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Kaushal JB, Takkar S, Batra SK, Siddiqui JA. Diverse landscape of genetically engineered mouse models: Genomic and molecular insights into prostate cancer. Cancer Lett 2024; 593:216954. [PMID: 38735382 DOI: 10.1016/j.canlet.2024.216954] [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] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
Prostate cancer (PCa) is a significant health concern for men worldwide and is particularly prevalent in the United States. It is a complex disease presenting different molecular subtypes and varying degrees of aggressiveness. Transgenic/genetically engineered mouse models (GEMMs) greatly enhanced our understanding of the intricate molecular processes that underlie PCa progression and have offered valuable insights into potential therapeutic targets for this disease. The integration of whole-exome and whole-genome sequencing, along with expression profiling, has played a pivotal role in advancing GEMMs by facilitating the identification of genetic alterations driving PCa development. This review focuses on genetically modified mice classified into the first and second generations of PCa models. We summarize whether models created by manipulating the function of specific genes replicate the consequences of genomic alterations observed in human PCa, including early and later disease stages. We discuss cases where GEMMs did not fully exhibit the expected human PCa phenotypes and possible causes of the failure. Here, we summarize the comprehensive understanding, recent advances, strengths and limitations of the GEMMs in advancing our insights into PCa, offering genetic and molecular perspectives for developing novel GEMM models.
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Affiliation(s)
- Jyoti B Kaushal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Simran Takkar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA.
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA.
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Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes, rather than cell type compositional effects that emerge from bulk tissue samples. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Chingpan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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3
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Ganji-Arjenaki M, Kamali Z, Sardari S, de Borst M, Snieder H, Vaez A. Prioritization of Kidney Cell Types Highlights Myofibroblast Cells in Regulating Human Blood Pressure. Kidney Int Rep 2024; 9:1849-1859. [PMID: 38899223 PMCID: PMC11184402 DOI: 10.1016/j.ekir.2024.03.001] [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: 11/04/2023] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 06/21/2024] Open
Abstract
Introduction Blood pressure (BP) is a highly heritable trait with over 2000 underlying genomic loci identified to date. Although the kidney plays a key role, little is known about specific cell types involved in the genetic regulation of BP. Methods Here, we applied stratified linkage disequilibrium score (LDSC) regression to connect BP genome-wide association studies (GWAS) results to specific cell types of the mature human kidney. We used the largest single-stage BP genome-wide analysis to date, including up to 1,028,980 adults of European ancestry, and single-cell transcriptomic data from 14 mature human kidneys, with mean age of 41 years. Results Our analyses prioritized myofibroblasts and endothelial cells, among the total of 33 annotated cell type, as specifically involved in BP regulation (P < 0.05/33, i.e., 0.001515). Enrichment of heritability for systolic BP (SBP) was observed in myofibroblast cells in mature human kidney cortex, and enrichment of heritability for diastolic BP (DBP) was observed in descending vasa recta and peritubular capillary endothelial cells as well as stromal myofibroblast cells. The new finding of myofibroblast, the significant cell type for both BP traits, was consistent in 8 replication efforts using 7 sets of independent data, including in human fetal kidney, in East-Asian (EAS) ancestry, using mouse single-cell RNA sequencing (scRNA-seq) data, and when using another prioritization method. Conclusion Our findings provide a solid basis for follow-up studies to further identify genes and mechanisms in myofibroblast cells that underlie the regulation of BP.
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Affiliation(s)
- Mahboube Ganji-Arjenaki
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Zoha Kamali
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Martin de Borst
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
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Calamari ZT, Flynn JJ. Gene expression supports a single origin of horns and antlers in hoofed mammals. Commun Biol 2024; 7:509. [PMID: 38769090 PMCID: PMC11106249 DOI: 10.1038/s42003-024-06134-4] [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: 11/27/2020] [Accepted: 04/02/2024] [Indexed: 05/22/2024] Open
Abstract
Horns, antlers, and other bony cranial appendages of even-toed hoofed mammals (ruminant artiodactyls) challenge traditional morphological homology assessments. Cranial appendages all share a permanent bone portion with family-specific integument coverings, but homology determination depends on whether the integument covering is an essential component or a secondary elaboration of each structure. To enhance morphological homology assessments, we tested whether juvenile cattle horn bud transcriptomes share homologous gene expression patterns with deer antlers relative to pig outgroup tissues, treating the integument covering as a secondary elaboration. We uncovered differentially expressed genes that support horn and antler homology, potentially distinguish them from non-cranial-appendage bone and other tissues, and highlight the importance of phylogenetic outgroups in homology assessments. Furthermore, we found differentially expressed genes that could support a shared cranial neural crest origin for horns and antlers and expression patterns that refine our understanding of the timing of horn and antler differentiation.
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Affiliation(s)
- Zachary T Calamari
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Department of Natural Sciences, Baruch College, City University of New York, 17 Lexington Avenue, Box A-920, New York, NY, 10010, USA.
| | - John J Flynn
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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Barak MM. Cortical and Trabecular Bone Modeling and Implications for Bone Functional Adaptation in the Mammalian Tibia. Bioengineering (Basel) 2024; 11:514. [PMID: 38790379 PMCID: PMC11118124 DOI: 10.3390/bioengineering11050514] [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: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Bone modeling involves the addition of bone material through osteoblast-mediated deposition or the removal of bone material via osteoclast-mediated resorption in response to perceived changes in loads by osteocytes. This process is characterized by the independent occurrence of deposition and resorption, which can take place simultaneously at different locations within the bone due to variations in stress levels across its different regions. The principle of bone functional adaptation states that cortical and trabecular bone tissues will respond to mechanical stimuli by adjusting (i.e., bone modeling) their morphology and architecture to mechanically improve their mechanical function in line with the habitual in vivo loading direction. This principle is relevant to various research areas, such as the development of improved orthopedic implants, preventative medicine for osteopenic elderly patients, and the investigation of locomotion behavior in extinct species. In the present review, the mammalian tibia is used as an example to explore cortical and trabecular bone modeling and to examine its implications for the functional adaptation of bones. Following a short introduction and an exposition on characteristics of mechanical stimuli that influence bone modeling, a detailed critical appraisal of the literature on cortical and trabecular bone modeling and bone functional adaptation is given. By synthesizing key findings from studies involving small mammals (rodents), large mammals, and humans, it is shown that examining both cortical and trabecular bone structures is essential for understanding bone functional adaptation. A combined approach can provide a more comprehensive understanding of this significant physiological phenomenon, as each structure contributes uniquely to the phenomenon.
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Affiliation(s)
- Meir M Barak
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY 11548, USA
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Wenzel TJ, Mousseau DD. Brain organoids engineered to give rise to glia and neural networks after 90 days in culture exhibit human-specific proteoforms. Front Cell Neurosci 2024; 18:1383688. [PMID: 38784709 PMCID: PMC11111902 DOI: 10.3389/fncel.2024.1383688] [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: 02/07/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Human brain organoids are emerging as translationally relevant models for the study of human brain health and disease. However, it remains to be shown whether human-specific protein processing is conserved in human brain organoids. Herein, we demonstrate that cell fate and composition of unguided brain organoids are dictated by culture conditions during embryoid body formation, and that culture conditions at this stage can be optimized to result in the presence of glia-associated proteins and neural network activity as early as three-months in vitro. Under these optimized conditions, unguided brain organoids generated from induced pluripotent stem cells (iPSCs) derived from male-female siblings are similar in growth rate, size, and total protein content, and exhibit minimal batch-to-batch variability in cell composition and metabolism. A comparison of neuronal, microglial, and macroglial (astrocyte and oligodendrocyte) markers reveals that profiles in these brain organoids are more similar to autopsied human cortical and cerebellar profiles than to those in mouse cortical samples, providing the first demonstration that human-specific protein processing is largely conserved in unguided brain organoids. Thus, our organoid protocol provides four major cell types that appear to process proteins in a manner very similar to the human brain, and they do so in half the time required by other protocols. This unique copy of the human brain and basic characteristics lay the foundation for future studies aiming to investigate human brain-specific protein patterning (e.g., isoforms, splice variants) as well as modulate glial and neuronal processes in an in situ-like environment.
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Affiliation(s)
- Tyler J. Wenzel
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, Saskatoon, SK, Canada
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Sullivan MA, Lane SD, McKenzie ADJ, Ball SR, Sunde M, Neely GG, Moreno CL, Maximova A, Werry EL, Kassiou M. iPSC-derived PSEN2 (N141I) astrocytes and microglia exhibit a primed inflammatory phenotype. J Neuroinflammation 2024; 21:7. [PMID: 38178159 PMCID: PMC10765839 DOI: 10.1186/s12974-023-02951-2] [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: 11/11/2022] [Accepted: 11/07/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Widescale evidence points to the involvement of glia and immune pathways in the progression of Alzheimer's disease (AD). AD-associated iPSC-derived glial cells show a diverse range of AD-related phenotypic states encompassing cytokine/chemokine release, phagocytosis and morphological profiles, but to date studies are limited to cells derived from PSEN1, APOE and APP mutations or sporadic patients. The aim of the current study was to successfully differentiate iPSC-derived microglia and astrocytes from patients harbouring an AD-causative PSEN2 (N141I) mutation and characterise the inflammatory and morphological profile of these cells. METHODS iPSCs from three healthy control individuals and three familial AD patients harbouring a heterozygous PSEN2 (N141I) mutation were used to derive astrocytes and microglia-like cells and cell identity and morphology were characterised through immunofluorescent microscopy. Cellular characterisation involved the stimulation of these cells by LPS and Aβ42 and analysis of cytokine/chemokine release was conducted through ELISAs and multi-cytokine arrays. The phagocytic capacity of these cells was then indexed by the uptake of fluorescently-labelled fibrillar Aβ42. RESULTS AD-derived astrocytes and microglia-like cells exhibited an atrophied and less complex morphological appearance than healthy controls. AD-derived astrocytes showed increased basal expression of GFAP, S100β and increased secretion and phagocytosis of Aβ42 while AD-derived microglia-like cells showed decreased IL-8 secretion compared to healthy controls. Upon immunological challenge AD-derived astrocytes and microglia-like cells showed exaggerated secretion of the pro-inflammatory IL-6, CXCL1, ICAM-1 and IL-8 from astrocytes and IL-18 and MIF from microglia. CONCLUSION Our study showed, for the first time, the differentiation and characterisation of iPSC-derived astrocytes and microglia-like cells harbouring a PSEN2 (N141I) mutation. PSEN2 (N141I)-mutant astrocytes and microglia-like cells presented with a 'primed' phenotype characterised by reduced morphological complexity, exaggerated pro-inflammatory cytokine secretion and altered Aβ42 production and phagocytosis.
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Affiliation(s)
- Michael A Sullivan
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Samuel D Lane
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - André D J McKenzie
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Sarah R Ball
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Margaret Sunde
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - G Gregory Neely
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, Australia
| | - Cesar L Moreno
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, Australia
| | - Alexandra Maximova
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Eryn L Werry
- School of Medical Sciences, The Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia.
- School of Chemistry, The Faculty of Science, The University of Sydney, Camperdown, Australia.
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia.
| | - Michael Kassiou
- School of Chemistry, The Faculty of Science, The University of Sydney, Camperdown, Australia.
