1
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Ronan G, Bahcecioglu G, Yang J, Zorlutuna P. Cardiac tissue-resident vesicles differentially modulate anti-fibrotic phenotype by age and sex through synergistic miRNA effects. Biomaterials 2024; 311:122671. [PMID: 38941684 DOI: 10.1016/j.biomaterials.2024.122671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024]
Abstract
Aging is a risk factor for cardiovascular disease, the leading cause of death worldwide. Cardiac fibrosis is a harmful result of repeated myocardial infarction that increases risk of morbidity and future injury. Interestingly, both rates and outcomes of cardiac fibrosis differ between young and aged individuals, as well as men and women. Here, for the first time, we identify and isolate matrix-bound extracellular vesicles from the left ventricles (LVs) of young or aged males and females in both human and murine models. These LV vesicles (LVVs) show differences in morphology and content between these four cohorts in both humans and mice. LVV effects on fibrosis were also investigated in vitro, and aged male LVVs were pro-fibrotic while other LVVs were anti-fibrotic. From these LVVs, we could identify therapeutic miRNAs to promote anti-fibrotic effects. Four miRNAs were identified and together, but not individually, demonstrated significant cardioprotective effects when transfected. This suggests that miRNA synergy can regulate cell response, not just individual miRNAs, and also indicates that biological agent-associated therapeutic effects may be recapitulated using non-immunologically active agents. Furthermore, that chronic changes in LVV miRNA content may be a major factor in sex- and age-dependent differences in clinical outcomes of cardiac fibrosis.
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Affiliation(s)
- George Ronan
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, 46556, USA; Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Gokhan Bahcecioglu
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, 46556, USA
| | - Jun Yang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Pinar Zorlutuna
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, 46556, USA; Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, 46556, USA; Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
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2
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Hofman B, Szyda J, Frąszczak M, Mielczarek M. Long non-coding RNA variability in porcine skeletal muscle. J Appl Genet 2024; 65:565-573. [PMID: 38539022 DOI: 10.1007/s13353-024-00860-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/14/2024] [Accepted: 03/21/2024] [Indexed: 08/09/2024]
Abstract
Recently, numerous studies including various tissues have been carried out on long non-coding RNAs (lncRNAs), but still, its variability has not yet been fully understood. In this study, we characterised the inter-individual variability of lncRNAs in pigs, in the context of number, length and expression. Transcriptomes collected from muscle tissue belonging to six Polish Landrace boars (PL1-PL6), including half-brothers (PL1-PL3), were investigated using bioinformatics (lncRNA identification and functional analysis) and statistical (lncRNA variability) methods. The number of lncRNA ranged from 1289 to 3500 per animal, and the total number of common lncRNAs among all boars was 232. The number, length and expression of lncRNAs significantly varied between individuals, and no consistent pattern has been found between pairs of half-brothers. In detail, PL5 exhibits lower expression than the others, while PL4 has significantly higher expression than PL2-PL3 and PL5-PL6. Noteworthy, comparing the inter-individual variability of lncRNA and mRNA expression, they exhibited concordant patterns. The enrichment analysis for common lncRNA target genes determined a variety of biological processes that play fundamental roles in cell biology, and they were mostly related to whole-body homeostasis maintenance, energy and protein synthesis as well as dynamics of multiple nucleoprotein complexes. The high variability of lncRNA landscape in the porcine genome has been revealed in this study. The inter-individual differences have been found in the context of three aspects: the number, length and expression of lncRNAs, which contribute to a better understanding of its complex nature.
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Affiliation(s)
- Bartłomiej Hofman
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Joanna Szyda
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Magdalena Frąszczak
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - Magda Mielczarek
- Biostatistics Group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland.
