIVA/ATMwt) were also used. Protein expression associated with AMPK signaling was examined by immunostaining and/or Western blotting. RESULTS Radiation-induced nuclear DNA damage activates ATM-dependent AMPK signaling pathways that regulate mitochondrial quality control. In contrast, hypoxia and glucose starvation caused ATP depletion and activated AMPK via a pathway independent of ATM. DNA-PK and AKT are not involved in AMPK-mediated mitochondrial signaling pathways. CONCLUSION Activation of the AMPK signaling pathway differs depending on the stimulus. Radiation activates AMPK through two pathways: depletion of ATP-mediated LKB1 signaling and nuclear DNA damage-induced ATM signaling. Nuclear DNA damage signaling to mitochondria therefore plays a pivotal role in determining the cell fates of irradiated cells.
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Affiliation(s)
- Tsutomu Shimura
- Department of Environmental Health, National Institute of Public Health Wako, Saitama, Japan
| | - Kenta Sunaga
- Faculty of Pharmaceutical Sciences Student, Meiji Pharmaceutical University, Kiyose, Japan
| | - Mayu Yamazaki
- Faculty of Pharmaceutical Sciences Student, Meiji Pharmaceutical University, Kiyose, Japan
| | - Nara Honoka
- Faculty of Pharmaceutical Sciences Student, Meiji Pharmaceutical University, Kiyose, Japan
| | - Megumi Sasatani
- Department of Experimental Oncology; Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Kenji Kamiya
- Department of Experimental Oncology; Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Akira Ushiyama
- Department of Environmental Health, National Institute of Public Health Wako, Saitama, Japan
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197
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Chou HT, Valencia F, Alexander JC, Bell AD, Deb D, Pollard DA, Paaby AB. Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains. Genetics 2024; 226:iyad191. [PMID: 37865119 PMCID: PMC10763538 DOI: 10.1093/genetics/iyad191] [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: 07/09/2023] [Revised: 07/09/2023] [Accepted: 08/12/2023] [Indexed: 10/23/2023] Open
Abstract
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.
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Affiliation(s)
- Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jacqueline C Alexander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Diptodip Deb
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Janelia Research Campus, Ashburn, VA 20147, USA
| | - Daniel A Pollard
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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198
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Sato F, Bhawal UK, Oikawa K, Muragaki Y. Loss of Dec1 inhibits alcohol-induced hepatic lipid accumulation and circadian rhythm disorder. BMC Mol Cell Biol 2024; 25:1. [PMID: 38166556 PMCID: PMC10763066 DOI: 10.1186/s12860-023-00497-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
Chronic alcohol exposure increases liver damage such as lipid accumulation and hepatitis, resulting in hepatic cirrhosis. Chronic alcohol intake is known to disturb circadian rhythms in humans and animals. DEC1, a basic helix-loop-helix transcription factor, plays an important role in the circadian rhythm, inflammation, immune responses, and tumor progression. We have previously shown that Dec1 deficiency inhibits stresses such as periodontal inflammation and perivascular fibrosis of the heart. However, the significance of Dec1 deficiency in chronic alcohol consumption remains unclear. In the present study, we investigated whether the biological stress caused by chronic alcohol intake is inhibited in Dec1 knockout mice. We treated control and Dec1 knockout mice for three months by providing free access to 10% alcohol. The Dec1 knockout mice consumed more alcohol than control mice, however, we observed severe hepatic lipid accumulation and circadian rhythm disturbance in control mice. In contrast, Dec1 knockout mice exhibited little effect on these outcomes. We also investigated the expression of peroxisome proliferator-activated receptors (PPARs) and AMP-activated protein kinase (AMPK), which are involved in the regulation of fatty acid metabolism. Immunohistochemical analysis revealed increases of phosphorylation AMPK and PPARa but decreases PPARg in Dec1 knockout mice compared to that in control mice. This indicates a molecular basis for the inhibition of hepatic lipid accumulation in alcohol-treated Dec1 knockout mice. These results suggest a novel function of Dec1 in alcohol-induced hepatic lipid accumulation and circadian rhythm disorders.
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Affiliation(s)
- Fuyuki Sato
- Department of Diagnostic Pathology, Shizuoka Cancer Center, Sunto-gun, 411-8777, Japan.