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Shamshad A, Kang C, Jenny LA, Persad-Paisley EM, Tsang SH. Translatability barriers between preclinical and clinical trials of AAV gene therapy in inherited retinal diseases. Vision Res 2023; 210:108258. [PMID: 37244011 PMCID: PMC10526971 DOI: 10.1016/j.visres.2023.108258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/29/2023]
Abstract
Inherited retinal diseases (IRDs) are progressive degenerative diseases which cause gradual vision loss or complete blindness. As over 270 gene mutations have been identified in the underlying pathology of IRDs, gene therapy as a treatment modality has been an increasingly active realm of investigation. Currently, the most common vehicle of ocular gene delivery is the adeno-associated virus (AAV) vector. This is injected into the immune-privileged subretinal space to mediate transgene expression in retinal cells. Although numerous animal models of IRDs have demonstrated successful outcomes following AAV-mediated gene delivery, many of these studies fail to translate into successful outcomes in clinical trials. The purpose of this review is to A) comparatively assess preclinical and clinical IRD trials in which the success of AAV-mediated therapy failed to translate between animal and human participants B) discuss factors which may complicate the translatability of gene therapy in animals to results in humans.
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Affiliation(s)
| | - Chaerim Kang
- Warren Alpert Medical School of Brown University, USA
| | - Laura A Jenny
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center/New York-Presbyterian Hospital, New York, NY, USA; Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
| | | | - Stephen H Tsang
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center/New York-Presbyterian Hospital, New York, NY, USA; Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA; Department of Biomedical Engineering, Columbia University, New York, NY, USA; Columbia Stem Cell Initiative, Columbia University, New York, NY, USA; Insitute of Human Nutrition, Columbia University, New York, NY, USA
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Cai H, Des Marais DL. Revisiting regulatory coherence: accounting for temporal bias in plant gene co-expression analyses. THE NEW PHYTOLOGIST 2023; 238:16-24. [PMID: 36617750 DOI: 10.1111/nph.18720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Haoran Cai
- Department of Civil and Environmental Engineering, MIT, 15 Vassar St., Cambridge, MA, 02139, USA
| | - David L Des Marais
- Department of Civil and Environmental Engineering, MIT, 15 Vassar St., Cambridge, MA, 02139, USA
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10
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Makdissi S, Parsons BD, Di Cara F. Towards early detection of neurodegenerative diseases: A gut feeling. Front Cell Dev Biol 2023; 11:1087091. [PMID: 36824371 PMCID: PMC9941184 DOI: 10.3389/fcell.2023.1087091] [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: 11/01/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
The gastrointestinal tract communicates with the nervous system through a bidirectional network of signaling pathways called the gut-brain axis, which consists of multiple connections, including the enteric nervous system, the vagus nerve, the immune system, endocrine signals, the microbiota, and its metabolites. Alteration of communications in the gut-brain axis is emerging as an overlooked cause of neuroinflammation. Neuroinflammation is a common feature of the pathogenic mechanisms involved in various neurodegenerative diseases (NDs) that are incurable and debilitating conditions resulting in progressive degeneration and death of neurons, such as in Alzheimer and Parkinson diseases. NDs are a leading cause of global death and disability, and the incidences are expected to increase in the following decades if prevention strategies and successful treatment remain elusive. To date, the etiology of NDs is unclear due to the complexity of the mechanisms of diseases involving genetic and environmental factors, including diet and microbiota. Emerging evidence suggests that changes in diet, alteration of the microbiota, and deregulation of metabolism in the intestinal epithelium influence the inflammatory status of the neurons linked to disease insurgence and progression. This review will describe the leading players of the so-called diet-microbiota-gut-brain (DMGB) axis in the context of NDs. We will report recent findings from studies in model organisms such as rodents and fruit flies that support the role of diets, commensals, and intestinal epithelial functions as an overlooked primary regulator of brain health. We will finish discussing the pivotal role of metabolisms of cellular organelles such as mitochondria and peroxisomes in maintaining the DMGB axis and how alteration of the latter can be used as early disease makers and novel therapeutic targets.
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Affiliation(s)
- Stephanie Makdissi
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
- IWK Health Centre, Department of Pediatrics, Halifax, Canada
| | - Brendon D. Parsons
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
| | - Francesca Di Cara
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
- IWK Health Centre, Department of Pediatrics, Halifax, Canada
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Stavrou MR, So SS, Finch AM, Ballouz S, Smith NJ. Gene expression analyses of TAS1R taste receptors relevant to the treatment of cardiometabolic disease. Chem Senses 2023; 48:bjad027. [PMID: 37539767 DOI: 10.1093/chemse/bjad027] [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: 12/15/2022] [Indexed: 08/05/2023] Open
Abstract
The sweet taste receptor (STR) is a G protein-coupled receptor (GPCR) responsible for mediating cellular responses to sweet stimuli. Early evidence suggests that elements of the STR signaling system are present beyond the tongue in metabolically active tissues, where it may act as an extraoral glucose sensor. This study aimed to delineate expression of the STR in extraoral tissues using publicly available RNA-sequencing repositories. Gene expression data was mined for all genes implicated in the structure and function of the STR, and control genes including highly expressed metabolic genes in relevant tissues, other GPCRs and effector G proteins with physiological roles in metabolism, and other GPCRs with expression exclusively outside the metabolic tissues. Since the physiological role of the STR in extraoral tissues is likely related to glucose sensing, expression was then examined in diseases related to glucose-sensing impairment such as type 2 diabetes. An aggregate co-expression network was then generated to precisely determine co-expression patterns among the STR genes in these tissues. We found that STR gene expression was negligible in human pancreatic and adipose tissues, and low in intestinal tissue. Genes encoding the STR did not show significant co-expression or connectivity with other functional genes in these tissues. In addition, STR expression was higher in mouse pancreatic and adipose tissues, and equivalent to human in intestinal tissue. Our results suggest that STR expression in mice is not representative of expression in humans, and the receptor is unlikely to be a promising extraoral target in human cardiometabolic disease.
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Affiliation(s)
- Mariah R Stavrou
- Orphan Receptor Laboratory, School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sean Souchiart So
- Orphan Receptor Laboratory, School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Angela M Finch
- Department of Pharmacology, School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sara Ballouz
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Computer Science and Engineering, Faculty of Engineering, UNSW Sydney, Sydney, NSW, Australia
| | - Nicola J Smith
- Orphan Receptor Laboratory, School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
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Shetty A, Lim S, Strell P, Steer CJ, Rivera-Mulia JC, Low WC. In Silico Stage-Matching of Human, Marmoset, Mouse, and Pig Embryos to Enhance Organ Development Through Interspecies Chimerism. Cell Transplant 2023; 32:9636897231158728. [PMID: 36929807 PMCID: PMC10026093 DOI: 10.1177/09636897231158728] [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: 03/18/2023] Open
Abstract
Currently, there is a significant shortage of transplantable organs for patients in need. Interspecies chimerism and blastocyst complementation are alternatives for generating transplantable human organs in host animals such as pigs to meet this shortage. While successful interspecies chimerism and organ generation have been observed between evolutionarily close species such as rat and mouse, barriers still exist for more distant species pairs such as human-mouse, marmoset-mouse, human-pig, and others. One of the proposed barriers to chimerism is the difference in developmental stages between the donor cells and the host embryo at the time the cells are introduced into the host embryo. Hence, there is a logical effort to stage-match the donor cells with the host embryos for enhancing interspecies chimerism. In this study, we used an in silico approach to simultaneously stage-match the early developing embryos of four species, including human, marmoset, mouse, and pig based on transcriptome similarities. We used an unsupervised clustering algorithm to simultaneously stage-match all four species as well as Spearman's correlation analyses to stage-match pairs of donor-host species. From our stage-matching analyses, we found that the four stages that best matched with each other are the human blastocyst (E6/E7), the gastrulating mouse embryo (E6-E6.75), the marmoset late inner cell mass, and the pig late blastocyst. We further demonstrated that human pluripotent stem cells best matched with the mouse post-implantation stages. We also performed ontology analysis of the genes upregulated and commonly expressed between donor-host species pairs at their best matched stages. The stage-matching results predicted by this study will inform in vivo and in vitro interspecies chimerism and blastocyst complementation studies and can be used to match donor cells with host embryos between multiple species pairs to enhance chimerism for organogenesis.
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Affiliation(s)
- Anala Shetty
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Seunghyun Lim
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Phoebe Strell
- Comparative and Molecular Biosciences Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Clifford J Steer
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Juan Carlos Rivera-Mulia
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Walter C Low
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
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13
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Bishop CR, Caten FT, Nakaya HI, Suhrbier A. Chikungunya patient transcriptional signatures faithfully recapitulated in a C57BL/6J mouse model. Front Immunol 2022; 13:1092370. [PMID: 36578476 PMCID: PMC9791225 DOI: 10.3389/fimmu.2022.1092370] [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: 11/08/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction An adult wild-type C57BL/6J mouse model of chikungunya virus (CHIKV) infection and disease has been extensively used to study the alphaviral arthritic immunopathology and to evaluate new interventions. How well mouse models recapitulate the gene expression profiles seen in humans remains controversial. Methods Herein we perform a comparative transcriptomics analysis using RNA-Seq datasets from the C57BL/6J CHIKV mouse model with datasets obtained from adults and children acutely infected with CHIKV. Results Despite sampling quite different tissues, peripheral blood from humans and feet from mice, gene expression profiles were quite similar, with an overlap of up to ≈50% for up-regulated single copy orthologue differentially expressed genes. Furthermore, high levels of significant concordance between mouse and human were seen for immune pathways and signatures, which were dominated by interferons, T cells and monocyte/macrophages. Importantly, predicted responses to a series of anti-inflammatory drug and biologic treatments also showed cogent similarities between species. Discussion Comparative transcriptomics and subsequent pathway analysis provides a detailed picture of how a given model recapitulates human gene expression. Using this method, we show that the C57BL/6J CHIKV mouse model provides a reliable and representative system in which to study CHIKV immunopathology and evaluate new treatments.
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Affiliation(s)
- Cameron R. Bishop
- Department of Infection and Inflammation, Queensland Institute of Medical Research, Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Felipe Ten Caten
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Helder I. Nakaya, ; Andreas Suhrbier,
| | - Andreas Suhrbier
- Department of Infection and Inflammation, Queensland Institute of Medical Research, Berghofer Medical Research Institute, Brisbane, QLD, Australia,Global Virus Network (GVN) Center of Excellence, Australian Infectious Disease Research Centre, Brisbane, QLD, Australia,*Correspondence: Helder I. Nakaya, ; Andreas Suhrbier,
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14
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Roe AL, Boyte ME, Elkins CA, Goldman VS, Heimbach J, Madden E, Oketch-Rabah H, Sanders ME, Sirois J, Smith A. Considerations for determining safety of probiotics: A USP perspective. Regul Toxicol Pharmacol 2022; 136:105266. [PMID: 36206977 PMCID: PMC10292223 DOI: 10.1016/j.yrtph.2022.105266] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/15/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
A history of safe use is a backbone of safety assessments for many current probiotic species, however, there is no global harmonization regarding requirements for establishing probiotic safety for use in foods and supplements. As probiotic manufacturers are increasingly seeking to use new strains, novel species, and next-generation probiotics, justification based on a significant history of use may be challenged. There are efforts underway by a variety of stakeholders, including the United States Pharmacopeia (USP), to develop best practices guidelines for assessing the quality and safety of probiotics. A current initiative of the USP seeks to provide expert advice specific to safety considerations for probiotics. Toward this goal, this review provides a helpful summary guide to global regulatory guidelines. We question the suitability of traditional animal toxicology studies designed for testing chemicals for relevance in assessing probiotic safety. This includes discussion of the use of excessive dose levels, the length of repeated dose toxicity studies needed, and the most suitable animal species used in toxicology studies. In addition, the importance of proper manufacturing practices with regard to final product safety are also included. Thus, an outline of essential parameters of a comprehensive safety assessment for a probiotic are provided.