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3
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Madan A, Kelly KP, Bahk P, Sullivan CE, Poling ME, Brent AE, Alassaf M, Dubrulle J, Rajan A. Atg8/LC3 controls systemic nutrient surplus signaling in flies and humans. Curr Biol 2024; 34:3327-3341.e9. [PMID: 38955177 PMCID: PMC11303106 DOI: 10.1016/j.cub.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 04/26/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
Organisms experience constant nutritional flux. Mechanisms at the interface of opposing nutritional states-scarcity and surplus-enable organismal energy homeostasis. Contingent on nutritional stores, adipocytes secrete adipokines, such as the fat hormone leptin, to signal nutrient status to the central brain. Increased leptin secretion underlies metabolic dysregulation during common obesity, but the molecular mechanisms regulating leptin secretion from human adipocytes are poorly understood. Here, we report that Atg8/LC3 family proteins, best known for their role in autophagy during nutrient scarcity, play an evolutionarily conserved role during nutrient surplus by promoting adipokine secretion. We show that in a well-fed state, Atg8/LC3 promotes the secretion of the Drosophila functional leptin ortholog unpaired 2 (Upd2) and leptin from human adipocytes. Proteomic analyses reveal that LC3 directs leptin to a secretory pathway in human cells. We identified LC3-dependent extracellular vesicle (EV) loading and secretion (LDELS) as a required step for leptin release, highlighting a unique secretory route adopted by leptin in human adipocytes. In Drosophila, mutations to Upd2's Atg8 interaction motif (AIM) result in constitutive adipokine retention. Atg8-mediated Upd2 retention alters lipid storage and hunger response and rewires the bulk organismal transcriptome in a manner conducive to starvation survival. Thus, Atg8/LC3's bidirectional role in nutrient sensing-conveying nutrient surplus and responding to nutrient deprivation-enables organisms to manage nutrient flux effectively. We posit that decoding how bidirectional molecular switches-such as Atg8/LC3-operate at the nexus of nutritional scarcity and surplus will inform therapeutic strategies to tackle chronic metabolic disorders.
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Affiliation(s)
- Aditi Madan
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Kevin P Kelly
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Patrick Bahk
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | | | | | - Ava E Brent
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Mroj Alassaf
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Julien Dubrulle
- Cellular Imaging Core, Shared Resources, Fred Hutch, Seattle, WA 98109, USA
| | - Akhila Rajan
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA.
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4
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Zhou Y, Tabib T, Huang M, Yuan K, Kim Y, Morse C, Sembrat J, Valenzi E, Lafyatis R. Molecular Changes Implicate Angiogenesis and Arterial Remodeling in Systemic Sclerosis-Associated and Idiopathic Pulmonary Hypertension. Arterioscler Thromb Vasc Biol 2024; 44:e210-e225. [PMID: 38841857 PMCID: PMC11269037 DOI: 10.1161/atvbaha.123.320005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Pulmonary hypertension (PH) is a common complication of systemic sclerosis (SSc) and a leading cause of mortality among patients with this disease. PH can also occur as an idiopathic condition (idiopathic pulmonary arterial hypertension). Investigation of transcriptomic alterations in vascular populations is critical to elucidating cellular mechanisms underlying pathobiology of SSc-associated and idiopathic PH. METHODS We analyzed single-cell RNA sequencing profiles of endothelial and perivascular mesenchymal populations from explanted lung tissue of patients with SSc-associated PH (n=16), idiopathic pulmonary arterial hypertension (n=3), and healthy controls (n=15). Findings were validated by immunofluorescence staining of explanted human lung tissue. RESULTS Three disease-associated endothelial populations emerged. Two angiogenic endothelial cell (EC) subtypes markedly expanded in SSc-associated PH lungs: tip ECs expressing canonical tip markers PGF and APLN and phalanx ECs expressing genes associated with vascular development, endothelial barrier integrity, and Notch signaling. Gene regulatory network analysis suggested enrichment of Smad1 (SMAD family member 1) and PPAR-γ (peroxisome proliferator-activated receptor-γ) regulon activities in these 2 populations, respectively. Mapping of potential ligand-receptor interactions highlighted Notch, apelin-APJ (apelin receptor), and angiopoietin-Tie (tyrosine kinase with immunoglobulin-like and EGF-like domains 1) signaling pathways between angiogenic ECs and perivascular cells. Transitional cells, expressing both endothelial and pericyte/smooth muscle cell markers, provided evidence for the presence of endothelial-to-mesenchymal transition. Transcriptional programs associated with arterial endothelial dysfunction implicated VEGF-A (vascular endothelial growth factor-A), TGF-β1 (transforming growth factor beta-1), angiotensin, and TNFSF12 (tumor necrosis factor ligand superfamily member 12)/TWEAK (TNF-related weak inducer of apoptosis) in the injury/remodeling phenotype of PH arterial ECs. CONCLUSIONS These data provide high-resolution insights into the complexity and plasticity of the pulmonary endothelium in SSc-associated PH and idiopathic pulmonary arterial hypertension and provide direct molecular insights into soluble mediators and transcription factors driving PH vasculopathy.