- Department of Pathology, Wakayama Medical University School of Medicine, Wakayama, 641- 8509, Japan.
| | - Ujjal K Bhawal
- Research Institute of Oral Science, Nihon University School of Dentistry at Matsudo, Chiba, 271-8587, Japan
- Center for Global Health Research , Saveetha Medical College and Hospitals , Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, India
| | - Kosuke Oikawa
- Department of Pathology, Wakayama Medical University School of Medicine, Wakayama, 641- 8509, Japan
| | - Yasuteru Muragaki
- Department of Pathology, Wakayama Medical University School of Medicine, Wakayama, 641- 8509, Japan
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Baeza-Pérez LG, Cabrera-Becerra SE, Romero-Nava R, Ramos-Tovar E, Hernández-Campos ME, López-Sánchez P. Cardiovascular effect of preeclampsia upon offspring development: Are (Pro) renin-renin receptor ((P)RR) and gender related? IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:621-629. [PMID: 38629095 PMCID: PMC11017840 DOI: 10.22038/ijbms.2024.72486.15790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/13/2023] [Indexed: 04/19/2024]
Abstract
Objectives Preeclampsia (PE) is a complication of pregnancy that might increase progeny risk of cardiovascular and metabolic problems, mainly in males. Renin angiotensin aldosterone system is known to be involved. (Pro) renin/renin receptor ((P)RR) has been shown to participate in cardiovascular pathology. The aim of this work was to evaluate (P)RR expression and function upon cardiovascular and renal tissues from PE dams' offspring. Materials and Methods We used offspring from normal pregnant and preeclamptic rats, evaluating body, heart, aorta and kidney weight, length, and blood pressure along 3 months after birth. Subsets of animals received handle region peptide (HRP) (0.2 mg/Kg, sc). Another group received vehicle. Animals were sacrificed at first, second, and third months of age, tissues were extracted and processed for immunoblot to detect (P)RR, PLZF, β-catenin, DVL-1, and PKCα. (P)RR and PLZF were also measured by RT-PCR. Results We found that offspring developed hypertension. Male descendants remained hypertensive throughout the whole experiment. Female animals tended to recover at second month and returned to normal blood pressure at third month. HRP treatment diminished hypertension in both male and female animals. Morphological evaluations showed changes in heart, aorta, and kidney weight, and HRP reverted this effect. Finally, we found that (P)RR, PLZF, and canonical WNT transduction pathway molecules were stimulated by PE, and HRP treatment abolished this increase. Conclusion These findings suggest that PE can induce hypertension in offspring, and (P)RR seems to play an important role through the canonical WNT pathway and that gender seems to influence this response.
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Affiliation(s)
- Lourdes Graciela Baeza-Pérez
- Laboratorio de Farmacología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Sto. Tomás, Ciudad de México, México
- These authors contributed eqully to this work
| | - Sandra Edith Cabrera-Becerra
- Laboratorio de Biología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Sto. Tomás, Ciudad de México, México
| | - Rodrigo Romero-Nava
- Laboratorio de Biología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Sto. Tomás, Ciudad de México, México
| | - Erika Ramos-Tovar
- Laboratorio de Farmacología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Sto. Tomás, Ciudad de México, México
- These authors contributed eqully to this work
| | - Maria Elena Hernández-Campos
- Laboratorio de Farmacología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Sto. Tomás, Ciudad de México, México
- These authors contributed eqully to this work
| | - Pedro López-Sánchez
- Laboratorio de Farmacología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Sto. Tomás, Ciudad de México, México
- These authors contributed eqully to this work
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Chanchal DK, Chaudhary JS, Kumar P, Agnihotri N, Porwal P. CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine. Curr Gene Ther 2024; 24:193-207. [PMID: 38310456 DOI: 10.2174/0115665232275754231204072320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 02/05/2024]
Abstract
With the discovery of CRISPR-Cas9, drug development and precision medicine have undergone a major change. This review article looks at the new ways that CRISPR-based therapies are being used and how they are changing the way medicine is done. CRISPR technology's ability to precisely and flexibly edit genes has opened up new ways to find, validate, and develop drug targets. Also, it has made way for personalized gene therapies, precise gene editing, and advanced screening techniques, all of which hold great promise for treating a wide range of diseases. In this article, we look at the latest research and clinical trials that show how CRISPR could be used to treat genetic diseases, cancer, infectious diseases, and other hard-to-treat conditions. However, ethical issues and problems with regulations are also discussed in relation to CRISPR-based therapies, which shows how important it is to use them safely and responsibly. As CRISPR continues to change how drugs are made and used, this review shines a light on the amazing things that have been done and what the future might hold in this rapidly changing field.
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Affiliation(s)
- Dilip Kumar Chanchal
- Department of Pharmacy, Smt. Vidyawati College of Pharmacy, Jhansi, Uttar Pradesh, India
- Glocal School of Pharmacy, Glocal University Mirzapur Pole, Saharanpur - 247121, Uttar Pradesh, India
| | | | - Pushpendra Kumar
- Faculty of Pharmacy, Uttar Pradesh University of Medical Sciences, Saifai, Etawah 206130, Uttar Pradesh, India
| | - Neha Agnihotri
- Department of Pharmacy, Maharana Pratap College of Pharmacy, Kothi, Mandhana, Kanpur-209217, Uttar Pradesh, India
| | - Prateek Porwal
- Glocal School of Pharmacy, Glocal University Mirzapur Pole, Saharanpur - 247121, Uttar Pradesh, India
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