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Affiliation(s)
- Amy L Roe
- The Procter & Gamble Company, Cincinnati, OH, USA.
| | | | - Chris A Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Virginia S Goldman
- Department of Dietary Supplements and Herbal Medicines, Science Division, US Pharmacopeial Convention, Rockville, MD, USA
| | | | - Emily Madden
- Department of Dietary Supplements and Herbal Medicines, Science Division, US Pharmacopeial Convention, Rockville, MD, USA
| | - Hellen Oketch-Rabah
- Department of Dietary Supplements and Herbal Medicines, Science Division, US Pharmacopeial Convention, Rockville, MD, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Sacramento, CA, USA
| | - Jay Sirois
- Consumer Health Products Association, Washington, DC, USA
| | - Amy Smith
- IFF Health & Biosciences, Wilmington, DE, USA
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15
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Raina P, Guinea R, Chatsirisupachai K, Lopes I, Farooq Z, Guinea C, Solyom CA, de Magalhães JP. GeneFriends: gene co-expression databases and tools for humans and model organisms. Nucleic Acids Res 2022; 51:D145-D158. [PMID: 36454018 PMCID: PMC9825523 DOI: 10.1093/nar/gkac1031] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022] Open
Abstract
Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring the relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have now updated the GeneFriends database and website. Here, we present the new version of GeneFriends, which includes gene and transcript co-expression networks based on RNA-seq data from 46 475 human and 34 322 mouse samples. The new database also encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on TCGA and GTEx projects and gene co-expression networks for additional seven model organisms (fruit fly, zebrafish, worm, rat, yeast, cow and chicken). GeneFriends is freely available at http://www.genefriends.org/.
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Affiliation(s)
- Priyanka Raina
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Rodrigo Guinea
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Zoya Farooq
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Cristina Guinea
- UCAL - Universidad de Ciencias y Artes de América Latina, Faculty of Design, Lima 15026, Perú
| | - Csaba-Attila Solyom
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
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16
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Pakalniškytė D, Schönberger T, Strobel B, Stierstorfer B, Lamla T, Schuler M, Lenter M. Rosa26-LSL-dCas9-VPR: a versatile mouse model for tissue specific and simultaneous activation of multiple genes for drug discovery. Sci Rep 2022; 12:19268. [PMID: 36357523 PMCID: PMC9649745 DOI: 10.1038/s41598-022-23127-7] [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: 06/29/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
Transgenic animals with increased or abrogated target gene expression are powerful tools for drug discovery research. Here, we developed a CRISPR-based Rosa26-LSL-dCas9-VPR mouse model for targeted induction of endogenous gene expression using different Adeno-associated virus (AAV) capsid variants for tissue-specific gRNAs delivery. To show applicability of the model, we targeted low-density lipoprotein receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9), either individually or together. We induced up to ninefold higher expression of hepatocellular proteins. In consequence of LDLR upregulation, plasma LDL levels almost abolished, whereas upregulation of PCSK9 led to increased plasma LDL and cholesterol levels. Strikingly, simultaneous upregulation of both LDLR and PCSK9 resulted in almost unaltered LDL levels. Additionally, we used our model to achieve expression of all α1-Antitrypsin (AAT) gene paralogues simultaneously. These results show the potential of our model as a versatile tool for optimized targeted gene expression, alone or in combination.
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Affiliation(s)
- Dalia Pakalniškytė
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Tanja Schönberger
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Benjamin Strobel
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Birgit Stierstorfer
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Nonclinical Drug Safety Germany, 88400 Biberach an der Riß, Germany
| | - Thorsten Lamla
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Discovery Research Coordination, 88400 Biberach an der Riß, Germany
| | - Michael Schuler
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
| | - Martin Lenter
- grid.420061.10000 0001 2171 7500Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400 Biberach an der Riß, Germany
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17
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Zhang Z, Bossila EA, Li L, Hu S, Zhao Y. Central gene transcriptional regulatory networks shaping monocyte development in bone marrow. Front Immunol 2022; 13:1011279. [PMID: 36304450 PMCID: PMC9595600 DOI: 10.3389/fimmu.2022.1011279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The development of monocytes in bone marrow is a complex process with multiple steps. We used RNA-seq data to analyze the transcriptome profiles in developing stages of monocytes, including hematopoietic stem cells (HSCs), common myeloid progenitors (CMPs), granulocyte-monocyte progenitors (GMPs), and monocytes. We found that genes related to potassium and other cation transmembrane activities and ion binding were upregulated during the differentiation of HSCs into CMPs. Protein transport and membrane surface functional molecules were significantly upregulated in the GMP stage. The CD42RAC and proteasome pathways are significantly upregulated during the development of HSCs into monocytes. Transcription factors Ank1, Runx2, Hmga2, Klf1, Nfia, and Bmyc were upregulated during the differentiation of HSCs into CMPs; Gfi1 and Hmgn2 were highly expressed during the differentiation of CMPs into GMPs; Seventeen transcription factors including Foxo1, Cdkn2d, Foxo3, Ep300, Pias1, Nfkb1, Creb1, Bcl6, Ppp3cb, Stat5b, Nfatc4, Mef2a, Stat6, Ifnar2, Irf7, Irf5, and Cebpb were identified as potentially involved in the development of GMPs into monocytes in mice and humans. In metabolism pathway regulation, HSCs have high glucose, lipid, and nucleic acid metabolism activities; CMPs mainly up regulate the TCA cycle related genes; and GMPs have extremely active metabolisms, with significantly elevated pentose phosphate pathway, TCA cycle, histidine metabolism, and purine metabolism. In the monocyte phase, the tricarboxylic acid (TCA) cycle is reduced, and the anaerobic glycolysis process becomes dominated. Overall, our studies offer the kinetics and maps of gene transcriptional expressions and cell metabolisms during monocyte development in bone marrow.
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Affiliation(s)
- Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Elhusseny A. Bossila
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Biotechnology Department, Faculty of Agriculture Al-Azhar University, Cairo, Egypt
| | - Ling Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regeneration, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regeneration, Beijing, China
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18
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Rucker R. Allometric Scaling: Comparison of Interspecies Nutritional Relationships and Requirements. J Nutr 2022; 152:2626-2627. [PMID: 36774128 PMCID: PMC9644180 DOI: 10.1093/jn/nxac189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Robert Rucker
- From the Department of Nutrition, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA.
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19
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Purushotham SS, Reddy NMN, D'Souza MN, Choudhury NR, Ganguly A, Gopalakrishna N, Muddashetty R, Clement JP. A perspective on molecular signalling dysfunction, its clinical relevance and therapeutics in autism spectrum disorder. Exp Brain Res 2022; 240:2525-2567. [PMID: 36063192 DOI: 10.1007/s00221-022-06448-x] [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: 06/01/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are neurodevelopmental disorders that have become a primary clinical and social concern, with a prevalence of 2-3% in the population. Neuronal function and behaviour undergo significant malleability during the critical period of development that is found to be impaired in ID/ASD. Human genome sequencing studies have revealed many genetic variations associated with ASD/ID that are further verified by many approaches, including many mouse and other models. These models have facilitated the identification of fundamental mechanisms underlying the pathogenesis of ASD/ID, and several studies have proposed converging molecular pathways in ASD/ID. However, linking the mechanisms of the pathogenic genes and their molecular characteristics that lead to ID/ASD has progressed slowly, hampering the development of potential therapeutic strategies. This review discusses the possibility of recognising the common molecular causes for most ASD/ID based on studies from the available models that may enable a better therapeutic strategy to treat ID/ASD. We also reviewed the potential biomarkers to detect ASD/ID at early stages that may aid in diagnosis and initiating medical treatment, the concerns with drug failure in clinical trials, and developing therapeutic strategies that can be applied beyond a particular mutation associated with ASD/ID.
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Affiliation(s)
- Sushmitha S Purushotham
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Neeharika M N Reddy
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Michelle Ninochka D'Souza
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - Nilpawan Roy Choudhury
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Anusa Ganguly
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Niharika Gopalakrishna
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Ravi Muddashetty
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - James P Clement
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India.
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20
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Bishop CR, Dumenil T, Rawle DJ, Le TT, Yan K, Tang B, Hartel G, Suhrbier A. Mouse models of COVID-19 recapitulate inflammatory pathways rather than gene expression. PLoS Pathog 2022; 18:e1010867. [PMID: 36155667 PMCID: PMC9536645 DOI: 10.1371/journal.ppat.1010867] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/06/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
How well mouse models recapitulate the transcriptional profiles seen in humans remains debatable, with both conservation and diversity identified in various settings. Herein we use RNA-Seq data and bioinformatics approaches to analyze the transcriptional responses in SARS-CoV-2 infected lungs, comparing 4 human studies with the widely used K18-hACE2 mouse model, a model where hACE2 is expressed from the mouse ACE2 promoter, and a model that uses a mouse adapted virus and wild-type mice. Overlap of single copy orthologue differentially expressed genes (scoDEGs) between human and mouse studies was generally poor (≈15-35%). Rather than being associated with batch, sample treatment, viral load, lung damage or mouse model, the poor overlaps were primarily due to scoDEG expression differences between species. Importantly, analyses of immune signatures and inflammatory pathways illustrated highly significant concordances between species. As immunity and immunopathology are the focus of most studies, these mouse models can thus be viewed as representative and relevant models of COVID-19.