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Affiliation(s)
- Yuechen Zhou
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
- School of Medicine, Tsinghua University; Beijing 100084, China
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Ke Yuan
- Division of Pulmonary Medicine, Boston Children’s Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Yunhye Kim
- Division of Pulmonary Medicine, Boston Children’s Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh; Pittsburgh, PA 15261, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh; Pittsburgh, PA 15261, USA
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5
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Ott BD, Hulse-Kemp AM, Duke MV, Griffin MJ, Peterson BC, Scheffler BE, Torrans EL, Allen PJ. Hypothalamic transcriptome response to simulated diel earthen pond hypoxia cycles in channel catfish ( Ictalurus punctatus). Physiol Genomics 2024; 56:519-530. [PMID: 38808773 DOI: 10.1152/physiolgenomics.00007.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/03/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024] Open
Abstract
Commercial culture of channel catfish (Ictalurus punctatus) occurs in earthen ponds that are characterized by diel swings in dissolved oxygen concentration that can fall to severe levels of hypoxia, which can suppress appetite and lead to suboptimal growth. Given the significance of the hypothalamus in regulating these processes in other fishes, an investigation into the hypothalamus transcriptome was conducted to identify specific genes and expression patterns responding to hypoxia. Channel catfish in normoxic water were compared with catfish subjected to 12 h of hypoxia (20% oxygen saturation; 1.8 mg O2/L; 27°C) followed by 12 h of recovery in normoxia to mimic 24 h in a catfish aquaculture pond. Fish were sampled at 0-, 6-, 12-, 18-, and 24-h timepoints, with the 6- and 12-h samplings occurring during hypoxia. A total of 190 genes were differentially expressed during the experiment, with most occurring during hypoxia and returning to baseline values within 6 h of normoxia. Differentially expressed genes were sorted by function into Gene Ontology biological processes and revealed that most were categorized as "response to hypoxia," "sprouting angiogenesis," and "cellular response to xenobiotic stimulus." The patterns of gene expression reported here suggest that transcriptome responses to hypoxia are broad and quickly reversibly with the onset of normoxia. Although no genes commonly reported to modulate appetite were found to be differentially expressed in this experiment, several candidates were identified for future studies investigating the interplay between hypoxia and appetite in channel catfish, including adm, igfbp1a, igfbp7, and stc2b.NEW & NOTEWORTHY Channel catfish are an economically important species that experience diel episodic periods of hypoxia that can reduce appetite. This is the first study to investigate their transcriptome from the hypothalamus in a simulated 24-h span in a commercial catfish pond, with 12 h of hypoxia and 12 h of normoxia. The research revealed functional groups of genes relating to hypoxia, angiogenesis, and glycolysis as well as individual target genes possibly involved in appetite regulation.