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Affiliation(s)
- Cameron R. Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Daniel J. Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thuy T. Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Gunter Hartel
- Statistics Unit, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland, Australia
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21
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Goh TX, Tan SL, Roebuck MM, Teo SH, Kamarul T. A systematic review of EV-piRNA in human body fluid and its role in disease progression. Tissue Eng Part C Methods 2022; 28:511-528. [PMID: 35959742 DOI: 10.1089/ten.tec.2022.0092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The state of host cells is reflected in the cargo carried by their extracellular vesicles (EVs). This makes EV a potential source of biomarkers for human diseases. Piwi-interacting RNA (piRNA) regulates gene expression through epigenetic regulation and post-transcriptional gene silencing. Thus, piRNA profiles in EVs derived from human clinical samples could identify markers that characterize disease stages, and unveil their roles in disease pathology. This review aimed to report the expression profiles of EV-derived piRNA (EV-piRNA) in various human samples, as well as their role in each pathology. A systematic review was conducted to collate the findings of human EV-piRNA from original research articles published in indexed scientific journals up to 16th Feb 2022. Article searches were performed in PubMed, Web of Science, and Scopus databases, using a combination of keywords including 'EV' and 'piRNA'. A total of 775 non-redundant original articles were identified. After subjecting articles to inclusion and exclusion criteria, 34 articles were accepted for this review. The piRNA expression levels among the small RNA profiles of human-derived EVs range from 0.09% to 43.84%, with the lowest expression level reported in urine-derived EVs and the highest percentage in plasma-derived EVs. Differentially expressed EV-piRNAs have been identified in patients with specific disease conditions compared to their counterparts (healthy control), suggesting an association between piRNA and progression in various diseases. Seven articles identified piRNA putative target genes and/or the pathway enrichment of piRNA target genes, and one study demonstrated a direct tole of piRNA candidates in disease pathology. In conclusion, EV-piRNA has been isolated successfully from various human body fluids. EV-piRNA is a new research niche in human disease pathology. The expression profiles of EV-piRNA in various tissue types and disease conditions remain largely unexplored. Furthermore, there is currently a lack of guidelines on piRNA bioinformatics analysis, which could lead to inconsistent results and thus hinder the progression of piRNA discoveries. Lastly, the lack of published scientific evidence on the role of EV-piRNA supports the need for future research to focus on the functional analysis of EV-piRNA as part of the route in piRNA discoveries.
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Affiliation(s)
- Tuan Xin Goh
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Malaysia;
| | - Sik Loo Tan
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Malaysia;
| | - Margaret M Roebuck
- University of Liverpool Faculty of Health and Life Sciences, Department of Musculoskeletal & Ageing Science Institute of Life Course & Medical Sciences (ILCaMS) Faculty of Health & Life Sciences William Henry Duncan Building University of Liverpool, Liverpool, 6 West Derby Street Liverpool L7 8TX, United Kingdom of Great Britain and Northern Ireland;
| | - Seow-Hui Teo
- Division of Sports Injuries and Arthroscopic Surgery, National Orthopaedic Center of Excellence for Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, MALAYSIA., Division of Sports Injuries and Arthroscopic Surgery, National Orthopaedic Center of Excellence for Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Federal Territory, Kuala Lumpur, Malaysia;
| | - Tunku Kamarul
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Wilayah Persekutuan, Malaysia;
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22
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Rashmi R, Majumdar S. Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense-Antisense Gene Pair in Human Cancers. Noncoding RNA 2022; 8:ncrna8040051. [PMID: 35893234 PMCID: PMC9326536 DOI: 10.3390/ncrna8040051] [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: 04/05/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Human THAP9, which encodes a domesticated transposase of unknown function, and lncRNA THAP9-AS1 (THAP9-antisense1) are arranged head-to-head on opposite DNA strands, forming a sense and antisense gene pair. We predict that there is a bidirectional promoter that potentially regulates the expression of THAP9 and THAP9-AS1. Although both THAP9 and THAP9-AS1 are reported to be involved in various cancers, their correlative roles on each other’s expression has not been explored. We analyzed the expression levels, prognosis, and predicted biological functions of the two genes across different cancer datasets (TCGA, GTEx). We observed that although the expression levels of the two genes, THAP9 and THAP9-AS1, varied in different tumors, the expression of the gene pair was strongly correlated with patient prognosis; higher expression of the gene pair was usually linked to poor overall and disease-free survival. Thus, THAP9 and THAP9-AS1 may serve as potential clinical biomarkers of tumor prognosis. Further, we performed a gene co-expression analysis (using WGCNA) followed by a differential gene correlation analysis (DGCA) across 22 cancers to identify genes that share the expression pattern of THAP9 and THAP9-AS1. Interestingly, in both normal and cancer samples, THAP9 and THAP9-AS1 often co-express; moreover, their expression is positively correlated in each cancer type, suggesting the coordinated regulation of this H2H gene pair.
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23
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Nelson RS, Dammer EB, Santiago JV, Seyfried NT, Rangaraju S. Brain Cell Type-Specific Nuclear Proteomics Is Imperative to Resolve Neurodegenerative Disease Mechanisms. Front Neurosci 2022; 16:902146. [PMID: 35784845 PMCID: PMC9243337 DOI: 10.3389/fnins.2022.902146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 01/19/2023] Open
Abstract
Neurodegenerative diseases (NDs) involve complex cellular mechanisms that are incompletely understood. Emerging findings have revealed that disruption of nuclear processes play key roles in ND pathogenesis. The nucleus is a nexus for gene regulation and cellular processes that together, may underlie pathomechanisms of NDs. Furthermore, many genetic risk factors for NDs encode proteins that are either present in the nucleus or are involved in nuclear processes (for example, RNA binding proteins, epigenetic regulators, or nuclear-cytoplasmic transport proteins). While recent advances in nuclear transcriptomics have been significant, studies of the nuclear proteome in brain have been relatively limited. We propose that a comprehensive analysis of nuclear proteomic alterations of various brain cell types in NDs may provide novel biological and therapeutic insights. This may be feasible because emerging technical advances allow isolation and investigation of intact nuclei from post-mortem frozen human brain tissue with cell type-specific and single-cell resolution. Accordingly, nuclei of various brain cell types harbor unique protein markers which can be used to isolate cell-type specific nuclei followed by down-stream proteomics by mass spectrometry. Here we review the literature providing a rationale for investigating proteomic changes occurring in nuclei in NDs and then highlight the potential for brain cell type-specific nuclear proteomics to enhance our understanding of distinct cellular mechanisms that drive ND pathogenesis.
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Affiliation(s)
- Ruth S. Nelson
- Department of Neurology, Emory University, Atlanta, GA, United States
| | - Eric B. Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, United States
| | | | | | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, United States,*Correspondence: Srikant Rangaraju
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24
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Steenwyk JL, Phillips MA, Yang F, Date SS, Graham TR, Berman J, Hittinger CT, Rokas A. An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. SCIENCE ADVANCES 2022; 8:eabn0105. [PMID: 35507651 PMCID: PMC9067921 DOI: 10.1126/sciadv.abn0105] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
The evolutionary rates of functionally related genes often covary. We present a gene coevolution network inferred from examining nearly 3 million orthologous gene pairs from 332 budding yeast species spanning ~400 million years of evolution. Network modules provide insight into cellular and genomic structure and function. Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker's yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity. Mapping the network onto the chromosomes of S. cerevisiae and Candida albicans revealed that coevolving orthologous genes are not physically clustered in either species; rather, they are often located on different chromosomes or far apart on the same chromosome. The coevolution network captures the hierarchy of cellular structure and function, provides a roadmap for genotype-to-phenotype discovery, and portrays the genome as a linked ensemble of genes.
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Affiliation(s)
- Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Megan A. Phillips
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Feng Yang
- Shmunis School of Biomedical and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Swapneeta S. Date
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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25
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Touchant M, Labonté B. Sex-Specific Brain Transcriptional Signatures in Human MDD and Their Correlates in Mouse Models of Depression. Front Behav Neurosci 2022; 16:845491. [PMID: 35592639 PMCID: PMC9110970 DOI: 10.3389/fnbeh.2022.845491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/05/2022] [Indexed: 01/13/2023] Open
Abstract
Major depressive disorder (MDD) is amongst the most devastating psychiatric conditions affecting several millions of people worldwide every year. Despite the importance of this disease and its impact on modern societies, still very little is known about the etiological mechanisms. Treatment strategies have stagnated over the last decades and very little progress has been made to improve the efficiency of current therapeutic approaches. In order to better understand the disease, it is necessary for researchers to use appropriate animal models that reproduce specific aspects of the complex clinical manifestations at the behavioral and molecular levels. Here, we review the current literature describing the use of mouse models to reproduce specific aspects of MDD and anxiety in males and females. We first describe some of the most commonly used mouse models and their capacity to display unique but also shared features relevant to MDD. We then transition toward an integral description, combined with genome-wide transcriptional strategies. The use of these models reveals crucial insights into the molecular programs underlying the expression of stress susceptibility and resilience in a sex-specific fashion. These studies performed on human and mouse tissues establish correlates into the mechanisms mediating the impact of stress and the extent to which different mouse models of chronic stress recapitulate the molecular changes observed in depressed humans. The focus of this review is specifically to highlight the sex differences revealed from different stress paradigms and transcriptional analyses both in human and animal models.
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Affiliation(s)
- Maureen Touchant
- CERVO Brain Research Centre, Québec, QC, Canada
- Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Benoit Labonté
- CERVO Brain Research Centre, Québec, QC, Canada
- Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec, QC, Canada
- *Correspondence: Benoit Labonté
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26
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Tello JA, Williams HE, Eppler RM, Steinhilb ML, Khanna M. Animal Models of Neurodegenerative Disease: Recent Advances in Fly Highlight Innovative Approaches to Drug Discovery. Front Mol Neurosci 2022; 15:883358. [PMID: 35514431 PMCID: PMC9063566 DOI: 10.3389/fnmol.2022.883358] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases represent a formidable challenge to global health. As advances in other areas of medicine grant healthy living into later decades of life, aging diseases such as Alzheimer's disease (AD) and other neurodegenerative disorders can diminish the quality of these additional years, owed largely to the lack of efficacious treatments and the absence of durable cures. Alzheimer's disease prevalence is predicted to more than double in the next 30 years, affecting nearly 15 million Americans, with AD-associated costs exceeding $1 billion by 2050. Delaying onset of AD and other neurodegenerative diseases is critical to improving the quality of life for patients and reducing the burden of disease on caregivers and healthcare systems. Significant progress has been made to model disease pathogenesis and identify points of therapeutic intervention. While some researchers have contributed to our understanding of the proteins and pathways that drive biological dysfunction in disease using in vitro and in vivo models, others have provided mathematical, biophysical, and computational technologies to identify potential therapeutic compounds using in silico modeling. The most exciting phase of the drug discovery process is now: by applying a target-directed approach that leverages the strengths of multiple techniques and validates lead hits using Drosophila as an animal model of disease, we are on the fast-track to identifying novel therapeutics to restore health to those impacted by neurodegenerative disease.
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Affiliation(s)
- Judith A. Tello
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
| | - Haley E. Williams
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
| | - Robert M. Eppler
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - Michelle L. Steinhilb
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Center of Innovation in Brain Science, Tucson, AZ, United States
- Department of Molecular Pathobiology, New York University, New York, NY, United States
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27
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Powell G, Long H, Zolkiewski L, Dumbell R, Mallon AM, Lindgren CM, Simon MM. Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci. Biol Lett 2022; 18:20210630. [PMID: 35317627 PMCID: PMC8941414 DOI: 10.1098/rsbl.2021.0630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding the genetic aetiology of loci associated with a disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited in part by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarize the alignment of genomic (exonic and multi-cell regulatory) annotations alongside Mendelian and complex disease-associated variant sites between humans and mice. Our results highlight the importance of understanding evolutionary divergence in transcription regulation when interpreting functional studies using mice as models for human disease variants.
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Affiliation(s)
- George Powell
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK.,MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire OX11 0RD, UK
| | - Helen Long
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK.,MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire OX11 0RD, UK
| | - Louisa Zolkiewski
- MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire OX11 0RD, UK.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Rebecca Dumbell
- Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire OX11 0RD, UK
| | - Cecilia M Lindgren
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michelle M Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire OX11 0RD, UK
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28
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Vázquez-Domínguez I, Garanto A. Considerations for Generating Humanized Mouse Models to Test Efficacy of Antisense Oligonucleotides. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2434:267-279. [PMID: 35213024 DOI: 10.1007/978-1-0716-2010-6_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the last decades, animal models have become increasingly important in therapeutic drug development and assessment. The use of these models, mainly mice and rats, allow evaluating drugs in the real-organism environment and context. However, several molecular therapeutic approaches are sequence-dependent, and therefore, the humanization of such models is required to assess the efficacy. The generation of genetically modified humanized mouse models is often an expensive and laborious process that may not always recapitulate the human molecular and/or physiological phenotype. In this chapter, we summarize basic aspects to consider before designing and generating humanized models, especially when they are aimed to test antisense-based therapies.
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Affiliation(s)
- Irene Vázquez-Domínguez
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Alejandro Garanto
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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29
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Strell P, Shetty A, Steer CJ, Low WC. Interspecies Chimeric Barriers for Generating Exogenic Organs and Cells for Transplantation. Cell Transplant 2022; 31:9636897221110525. [PMID: 36173102 PMCID: PMC9527994 DOI: 10.1177/09636897221110525] [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] [Indexed: 11/29/2022] Open
Abstract
A growing need for organs and novel cell-based therapies has provided a niche for approaches like interspecies chimeras. To generate organs from one donor species in another host species requires techniques such as blastocyst complementation and gene editing to successfully create an embryo that has cells from both the donor and the host. However, the task of developing highly efficacious and competent interspecies chimeras is met by many challenges. These interspecies chimeric barriers impede the formation of chimeras, often leading to lower levels of chimeric competency. The barriers that need to be addressed include the evolutionary distance between species, stage-matching, temporal and spatial synchronization of developmental timing, interspecies cell competition and the survival of pluripotent stem cells and embryos, compatibility of ligand–receptor signaling between species, and the ethical concerns of forming such models. By overcoming the interspecies chimera barriers and creating highly competent chimeras, the technology of organ and cellular generation can be honed and refined to develop fully functioning exogenic organs, tissues, and cells for transplantation.
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Affiliation(s)
- Phoebe Strell
- Comparative and Molecular Bioscience Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Anala Shetty
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Clifford J Steer
- Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Department of Medicine, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Department of Genetics, Cell Biology and Genetics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Walter C Low
- Comparative and Molecular Bioscience Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota, Twin Cities, Minneapolis, MN, USA.,Department of Neurosurgery, University of Minnesota, Twin Cities, Minneapolis, MN, USA
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30
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Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology. J Neurosci 2021; 41:9008-9030. [PMID: 34462306 PMCID: PMC8549541 DOI: 10.1523/jneurosci.2534-20.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 06/18/2021] [Accepted: 07/10/2021] [Indexed: 12/14/2022] Open
Abstract
Recent large genome-wide association studies have identified multiple confident risk loci linked to addiction-associated behavioral traits. Most genetic variants linked to addiction-associated traits lie in noncoding regions of the genome, likely disrupting cis-regulatory element (CRE) function. CREs tend to be highly cell type-specific and may contribute to the functional development of the neural circuits underlying addiction. Yet, a systematic approach for predicting the impact of risk variants on the CREs of specific cell populations is lacking. To dissect the cell types and brain regions underlying addiction-associated traits, we applied stratified linkage disequilibrium score regression to compare genome-wide association studies to genomic regions collected from human and mouse assays for open chromatin, which is associated with CRE activity. We found enrichment of addiction-associated variants in putative CREs marked by open chromatin in neuronal (NeuN+) nuclei collected from multiple prefrontal cortical areas and striatal regions known to play major roles in reward and addiction. To further dissect the cell type-specific basis of addiction-associated traits, we also identified enrichments in human orthologs of open chromatin regions of female and male mouse neuronal subtypes: cortical excitatory, D1, D2, and PV. Last, we developed machine learning models to predict mouse cell type-specific open chromatin, enabling us to further categorize human NeuN+ open chromatin regions into cortical excitatory or striatal D1 and D2 neurons and predict the functional impact of addiction-associated genetic variants. Our results suggest that different neuronal subtypes within the reward system play distinct roles in the variety of traits that contribute to addiction.SIGNIFICANCE STATEMENT We combine statistical genetic and machine learning techniques to find that the predisposition to for nicotine, alcohol, and cannabis use behaviors can be partially explained by genetic variants in conserved regulatory elements within specific brain regions and neuronal subtypes of the reward system. Our computational framework can flexibly integrate open chromatin data across species to screen for putative causal variants in a cell type- and tissue-specific manner for numerous complex traits.
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Affiliation(s)
- Chaitanya Srinivasan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - BaDoi N Phan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Medical Scientist Training Program, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Alyssa J Lawler
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Easwaran Ramamurthy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Michael Kleyman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Ashley R Brown
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Irene M Kaplow
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Morgan E Wirthlin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Andreas R Pfenning
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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31
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O'Brien CB, Locklear CE, Glovak ZT, Zebadúa Unzaga D, Baghdoyan HA, Lydic R. Opioids cause dissociated states of consciousness in C57BL/6J mice. J Neurophysiol 2021; 126:1265-1275. [PMID: 34469699 DOI: 10.1152/jn.00266.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The electroencephalogram (EEG) provides an objective, neural correlate of consciousness. Opioid receptors modulate mammalian neuronal excitability, and this fact was used to characterize how opioids administered to mice alter EEG power and states of consciousness. The present study tested the hypothesis that antinociceptive doses of fentanyl, morphine, or buprenorphine differentially alter the EEG and states of sleep and wakefulness in adult, male C57BL/6J mice. Mice were anesthetized and implanted with telemeters that enabled wireless recordings of cortical EEG and electromyogram (EMG). After surgical recovery, EEG and EMG were used to objectively score states of consciousness as wakefulness, rapid eye movement (REM) sleep, or non-REM (NREM) sleep. Measures of EEG power (dB) were quantified as δ (0.5-4 Hz), θ (4-8 Hz), α (8-13 Hz), σ (12-15 Hz), β (13-30 Hz), and γ (30-60 Hz). Compared with saline (control), fentanyl and morphine decreased NREM sleep, morphine eliminated REM sleep, and buprenorphine eliminated NREM sleep and REM sleep. Opioids significantly and differentially disrupted the temporal organization of sleep/wake states, altered specific EEG frequency bands, and caused dissociated states of consciousness. The results are discussed relative to the fact that opioids, pain, and sleep modulate interacting states of consciousness.NEW & NOTEWORTHY This study discovered that antinociceptive doses of fentanyl, morphine, and buprenorphine significantly and differentially disrupt EEG-defined states of consciousness in C57BL/6J mice. These data are noteworthy because: 1) buprenorphine is commonly used in medication-assisted therapy for opioid addiction, and 2) there is evidence that disordered sleep can promote addiction relapse. The results contribute to community phenotyping efforts by making publicly available all descriptive and inferential statistics from this study (Supplemental Tables S1-S8).
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Affiliation(s)
| | | | - Zachary T Glovak
- Department of Psychology, The University of Tennessee, Knoxville, Tennessee
| | | | - Helen A Baghdoyan
- Department of Psychology, The University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Ralph Lydic
- Department of Psychology, The University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
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32
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Ovens K, Eames BF, McQuillan I. Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution. Front Genet 2021; 12:695399. [PMID: 34484293 PMCID: PMC8414652 DOI: 10.3389/fgene.2021.695399] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Similarities and differences in the associations of biological entities among species can provide us with a better understanding of evolutionary relationships. Often the evolution of new phenotypes results from changes to interactions in pre-existing biological networks and comparing networks across species can identify evidence of conservation or adaptation. Gene co-expression networks (GCNs), constructed from high-throughput gene expression data, can be used to understand evolution and the rise of new phenotypes. The increasing abundance of gene expression data makes GCNs a valuable tool for the study of evolution in non-model organisms. In this paper, we cover motivations for why comparing these networks across species can be valuable for the study of evolution. We also review techniques for comparing GCNs in the context of evolution, including local and global methods of graph alignment. While some protein-protein interaction (PPI) bioinformatic methods can be used to compare co-expression networks, they often disregard highly relevant properties, including the existence of continuous and negative values for edge weights. Also, the lack of comparative datasets in non-model organisms has hindered the study of evolution using PPI networks. We also discuss limitations and challenges associated with cross-species comparison using GCNs, and provide suggestions for utilizing co-expression network alignments as an indispensable tool for evolutionary studies going forward.
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Affiliation(s)
- Katie Ovens
- Augmented Intelligence & Precision Health Laboratory (AIPHL), Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - B. Frank Eames
- Department of Anatomy, Physiology, & Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ian McQuillan
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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33
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Bonilla DA, Moreno Y, Rawson ES, Forero DA, Stout JR, Kerksick CM, Roberts MD, Kreider RB. A Convergent Functional Genomics Analysis to Identify Biological Regulators Mediating Effects of Creatine Supplementation. Nutrients 2021; 13:2521. [PMID: 34444681 PMCID: PMC8397972 DOI: 10.3390/nu13082521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
Creatine (Cr) and phosphocreatine (PCr) are physiologically essential molecules for life, given they serve as rapid and localized support of energy- and mechanical-dependent processes. This evolutionary advantage is based on the action of creatine kinase (CK) isozymes that connect places of ATP synthesis with sites of ATP consumption (the CK/PCr system). Supplementation with creatine monohydrate (CrM) can enhance this system, resulting in well-known ergogenic effects and potential health or therapeutic benefits. In spite of our vast knowledge about these molecules, no integrative analysis of molecular mechanisms under a systems biology approach has been performed to date; thus, we aimed to perform for the first time a convergent functional genomics analysis to identify biological regulators mediating the effects of Cr supplementation in health and disease. A total of 35 differentially expressed genes were analyzed. We identified top-ranked pathways and biological processes mediating the effects of Cr supplementation. The impact of CrM on miRNAs merits more research. We also cautiously suggest two dose-response functional pathways (kinase- and ubiquitin-driven) for the regulation of the Cr uptake. Our functional enrichment analysis, the knowledge-based pathway reconstruction, and the identification of hub nodes provide meaningful information for future studies. This work contributes to a better understanding of the well-reported benefits of Cr in sports and its potential in health and disease conditions, although further clinical research is needed to validate the proposed mechanisms.