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Affiliation(s)
- Brian D Ott
- Warmwater Aquaculture Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Mary V Duke
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Matt J Griffin
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, United States
| | - Brian C Peterson
- National Cold Water Marine Aquaculture Center, Agricultural Research Service, United States Department of Agriculture, Franklin, Maine, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Eugene L Torrans
- Warmwater Aquaculture Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Peter J Allen
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, Mississippi State, Mississippi, United States
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6
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Beer MA, Trumbo DR, Rautsaw RM, Kozakiewicz CP, Epstein B, Hohenlohe PA, Alford RA, Schwarzkopf L, Storfer A. Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia. Mol Ecol 2024; 33:e17464. [PMID: 38994885 DOI: 10.1111/mec.17464] [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: 09/25/2023] [Revised: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Daryl R Trumbo
- Department of Biology, Colorado State University Pueblo, Pueblo, Colorado, USA
| | - Rhett M Rautsaw
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Christopher P Kozakiewicz
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, Michigan, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Ross A Alford
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Lin Schwarzkopf
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
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7
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Choa R, Harris JC, Yang E, Yokoyama Y, Okumura M, Kim M, To J, Lou M, Nelson A, Kambayashi T. Thymic stromal lymphopoietin induces IL-4/IL-13 from T cells to promote sebum secretion and adipose loss. J Allergy Clin Immunol 2024; 154:480-491. [PMID: 38157943 PMCID: PMC11211244 DOI: 10.1016/j.jaci.2023.11.923] [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: 04/20/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The cytokine TSLP promotes type 2 immune responses and can induce adipose loss by stimulating lipid loss from the skin through sebum secretion by sebaceous glands, which enhances the skin barrier. However, the mechanism by which TSLP upregulates sebaceous gland function is unknown. OBJECTIVES This study investigated the mechanism by which TSLP stimulates sebum secretion and adipose loss. METHODS RNA-sequencing analysis was performed on sebaceous glands isolated by laser capture microdissection and single-cell RNA-sequencing analysis was performed on sorted skin T cells. Sebocyte function was analyzed by histological analysis and sebum secretion in vivo and by measuring lipogenesis and proliferation in vitro. RESULTS This study found that TSLP sequentially stimulated the expression of lipogenesis genes followed by cell death genes in sebaceous glands to induce holocrine secretion of sebum. TSLP did not affect sebaceous gland activity directly. Rather, single-cell RNA-sequencing revealed that TSLP recruited distinct T-cell clusters that produce IL-4 and IL-13, which were necessary for TSLP-induced adipose loss and sebum secretion. Moreover, IL-13 was sufficient to cause sebum secretion and adipose loss in vivo and to induce lipogenesis and proliferation of a human sebocyte cell line in vitro. CONCLUSIONS This study proposes that TSLP stimulates T cells to deliver IL-4 and IL-13 to sebaceous glands, which enhances sebaceous gland function, turnover, and subsequent adipose loss.
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Affiliation(s)
- Ruth Choa
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Jordan C Harris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - EnJun Yang
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore
| | - Yuichi Yokoyama
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Mariko Okumura
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - MinJu Kim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Jerrick To
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Meng Lou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Amanda Nelson
- Department of Dermatology, Penn State Milton S. Hershey Medical Center, Hershey, Pa
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa.
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8
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Tandon I, Woessner AE, Ferreira LA, Shamblin C, Vaca-Diez G, Walls A, Kuczwara P, Applequist A, Nascimento DF, Tandon S, Kim JW, Rausch M, Timek T, Padala M, Kinter MT, Province D, Byrum SD, Quinn KP, Balachandran K. A three-dimensional valve-on-chip microphysiological system implicates cell cycle progression, cholesterol metabolism and protein homeostasis in early calcific aortic valve disease progression. Acta Biomater 2024:S1742-7061(24)00417-3. [PMID: 39084496 DOI: 10.1016/j.actbio.2024.07.036] [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: 09/11/2023] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Calcific aortic valve disease (CAVD) is one of the most common forms of valvulopathy, with a 50 % elevated risk of a fatal cardiovascular event, and greater than 15,000 annual deaths in North America alone. The treatment standard is valve replacement as early diagnostic, mitigation, and drug strategies remain underdeveloped. The development of early diagnostic and therapeutic strategies requires the fabrication of effective in vitro valve mimetic models to elucidate early CAVD mechanisms. METHODS In this study, we developed a multilayered physiologically relevant 3D valve-on-chip (VOC) system that incorporated aortic valve mimetic extracellular matrix (ECM), porcine aortic valve interstitial cell (VIC) and endothelial cell (VEC) co-culture and dynamic mechanical stimuli. Collagen and glycosaminoglycan (GAG) based hydrogels were assembled in a bilayer to mimic healthy or diseased compositions of the native fibrosa and spongiosa. Multiphoton imaging and proteomic analysis of healthy and diseased VOCs were performed. RESULTS Collagen-based bilayered hydrogel maintained the phenotype of the VICs. Proteins related to cellular processes like cell cycle progression, cholesterol biosynthesis, and protein homeostasis were found to be significantly altered and correlated with changes in cell metabolism in diseased VOCs. This study suggested that diseased VOCs may represent an early, adaptive disease initiation stage, which was corroborated by human aortic valve proteomic assessment. CONCLUSIONS In this study, we developed a collagen-based bilayered hydrogel to mimic healthy or diseased compositions of the native fibrosa and spongiosa layers. When the gels were assembled in a VOC with VECs and VICs, the diseased VOCs revealed key insights about the CAVD initiation process. STATEMENT OF SIGNIFICANCE Calcific aortic valve disease (CAVD) elevates the risk of death due to cardiovascular pathophysiology by 50 %, however, prevention and mitigation strategies are lacking, clinically. Developing tools to assess early disease would significantly aid in the prevention of disease and in the development of therapeutics. Previously, studies have utilized collagen and glycosaminoglycan-based hydrogels for valve cell co-cultures, valve cell co-cultures in dynamic environments, and inorganic polymer-based multilayered hydrogels; however, these approaches have not been combined to make a physiologically relevant model for CAVD studies. We fabricated a bi-layered hydrogel that closely mimics the aortic valve and used it for valve cell co-culture in a dynamic platform to gain mechanistic insights into the CAVD initiation process using proteomic and multiphoton imaging assessment.
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Affiliation(s)
- Ishita Tandon
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Alan E Woessner
- Arkansas Integrative Metabolic Research Center, University of Arkansas, Fayetteville, AR, USA
| | - Laίs A Ferreira
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | | | - Gustavo Vaca-Diez
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Amanda Walls
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Patrick Kuczwara
- Department of Biological and Agricultural Engineering, Materials Science & Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Alexis Applequist
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Denise F Nascimento
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Swastika Tandon
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Jin-Woo Kim
- Department of Biological and Agricultural Engineering, Materials Science & Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Manuel Rausch
- Departments of Aerospace Engineering and Engineering Mechanics and Biomedical Engineering, Institute for Computational Engineering and Science, University of Texas at Austin, Austin, TX, USA
| | - Tomasz Timek
- Meijer Heart and Vascular Institute at Spectrum Health, Grand Rapids, MI, USA
| | - Muralidhar Padala
- Division of Cardiothoracic Surgery, Joseph P. Whitehead Department of Surgery, Emory University, Atlanta, GA, USA
| | - Michael T Kinter
- Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Dennis Province
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kyle P Quinn
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA; Arkansas Integrative Metabolic Research Center, University of Arkansas, Fayetteville, AR, USA
| | - Kartik Balachandran
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR, USA.
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9
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Matsuzaki T, Weistuch C, de Graff A, Dill KA, Balázsi G. Transcriptional drift in aging cells: A global decontroller. Proc Natl Acad Sci U S A 2024; 121:e2401830121. [PMID: 39012826 PMCID: PMC11287169 DOI: 10.1073/pnas.2401830121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024] Open
Abstract
As cells age, they undergo a remarkable global change: In transcriptional drift, hundreds of genes become overexpressed while hundreds of others become underexpressed. Using archetype modeling and Gene Ontology analysis on data from aging Caenorhabditis elegans worms, we find that the up-regulated genes code for sensory proteins upstream of stress responses and down-regulated genes are growth- and metabolism-related. We observe similar trends within human fibroblasts, suggesting that this process is conserved in higher organisms. We propose a simple mechanistic model for how such global coordination of multiprotein expression levels may be achieved by the binding of a single factor that concentrates with age in C. elegans. A key implication is that a cell's own responses are part of its aging process, so unlike wear-and-tear processes, intervention might be able to modulate these effects.