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Affiliation(s)
- Diego A. Bonilla
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogotá 110861, Colombia;
- Research Group in Biochemistry and Molecular Biology, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
- Research Group in Physical Activity, Sports and Health Sciences (GICAFS), Universidad de Córdoba, Montería 230002, Colombia
- kDNA Genomics, Joxe Mari Korta Research Center, University of the Basque Country UPV/EHU, 20018 Donostia-San Sebastián, Spain
| | - Yurany Moreno
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogotá 110861, Colombia;
- Research Group in Biochemistry and Molecular Biology, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
| | - Eric S. Rawson
- Department of Health, Nutrition and Exercise Science, Messiah University, Mechanicsburg, PA 17055, USA;
| | - Diego A. Forero
- Professional Program in Sport Training, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá 111221, Colombia;
| | - Jeffrey R. Stout
- Physiology of Work and Exercise Response (POWER) Laboratory, Institute of Exercise Physiology and Rehabilitation Science, University of Central Florida, Orlando, FL 32816, USA;
| | - Chad M. Kerksick
- Exercise and Performance Nutrition Laboratory, School of Health Sciences, Lindenwood University, Saint Charles, MO 63301, USA;
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA;
- Edward via College of Osteopathic Medicine, Auburn, AL 36849, USA
| | - Richard B. Kreider
- Exercise & Sport Nutrition Laboratory, Human Clinical Research Facility, Texas A&M University, College Station, TX 77843, USA;
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34
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Cui C, Zhou Y, Cui Q. Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation. Brief Bioinform 2021; 22:6314723. [PMID: 34226920 DOI: 10.1093/bib/bbab253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Animal models have a certain degree of similarity with human in genes and physiological processes, which leads them to be valuable tools for studying human diseases and for assisting drug development. However, translational researches adopting animal models are largely restricted by the species heterogeneity, which is also a major reason for the failure of drug research. Currently, computational method for exploring the functional differences between orthologous genes is still insufficient. For this purpose, here, we presented an algorithm, functional divergence score (FDS), by comprehensively evaluating the functional differences between the microRNAs regulating the paired orthologous genes. Given that mouse is one of the most popular model animals, currently, FDS was designed to dissect the functional divergence of orthologous genes between human and mouse. The results showed that gene FDS value is significantly associated with gene evolutionary characteristics and can discover expression divergence of human-mouse orthologous genes. Moreover, FDS performed well in distinguishing the targets of approved drugs and the failed ones. These results suggest that FDS is a valuable tool to evaluate the functional divergence of paired human and mouse orthologous genes. In addition, for each orthologous gene pair, FDS can provide detailed differences in functions and phenotypes. Our study provided a useful tool for quantifying the functional difference between human and mouse, and the presented framework is easily to be extended to the orthologous genes between human and other species. An online server of FDS is available at http://www.cuilab.cn/fds/.
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Affiliation(s)
- Chunmei Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
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35
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Ovens K, Maleki F, Eames BF, McQuillan I. Juxtapose: a gene-embedding approach for comparing co-expression networks. BMC Bioinformatics 2021; 22:125. [PMID: 33726666 PMCID: PMC7968242 DOI: 10.1186/s12859-021-04055-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Gene co-expression networks (GCNs) are not easily comparable due to their complex structure. In this paper, we propose a tool, Juxtapose, together with similarity measures that can be utilized for comparative transcriptomics between a set of organisms. While we focus on its application to comparing co-expression networks across species in evolutionary studies, Juxtapose is also generalizable to co-expression network comparisons across tissues or conditions within the same species. METHODS A word embedding strategy commonly used in natural language processing was utilized in order to generate gene embeddings based on walks made throughout the GCNs. Juxtapose was evaluated based on its ability to embed the nodes of synthetic structures in the networks consistently while also generating biologically informative results. Evaluation of the techniques proposed in this research utilized RNA-seq datasets from GTEx, a multi-species experiment of prefrontal cortex samples from the Gene Expression Omnibus, as well as synthesized datasets. Biological evaluation was performed using gene set enrichment analysis and known gene relationships in literature. RESULTS We show that Juxtapose is capable of globally aligning synthesized networks as well as identifying areas that are conserved in real gene co-expression networks without reliance on external biological information. Furthermore, output from a matching algorithm that uses cosine distance between GCN embeddings is shown to be an informative measure of similarity that reflects the amount of topological similarity between networks. CONCLUSIONS Juxtapose can be used to align GCNs without relying on known biological similarities and enables post-hoc analyses using biological parameters, such as orthology of genes, or conserved or variable pathways. AVAILABILITY A development version of the software used in this paper is available at https://github.com/klovens/juxtapose.
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Affiliation(s)
- Katie Ovens
- Department of Computer Science, University of Saskatchewan, Saskatoon, S7N 5C9 Canada
| | - Farhad Maleki
- Augmented Intelligence & Precision Health Laboratory (AIPHL), Research Institute of the McGill University Health Centre, Montreal, H4A 3S5 Canada
| | - B. Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Ian McQuillan
- Department of Computer Science, University of Saskatchewan, Saskatoon, S7N 5C9 Canada
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Optical Coherence Tomography Angiography Monitors Cutaneous Wound Healing under Angiogenesis-Promoting Treatment in Diabetic and Non-Diabetic Mice. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
During wound healing, the rapid re-establishment of a functional microcirculation in the wounded tissue is of utmost importance. We applied optical coherence tomography (OCT) angiography to evaluate vascular remodeling in an excisional wound model in the pinnae of C57BL/6 and db/db mice receiving different proangiogenic topical treatments. Analysis of the high-resolution OCT angiograms, including the four quantitative parameters vessel density, vessel length, number of bifurcations, and vessel tortuosity, revealed changes of the microvasculature and allowed identification of the overlapping wound healing phases hemostasis, inflammation, proliferation, and remodeling. Angiograms acquired in the inflammatory phase in the first days showed a dilation of vessels and recruitment of pre-existing capillaries. In the proliferative phase, angiogenesis with the sprouting of new capillaries into the wound tissue led to an increase of the OCT angiography parameters vessel density, normalized vessel length, number of bifurcations, and vessel tortuosity by 28–47%, 39–52%, 33–48%, and 3–8% versus baseline, respectively. After the peak observed on study days four to seven, the parameters slowly decreased but remained still elevated 18 days after wounding, indicating a continuing remodeling phase. Our study suggests that OCT angiography has the potential to serve as a valuable preclinical research tool in studies investigating impaired vascular remodeling during wound healing and potential new treatment strategies.
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Basson AR, Chen C, Sagl F, Trotter A, Bederman I, Gomez-Nguyen A, Sundrud MS, Ilic S, Cominelli F, Rodriguez-Palacios A. Regulation of Intestinal Inflammation by Dietary Fats. Front Immunol 2021; 11:604989. [PMID: 33603741 PMCID: PMC7884479 DOI: 10.3389/fimmu.2020.604989] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
With the epidemic of human obesity, dietary fats have increasingly become a focal point of biomedical research. Epidemiological studies indicate that high-fat diets (HFDs), especially those rich in long-chain saturated fatty acids (e.g., Western Diet, National Health Examination survey; NHANES 'What We Eat in America' report) have multi-organ pro-inflammatory effects. Experimental studies have confirmed some of these disease associations, and have begun to elaborate mechanisms of disease induction. However, many of the observed effects from epidemiological studies appear to be an over-simplification of the mechanistic complexity that depends on dynamic interactions between the host, the particular fatty acid, and the rather personalized genetics and variability of the gut microbiota. Of interest, experimental studies have shown that certain saturated fats (e.g., lauric and myristic fatty acid-rich coconut oil) could exert the opposite effect; that is, desirable anti-inflammatory and protective mechanisms promoting gut health by unanticipated pathways. Owing to the experimental advantages of laboratory animals for the study of mechanisms under well-controlled dietary settings, we focus this review on the current understanding of how dietary fatty acids impact intestinal biology. We center this discussion on studies from mice and rats, with validation in cell culture systems or human studies. We provide a scoping overview of the most studied diseases mechanisms associated with the induction or prevention of Inflammatory Bowel Disease in rodent models relevant to Crohn's Disease and Ulcerative Colitis after feeding either high-fat diet (HFD) or feed containing specific fatty acid or other target dietary molecule. Finally, we provide a general outlook on areas that have been largely or scarcely studied, and assess the effects of HFDs on acute and chronic forms of intestinal inflammation.
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Affiliation(s)
- Abigail R. Basson
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Christy Chen
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Filip Sagl
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Ashley Trotter
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Hospital Medicine, Pritzker School of Medicine, NorthShore University Health System, Chicago, IL, United States
| | - Ilya Bederman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Adrian Gomez-Nguyen
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Mark S. Sundrud
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States
| | - Sanja Ilic
- Department of Human Sciences, Human Nutrition, College of Education and Human Ecology, The Ohio State University, Columbus, OH, United States
| | - Fabio Cominelli
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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Pembroke WG, Hartl CL, Geschwind DH. Evolutionary conservation and divergence of the human brain transcriptome. Genome Biol 2021; 22:52. [PMID: 33514394 PMCID: PMC7844938 DOI: 10.1186/s13059-020-02257-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022] Open
Abstract
Background Mouse models have allowed for the direct interrogation of genetic effects on molecular, physiological, and behavioral brain phenotypes. However, it is unknown to what extent neurological or psychiatric traits may be human- or primate-specific and therefore which components can be faithfully recapitulated in mouse models. Results We compare conservation of co-expression in 116 independent data sets derived from human, mouse, and non-human primate representing more than 15,000 total samples. We observe greater changes occurring on the human lineage than mouse, and substantial regional variation that highlights cerebral cortex as the most diverged region. Glia, notably microglia, astrocytes, and oligodendrocytes are the most divergent cell type, three times more on average than neurons. We show that cis-regulatory sequence divergence explains a significant fraction of co-expression divergence. Moreover, protein coding sequence constraint parallels co-expression conservation, such that genes with loss of function intolerance are enriched in neuronal, rather than glial modules. We identify dozens of human neuropsychiatric and neurodegenerative disease risk genes, such as COMT, PSEN-1, LRRK2, SHANK3, and SNCA, with highly divergent co-expression between mouse and human and show that 3D human brain organoids recapitulate in vivo co-expression modules representing several human cell types. Conclusions We identify robust co-expression modules reflecting whole-brain and regional patterns of gene expression. Compared with those that represent basic metabolic processes, cell-type-specific modules, most prominently glial modules, are the most divergent between species. These data and analyses serve as a foundational resource to guide human disease modeling and its interpretation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-020-02257-z.
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Affiliation(s)
- William G Pembroke
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Christopher L Hartl
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA. .,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA. .,Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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Zhang J, Dulawa SC. The Utility of Animal Models for Studying the Metabo-Psychiatric Origins of Anorexia Nervosa. Front Psychiatry 2021; 12:711181. [PMID: 34721100 PMCID: PMC8551379 DOI: 10.3389/fpsyt.2021.711181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/17/2021] [Indexed: 11/15/2022] Open
Abstract
Anorexia nervosa (AN) is a severe eating disorder that primarily affects young women and girls, and is characterized by abnormal restrictive feeding and a dangerously low body-mass index. AN has one of the highest mortality rates of any psychiatric disorder, and no approved pharmacological treatments exist. Current psychological and behavioral treatments are largely ineffective, and relapse is common. Relatively little basic research has examined biological mechanisms that underlie AN compared to other major neuropsychiatric disorders. A recent large-scale genome-wide association study (GWAS) revealed that the genetic architecture of AN has strong metabolic as well as psychiatric origins, suggesting that AN should be reconceptualized as a metabo-psychiatric disorder. Therefore, identifying the metabo-psychiatric mechanisms that contribute to AN may be essential for developing effective treatments. This review focuses on animal models for studying the metabo-psychiatric mechanisms that may contribute to AN, with a focus on the activity-based anorexia (ABA) paradigm. We also highlight recent work using modern circuit-dissecting neuroscience techniques to uncover metabolic mechanisms that regulate ABA, and encourage further work to ultimately identify novel treatment strategies for AN.