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Affiliation(s)
- Tyler Matsuzaki
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY11794
| | - Corey Weistuch
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | | | - Ken A. Dill
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY11794
| | - Gábor Balázsi
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY11794
- Department of Biomedical Engineering, Stony Brook University, New York, NY11794
- Stony Brook Cancer Center, Stony Brook University, New York, NY11794
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10
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Di Luca A, Bennato F, Ianni A, Martino C, Henry M, Meleady P, Martino G. Label-free liquid chromatography-mass spectrometry comparison of the breast muscle proteome profiles in two fast-growing broilers. Sci Rep 2024; 14:16886. [PMID: 39043903 PMCID: PMC11266551 DOI: 10.1038/s41598-024-67993-9] [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: 11/29/2023] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Poultry meat-production is increasing worldwide; leading to the selection of chickens for meat-production that show a fast growth. A label-free quantitative proteomic-approach and Western-blot were applied to investigate the dynamics of muscle protein under rapid growth conditions in two common fast-growing broiler genetic-lines (Ross 508 and AZ Extra Heavy Red-chicken). Muscle exudate from chicken Pectoralis major was used as substrate to unveil the proteome of these genetic-lines. Six-hundred forty-five proteins were identified in total from all samples, and after statistical-analysis 172 proteins were found to be differentially-expressed, clearly distinguishing the two chicken genetic-lines. Several of these differentially-expressed proteins were involved with the proteasome and glycolysis/gluconeogenesis-pathways. Changes in meat-quality traits were also observed, which were reflected in the proteomic-profile. Proteins involved in the ubiquitin-proteasome system were associated with the bigger muscle mass of Ross 508, while phosphoglucomutase 1 was associated with a possible higher capability of AZ Extra Heavy Red-chickens to cope with stressors. This pilot proteomic-approach applied on muscle exudate samples provided key evidence about the pathways and processes underlying these two chicken genetic-lines and their meat-quality parameters. We also identified potential biomarkers that could determine the peculiar production potentials (e.g. breast-growth) of these broilers-lines, which arise from differences in their genetic-backgrounds.
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Affiliation(s)
- Alessio Di Luca
- Department of Bioscience and Technology for Food Agro-Food and Environmental Technology, University of Teramo, 64100, Teramo, Italy
| | - Francesca Bennato
- Department of Bioscience and Technology for Food Agro-Food and Environmental Technology, University of Teramo, 64100, Teramo, Italy
| | - Andrea Ianni
- Department of Bioscience and Technology for Food Agro-Food and Environmental Technology, University of Teramo, 64100, Teramo, Italy
| | - Camillo Martino
- Department of Veterinary Medicine, University of Perugia, 06126, Perugia, Italy
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Dublin, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Dublin, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Dublin, Ireland
| | - Giuseppe Martino
- Department of Bioscience and Technology for Food Agro-Food and Environmental Technology, University of Teramo, 64100, Teramo, Italy.
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11
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Garma LD, Harder L, Barba-Reyes JM, Marco Salas S, Díez-Salguero M, Nilsson M, Serrano-Pozo A, Hyman BT, Muñoz-Manchado AB. Interneuron diversity in the human dorsal striatum. Nat Commun 2024; 15:6164. [PMID: 39039043 PMCID: PMC11263574 DOI: 10.1038/s41467-024-50414-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/01/2024] [Indexed: 07/24/2024] Open
Abstract
Deciphering the striatal interneuron diversity is key to understanding the basal ganglia circuit and to untangling the complex neurological and psychiatric diseases affecting this brain structure. We performed snRNA-seq and spatial transcriptomics of postmortem human caudate nucleus and putamen samples to elucidate the diversity and abundance of interneuron populations and their inherent transcriptional structure in the human dorsal striatum. We propose a comprehensive taxonomy of striatal interneurons with eight main classes and fourteen subclasses, providing their full transcriptomic identity and spatial expression profile as well as additional quantitative FISH validation for specific populations. We have also delineated the correspondence of our taxonomy with previous standardized classifications and shown the main transcriptomic and class abundance differences between caudate nucleus and putamen. Notably, based on key functional genes such as ion channels and synaptic receptors, we found matching known mouse interneuron populations for the most abundant populations, the recently described PTHLH and TAC3 interneurons. Finally, we were able to integrate other published datasets with ours, supporting the generalizability of this harmonized taxonomy.
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Affiliation(s)
- Leonardo D Garma
- Karolinska Institutet, Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Stockholm, Sweden
| | - Lisbeth Harder
- Karolinska Institutet, Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Stockholm, Sweden
| | - Juan M Barba-Reyes
- Departamento de Anatomía Patológica, Biología Celular, Histología, Historia de la Ciencia, Medicina Legal y Forense y Toxicología. Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA). University of Cádiz, Cádiz, Spain
| | - Sergio Marco Salas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mónica Díez-Salguero
- Departamento de Anatomía Patológica, Biología Celular, Histología, Historia de la Ciencia, Medicina Legal y Forense y Toxicología. Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA). University of Cádiz, Cádiz, Spain
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alberto Serrano-Pozo
- Massachusetts General Hospital, Neurology Department, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Bradley T Hyman
- Massachusetts General Hospital, Neurology Department, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Ana B Muñoz-Manchado
- Karolinska Institutet, Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Stockholm, Sweden.
- Departamento de Anatomía Patológica, Biología Celular, Histología, Historia de la Ciencia, Medicina Legal y Forense y Toxicología. Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA). University of Cádiz, Cádiz, Spain.
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12
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Pulawska-Moon K, Ponikwicka-Tyszko D, Lebiedzinska W, Pilaszewicz-Puza A, Bernaczyk P, Koda M, Lupu O, Milewska G, Huang CCJ, Zheng H, Schiele P, Na IK, Frentsch M, Li X, Toppari J, Wolczynski S, Coelingh Bennink HJT, Huhtaniemi I, Rahman NA. Novel ectopic expression of zona pellucida 3 glycoprotein in lung cancer promotes tumor growth. Int J Cancer 2024. [PMID: 39039845 DOI: 10.1002/ijc.35098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/24/2024]
Abstract
Zona pellucida 3 (ZP3) expression is classically found in the ZP-layer of the oocytes, lately shown in ovarian and prostate cancer. A successful ZP3 ovarian cancer immunotherapy in transgenic mice suggested its use as an attractive therapeutic target. The biological role of ZP3 in cancer growth and progression is still unknown. We found that ~88% of the analyzed adenocarcinoma, squamous and small cell lung carcinomas to express ZP3. Knockout of ZP3 in a ZP3-expressing lung adenocarcinoma cell line, significantly decreased cell viability, proliferation, and migration rates in vitro. Zona pellucida 3 knock out (ZP3-KO) cell tumors inoculated in vivo in immunodeficient non-obese diabetic, severe combined immunodeficient mice showed significant inhibition of tumor growth and mitigation of the malignant phenotype. RNA sequencing revealed the deregulation of cell migration/adhesion signaling pathways in ZP3-KO cells. This novel functional relevance of ZP3 in lung cancer emphasized the suitability of ZP3 as a target in cancer immunotherapy and as a potential cancer biomarker.