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Affiliation(s)
- Jie Zhang
- Department of Psychiatry, University of California, San Diego, San Diego, CA, United States
| | - Stephanie C Dulawa
- Department of Psychiatry, University of California, San Diego, San Diego, CA, United States
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Lee J, Shah M, Ballouz S, Crow M, Gillis J. CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Res 2020; 48:W566-W571. [PMID: 32392296 PMCID: PMC7319556 DOI: 10.1093/nar/gkaa348] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.
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Affiliation(s)
- John Lee
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Manthan Shah
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Sara Ballouz
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd., Woodbury, NY 11797, USA
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Dolganova IN, Aleksandrova PV, Nikitin PV, Alekseeva AI, Chernomyrdin NV, Musina GR, Beshplav ST, Reshetov IV, Potapov AA, Kurlov VN, Tuchin VV, Zaytsev KI. Capability of physically reasonable OCT-based differentiation between intact brain tissues, human brain gliomas of different WHO grades, and glioma model 101.8 from rats. BIOMEDICAL OPTICS EXPRESS 2020; 11:6780-6798. [PMID: 33282523 PMCID: PMC7687948 DOI: 10.1364/boe.409692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 05/17/2023]
Abstract
Optical coherence tomography (OCT) of the ex vivo rat and human brain tissue samples is performed. The set of samples comprises intact white and gray matter, as well as human brain gliomas of the World Health Organization (WHO) Grades I-IV and glioma model 101.8 from rats. Analysis of OCT signals is aimed at comparing the physically reasonable properties of tissues, and determining the attenuation coefficient, parameter related to effective refractive index, and their standard deviations. Data analysis is based on the linear discriminant analysis and estimation of their dispersion in a four-dimensional principal component space. The results demonstrate the distinct contrast between intact tissues and low-grade gliomas and moderate contrast between intact tissues and high-grade gliomas. Particularly, the mean values of attenuation coefficient are 7.56±0.91, 3.96±0.98, and 5.71±1.49 mm-1 for human white matter, glioma Grade I, and glioblastoma, respectively. The significant variability of optical properties of high Grades and essential differences between rat and human brain tissues are observed. The dispersion of properties enlarges with increase of the glioma WHO Grade, which can be attributed to the growing heterogeneity of pathological brain tissues. The results of this study reveal the advantages and drawbacks of OCT for the intraoperative diagnosis of brain gliomas and compare its abilities separately for different grades of malignancy. The perspective of OCT to differentiate low-grade gliomas is highlighted by the low performance of the existing intraoperational methods and instruments.
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Affiliation(s)
- I. N. Dolganova
- Institute of Solid State Physics of the Russian Academy of Sciences, Chernogolovka 142432, Russia
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - P. V. Aleksandrova
- Institute of Solid State Physics of the Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - P. V. Nikitin
- Burdenko Neurosurgery Institute, Moscow 125047, Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | - A. I. Alekseeva
- Institute of Solid State Physics of the Russian Academy of Sciences, Chernogolovka 142432, Russia
- Research Institute of Human Morphology, Moscow 117418, Russia
| | - N. V. Chernomyrdin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | - G. R. Musina
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | - S. T. Beshplav
- Burdenko Neurosurgery Institute, Moscow 125047, Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | - I. V. Reshetov
- Institute for Cluster Oncology, Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
- Academy of Postgraduate Education FSCC FMBA, Moscow 125310, Russia
| | - A. A. Potapov
- Burdenko Neurosurgery Institute, Moscow 125047, Russia
| | - V. N. Kurlov
- Institute of Solid State Physics of the Russian Academy of Sciences, Chernogolovka 142432, Russia
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - V. V. Tuchin
- Saratov State University, Saratov 410012, Russia
- Institute of Precision Mechanics and Control of the Russian Academy of Sciences, Saratov 410028, Russia
- Tomsk State University, Tomsk 634050, Russia
| | - K. I. Zaytsev
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
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Tevlin R, Longaker MT, Wan DC. Skeletal Stem Cells-A Paradigm Shift in the Field of Craniofacial Bone Tissue Engineering. FRONTIERS IN DENTAL MEDICINE 2020; 1:596706. [PMID: 35664558 PMCID: PMC9161996 DOI: 10.3389/fdmed.2020.596706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Defects of the craniofacial skeleton arise as a direct result of trauma, diseases, oncological resection, or congenital anomalies. Current treatment options are limited, highlighting the importance for developing new strategies to restore form, function, and aesthetics of missing or damaged bone in the face and the cranium. For optimal reconstruction, the goal is to replace "like with like." With the inherent challenges of existing options, there is a clear need to develop alternative strategies to reconstruct the craniofacial skeleton. The success of mesenchymal stem cell-based approaches has been hampered by high heterogeneity of transplanted cell populations with inconsistent preclinical and clinical trial outcomes. Here, we discuss the novel characterization and isolation of mouse skeletal stem cell (SSC) populations and their response to injury, systemic disease, and how their re-activation in vivo can contribute to tissue regeneration. These studies led to the characterization of human SSCs which are able to self-renew, give rise to increasingly fate restricted progenitors, and differentiate into bone, cartilage, and bone marrow stroma, all on the clonal level in vivo without prior in vitro culture. SSCs hold great potential for implementation in craniofacial bone tissue engineering and regenerative medicine. As we begin to better understand the diversity and the nature of skeletal stem and progenitor cells, there is a tangible future whereby a subset of human adult SSCs can be readily purified from bone or activated in situ with broad potential applications in craniofacial tissue engineering.
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Affiliation(s)
- Ruth Tevlin
- Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Hagey Laboratory for Pediatric Regenerative Medicine, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Michael T. Longaker
- Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Hagey Laboratory for Pediatric Regenerative Medicine, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Derrick C. Wan
- Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Hagey Laboratory for Pediatric Regenerative Medicine, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
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Kashyap AS, Fernandez-Rodriguez L, Zhao Y, Monaco G, Trefny MP, Yoshida N, Martin K, Sharma A, Olieric N, Shah P, Stanczak M, Kirchhammer N, Park SM, Wieckowski S, Laubli H, Zagani R, Kasenda B, Steinmetz MO, Reinecker HC, Zippelius A. GEF-H1 Signaling upon Microtubule Destabilization Is Required for Dendritic Cell Activation and Specific Anti-tumor Responses. Cell Rep 2020; 28:3367-3380.e8. [PMID: 31553907 PMCID: PMC6876861 DOI: 10.1016/j.celrep.2019.08.057] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/06/2019] [Accepted: 08/16/2019] [Indexed: 12/31/2022] Open
Abstract
Dendritic cell (DC) activation is a critical step for anti-tumor T cell responses. Certain chemotherapeutics can influence DC function. Here we demonstrate that chemotherapy capable of microtubule destabilization has direct effects on DC function; namely, it induces potent DC maturation and elicits anti-tumor immunity. Guanine nucleotide exchange factor-H1 (GEF-H1) is specifically released upon microtubule destabilization and is required for DC activation. In response to chemotherapy, GEF-H1 drives a distinct cell signaling program in DCs dominated by the c-Jun N-terminal kinase (JNK) pathway and AP-1/ATF transcriptional response for control of innate and adaptive immune responses. Microtubule destabilization, and subsequent GEF-H1 signaling, enhances cross-presentation of tumor antigens to CD8 T cells. In absence of GEF-H1, anti-tumor immunity is hampered. In cancer patients, high expression of the GEF-H1 immune gene signature is associated with prolonged survival. Our study identifies an alternate intracellular axis in DCs induced upon microtubule destabilization in which GEF-H1 promotes protective anti-tumor immunity. Certain chemotherapeutics elicit potent anti-tumor immunity. Kashyap et al. demonstrate that microtubule-destabilizing chemotherapeutics induce maturation of dendritic cells through activation of microtubule-associated protein GEF-H1. This leads to effective priming of CD8 T cells against tumor antigens. GEF-H1 is critical for anti-tumor immunity of microtubule-targeting chemotherapy.
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Affiliation(s)
- Abhishek S Kashyap
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Laura Fernandez-Rodriguez
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Yun Zhao
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Gianni Monaco
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Marcel P Trefny
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Naohiro Yoshida
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kea Martin
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Ashwani Sharma
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Pankaj Shah
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michal Stanczak
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Nicole Kirchhammer
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Sung-Moo Park
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sebastien Wieckowski
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Heinz Laubli
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland; Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland
| | - Rachid Zagani
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kasenda
- Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland; University of Basel, Biozentrum, 4056 Basel, Switzerland
| | - Hans-Christian Reinecker
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Alfred Zippelius
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland; Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland.
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Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases. PLoS One 2020; 15:e0239219. [PMID: 32941527 PMCID: PMC7498011 DOI: 10.1371/journal.pone.0239219] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/01/2020] [Indexed: 01/10/2023] Open
Abstract
Neurodegenerative diseases (NDDs) are increasing serious menaces to human health in the recent years. Despite exhibiting different clinical phenotypes and selective neuronal loss, there are certain common features in these disorders, suggesting the presence of commonly dysregulated pathways. Identifying causal genes and dysregulated pathways can be helpful in providing effective treatment in these diseases. Interestingly, in spite of the considerable researches on NDDs, to the best of our knowledge, no dysregulated genes and/or pathways were reported in common across all the major NDDs so far. In this study, for the first time, we have applied the three-way interaction model, as an approach to unravel sophisticated gene interactions, to trace switch genes and significant pathways that are involved in six major NDDs. Subsequently, a gene regulatory network was constructed to investigate the regulatory communication of statistically significant triplets. Finally, KEGG pathway enrichment analysis was applied to find possible common pathways. Because of the central role of neuroinflammation and immune system responses in both pathogenic and protective mechanisms in the NDDs, we focused on immune genes in this study. Our results suggest that "cytokine-cytokine receptor interaction" pathway is enriched in all of the studied NDDs, while "osteoclast differentiation" and "natural killer cell mediated cytotoxicity" pathways are enriched in five of the NDDs each. The results of this study indicate that three pathways that include "osteoclast differentiation", "natural killer cell mediated cytotoxicity" and "cytokine-cytokine receptor interaction" are common in five, five and six NDDs, respectively. Additionally, our analysis showed that Rps27a as a switch gene, together with the gene pair {Il-18, Cx3cl1} form a statistically significant and biologically relevant triplet in the major NDDs. More specifically, we suggested that Cx3cl1 might act as a potential upstream regulator of Il-18 in microglia activation, and in turn, might be controlled with Rps27a in triggering NDDs.
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Valadão PAC, Santos KBS, Ferreira E Vieira TH, Macedo E Cordeiro T, Teixeira AL, Guatimosim C, de Miranda AS. Inflammation in Huntington's disease: A few new twists on an old tale. J Neuroimmunol 2020; 348:577380. [PMID: 32896821 DOI: 10.1016/j.jneuroim.2020.577380] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 12/15/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disease characterized by prominent loss of neurons in the striatum and cortex. Traditionally research in HD has focused on brain changes as they cause progressive motor dysfunction, cognitive decline and psychiatric disorders. The discovery that huntingtin protein (HTT) and its mutated form (mHTT) are expressed not only in the brain but also in different organs and tissues paved the way for the hypothesis that HD might affect regions beyond the central nervous system (CNS). Besides pathological deposition of mHTT, other mechanisms, including inflammation, seem to underlie HD pathogenesis and progression. Altered inflammation can be evidenced even before the onset of classical symptoms of HD. Herein, we will discuss current pre-clinical and clinical evidence on immune/inflammatory changes in peripheral organs during HD development and progression. The understanding of the impact of inflammation on peripheral organs may open new venues for the development of novel therapeutic targets in HD.
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Affiliation(s)
| | - Kívia Barretos S Santos
- Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Talita Hélen Ferreira E Vieira
- Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Departamento de Fisioterapia, Faculdade Sete Lagoas, Sete Lagoas, MG, Brazil
| | - Thiago Macedo E Cordeiro
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Antonio Lucio Teixeira
- Santa Casa BH Ensino e Pesquisa, Belo Horizonte, Brazil; Neuropsychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Cristina Guatimosim
- Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Aline Silva de Miranda
- Departamento de Morfologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, UFMG, Belo Horizonte, Minas Gerais, Brazil.
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Pan D, Hunter DA, Schellhardt L, Fuchs A, Halevi AE, Snyder-Warwick AK, Mackinnon SE, Wood MD. T cells modulate IL-4 expression by eosinophil recruitment within decellularized scaffolds to repair nerve defects. Acta Biomater 2020; 112:149-163. [PMID: 32434080 DOI: 10.1016/j.actbio.2020.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 12/20/2022]
Abstract
Decellularized nerve, or acellular nerve allografts (ANAs), are an increasingly used alternative to nerve autografts to repair nerve gaps to facilitate regeneration. The adaptive immune system, specifically T cells, plays a role in promoting regeneration upon these ANA scaffolds. However, how T cells promote regeneration across ANAs is not clear. Here, we show that T cells accumulate within ANAs repairing nerve gaps resulting in regulation of cytokine expression within the ANA environment. This in turn ultimately leads to robust nerve regeneration and functional recovery. Nerve regeneration across ANAs and functional recovery in Rag1KO mice was limited compared to wild-type (WT) mice. Prior to appreciable nerve regeneration, ANAs from Rag1KO mice contained fewer eosinophils and reduced IL-4 expression compared to ANAs from WT mice. During this period, both T cells and eosinophils regulated IL-4 expression within ANAs. Eosinophils represented the majority of IL-4 expressing cells within ANAs, while T cells regulated IL-4 expression. Finally, an essential role for IL-4 during nerve regeneration across ANAs was confirmed as nerves repaired using ANAs had reduced regeneration in IL-4 KO mice compared to WT mice. Our data demonstrate T cells regulate the expression of IL-4 within the ANA environment via their effects on eosinophils. STATEMENT OF SIGNIFICANCE: The immune system has been emerging as a critical component for tissue regeneration, especially when regeneration is supported upon biomaterials. The role of T cells, and their roles in the regeneration of nerve repaired with biomaterials, is still unclear. We demonstrated that when nerves are repaired with decellularized nerve scaffolds, T cells contribute to regeneration by regulating cytokines. We focused on their regulation of cytokine IL-4. Unexpectedly, T cells do not produce IL-4, but instead regulate IL-4 by recruiting eosinophils, which are major cellular sources of IL-4 within these scaffolds. Thus, our work demonstrated how IL-4 is regulated in a model biomaterial, and has implications for improving the design of biomaterials and understanding immune responses to biomaterials.
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Affiliation(s)
- Deng Pan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Daniel A Hunter
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Lauren Schellhardt
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Anja Fuchs
- Section of Acute and Critical Care Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexandra E Halevi
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Alison K Snyder-Warwick
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Susan E Mackinnon
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Matthew D Wood
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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Pei J, Harakalova M, Treibel TA, Lumbers RT, Boukens BJ, Efimov IR, van Dinter JT, González A, López B, El Azzouzi H, van den Dungen N, van Dijk CGM, Krebber MM, den Ruijter HM, Pasterkamp G, Duncker DJ, Nieuwenhuis EES, de Weger R, Huibers MM, Vink A, Moore JH, Moon JC, Verhaar MC, Kararigas G, Mokry M, Asselbergs FW, Cheng C. H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts. Clin Epigenetics 2020; 12:106. [PMID: 32664951 PMCID: PMC7362435 DOI: 10.1186/s13148-020-00895-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND H3K27ac histone acetylome changes contribute to the phenotypic response in heart diseases, particularly in end-stage heart failure. However, such epigenetic alterations have not been systematically investigated in remodeled non-failing human hearts. Therefore, valuable insight into cardiac dysfunction in early remodeling is lacking. This study aimed to reveal the acetylation changes of chromatin regions in response to myocardial remodeling and their correlations to transcriptional changes of neighboring genes. RESULTS We detected chromatin regions with differential acetylation activity (DARs; Padj. < 0.05) between remodeled non-failing patient hearts and healthy donor hearts. The acetylation level of the chromatin region correlated with its RNA polymerase II occupancy level and the mRNA expression level of its adjacent gene per sample. Annotated genes from DARs were enriched in disease-related pathways, including fibrosis and cell metabolism regulation. DARs that change in the same direction have a tendency to cluster together, suggesting the well-reorganized chromatin architecture that facilitates the interactions of regulatory domains in response to myocardial remodeling. We further show the differences between the acetylation level and the mRNA expression level of cell-type-specific markers for cardiomyocytes and 11 non-myocyte cell types. Notably, we identified transcriptome factor (TF) binding motifs that were enriched in DARs and defined TFs that were predicted to bind to these motifs. We further showed 64 genes coding for these TFs that were differentially expressed in remodeled myocardium when compared with controls. CONCLUSIONS Our study reveals extensive novel insight on myocardial remodeling at the DNA regulatory level. Differences between the acetylation level and the transcriptional level of cell-type-specific markers suggest additional mechanism(s) between acetylome and transcriptome. By integrating these two layers of epigenetic profiles, we further provide promising TF-encoding genes that could serve as master regulators of myocardial remodeling. Combined, our findings highlight the important role of chromatin regulatory signatures in understanding disease etiology.
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Affiliation(s)
- Jiayi Pei
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Thomas A Treibel
- Institute of Cardiovascular Science, University College London, London, UK
| | - R Thomas Lumbers
- Institute of Cardiovascular Science, University College London, London, UK
| | | | - Igor R Efimov
- Department of Biomedical Engineering, GWU, Washington, D.C, USA
| | - Jip T van Dinter
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Arantxa González
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Begoña López
- Program of Cardiovascular Diseases, CIMA Universidad de Navarra and IdiSNA, Pamplona, Spain
- CIBERCV, Carlos III Institute of Health, Madrid, Spain
| | - Hamid El Azzouzi
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | | | - Christian G M van Dijk
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Merle M Krebber
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Hester M den Ruijter
- Department of Experimental Cardiology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Hematology, UMC Utrecht, Utrecht, Netherlands
| | - Dirk J Duncker
- Division of Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Roel de Weger
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Manon M Huibers
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Aryan Vink
- Department of Pathology, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Jason H Moore
- Institute for Biomedical Informatics, UPENN, Philadelphia, USA
| | - James C Moon
- Institute of Cardiovascular Science, University College London, London, UK
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Georgios Kararigas
- Charité - Universitätsmedizin Berlin, and DZHK (German Centre for Cardiovascular Research), partner site, Berlin, Germany
| | - Michal Mokry
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Laboratory of Clinical Chemistry and Hematology, UMC Utrecht, Utrecht, Netherlands.
- Division of Paediatrics, UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Institute of Cardiovascular Science, Faculty of Population Health Science, University College London, London, UK.
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK.
| | - Caroline Cheng
- Department of Nephrology and Hypertension, DIGD, UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Regenerative Medicine Utrecht (RMU), UMC Utrecht, University of Utrecht, Utrecht, Netherlands.
- Division of Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, Rotterdam, Netherlands.
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Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. Sci Rep 2020; 10:10882. [PMID: 32616808 PMCID: PMC7331712 DOI: 10.1038/s41598-020-67878-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022] Open
Abstract
The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil microorganisms have evolved a variety of ways to adapt to environmental perturbations, including regulation of gene expression. However, it is challenging to untangle the complex phenotypic response of the soil to environmental change, partly due to the absence of predictive modeling frameworks that can mechanistically link molecular-level changes in soil microorganisms to a community’s functional phenotypes (or metaphenome). Towards filling this gap, we performed a combined analysis of metabolic and gene co-expression networks to explore how the soil microbiome responded to changes in soil moisture and nutrient conditions and to determine which genes were expressed under a given condition. Our integrated modeling approach revealed previously unknown, but critically important aspects of the soil microbiomes’ response to environmental perturbations. Incorporation of metabolomic and transcriptomic data into metabolic reaction networks identified condition-specific signature genes that are uniquely associated with dry, wet, and glycine-amended conditions. A subsequent gene co-expression network analysis revealed that drought-associated genes occupied more central positions in a network model of the soil community, compared to the genes associated with wet, and glycine-amended conditions. These results indicate the occurrence of system-wide metabolic coordination when soil microbiomes cope with moisture or nutrient perturbations. Importantly, the approach that we demonstrate here to analyze large-scale multi-omics data from a natural soil environment is applicable to other microbiome systems for which multi-omics data are available.
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Chowdhury HA, Bhattacharyya DK, Kalita JK. (Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1154-1173. [PMID: 30668502 DOI: 10.1109/tcbb.2019.2893170] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Analysis of gene expression data is widely used in transcriptomic studies to understand functions of molecules inside a cell and interactions among molecules. Differential co-expression analysis studies diseases and phenotypic variations by finding modules of genes whose co-expression patterns vary across conditions. We review the best practices in gene expression data analysis in terms of analysis of (differential) co-expression, co-expression network, differential networking, and differential connectivity considering both microarray and RNA-seq data along with comparisons. We highlight hurdles in RNA-seq data analysis using methods developed for microarrays. We include discussion of necessary tools for gene expression analysis throughout the paper. In addition, we shed light on scRNA-seq data analysis by including preprocessing and scRNA-seq in co-expression analysis along with useful tools specific to scRNA-seq. To get insights, biological interpretation and functional profiling is included. Finally, we provide guidelines for the analyst, along with research issues and challenges which should be addressed.
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Vaneechoutte D, Vandepoele K. Curse: building expression atlases and co-expression networks from public RNA-Seq data. Bioinformatics 2020; 35:2880-2881. [PMID: 30590391 DOI: 10.1093/bioinformatics/bty1052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/26/2018] [Accepted: 12/20/2018] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Public RNA-Sequencing (RNA-Seq) datasets are a valuable resource for transcriptome analyses, but their accessibility is hindered by the imperfect quality and presentation of their metadata and by the complexity of processing raw sequencing data. The Curse suite was created to alleviate these problems. It consists of an online curation tool named Curse to efficiently build compendia of experiments hosted on the Sequence Read Archive, and a lightweight pipeline named Prose to download and process the RNA-Seq data into expression atlases and co-expression networks. Curse networks showed improved linking of functionally related genes compared to the state-of-the-art. AVAILABILITY AND IMPLEMENTATION Curse, Prose and their manuals are available at http://bioinformatics.psb.ugent.be/webtools/Curse/. Prose was implemented in Java. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dries Vaneechoutte
- VIB Center for Plant Systems Biology, VIB, Ghent B, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B, Belgium
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, VIB, Ghent B, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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