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Affiliation(s)
| | - Donata Ponikwicka-Tyszko
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Biology and Pathology of Human Reproduction, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Weronika Lebiedzinska
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
| | | | - Piotr Bernaczyk
- Department of Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Mariusz Koda
- Department of General Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Oana Lupu
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
| | - Gabriela Milewska
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
| | - Chen-Che Jeff Huang
- Department of Anatomy, Physiology and Pharmacology, Auburn University College of Veterinary Medicine, Auburn, Alabama, USA
| | - Huifei Zheng
- Department of Anatomy, Physiology and Pharmacology, Auburn University College of Veterinary Medicine, Auburn, Alabama, USA
| | - Phillip Schiele
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Il-Kang Na
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, and ECRC Experimental and Clinical Research Center, both Charité-Universitätsmedizin Berlin, Corporate members of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | - Marco Frentsch
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xiangdong Li
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Jorma Toppari
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Slawomir Wolczynski
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
| | | | - Ilpo Huhtaniemi
- Institute of Biomedicine, University of Turku, Turku, Finland
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Nafis A Rahman
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland
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13
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Farazuddin M, Acker G, Zourob J, O’Konek JJ, Wong PT, Morris S, Rasky AJ, Kim CH, Lukacs NW, Baker JR. Inhibiting retinoic acid signaling in dendritic cells suppresses respiratory syncytial virus infection through enhanced antiviral immunity. iScience 2024; 27:110103. [PMID: 39045100 PMCID: PMC11263793 DOI: 10.1016/j.isci.2024.110103] [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: 10/09/2023] [Revised: 12/21/2023] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Retinoic acid (RA), controls the immunoregulatory functions of many immune cells, including dendritic cells (DCs), and is important for mucosal immunity. In DCs, RA regulates the expression of pattern recognition receptors and stimulates interferon production. Here, we investigated the role of RA in DCs in mounting immunity to respiratory syncytial virus (RSV). To abolish RA signaling in DCs, we used mice expressing a dominant negative form of retinoic acid receptor-α (RARα) under the CD11c promoter (CD11c-dnRARα). Paradoxically, upon RSV challenge, these animals had lower viral burden, reduced pathology, and greater Th1 polarized immunity than wild-type (WT) mice. Moreover, CD11c-dnRARα DCs infected with RSV showed enhancement in innate and adaptive immunity genes, while genes associated with viral replication were downregulated. These findings suggest that the absence of RA signaling in DCs enhances innate immunity against RSV infection leading to decreased viral load and reduced pathogenicity.
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Affiliation(s)
- Mohammad Farazuddin
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Grant Acker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph Zourob
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jessica J. O’Konek
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Pamela T. Wong
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Susan Morris
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrew J. Rasky
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chang H. Kim
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas W. Lukacs
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James R. Baker
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
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14
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Trogdon M, Abbott K, Arang N, Lande K, Kaur N, Tong M, Bakhoum M, Gutkind JS, Stites EC. Systems modeling of oncogenic G-protein and GPCR signaling reveals unexpected differences in downstream pathway activation. NPJ Syst Biol Appl 2024; 10:75. [PMID: 39013872 PMCID: PMC11252164 DOI: 10.1038/s41540-024-00400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/27/2024] [Indexed: 07/18/2024] Open
Abstract
Mathematical models of biochemical reaction networks are an important and emerging tool for the study of cell signaling networks involved in disease processes. One promising potential application of such mathematical models is the study of how disease-causing mutations promote the signaling phenotype that contributes to the disease. It is commonly assumed that one must have a thorough characterization of the network readily available for mathematical modeling to be useful, but we hypothesized that mathematical modeling could be useful when there is incomplete knowledge and that it could be a tool for discovery that opens new areas for further exploration. In the present study, we first develop a mechanistic mathematical model of a G-protein coupled receptor signaling network that is mutated in almost all cases of uveal melanoma and use model-driven explorations to uncover and explore multiple new areas for investigating this disease. Modeling the two major, mutually-exclusive, oncogenic mutations (Gαq/11 and CysLT2R) revealed the potential for previously unknown qualitative differences between seemingly interchangeable disease-promoting mutations, and our experiments confirmed oncogenic CysLT2R was impaired at activating the FAK/YAP/TAZ pathway relative to Gαq/11. This led us to hypothesize that CYSLTR2 mutations in UM must co-occur with other mutations to activate FAK/YAP/TAZ signaling, and our bioinformatic analysis uncovers a role for co-occurring mutations involving the plexin/semaphorin pathway, which has been shown capable of activating this pathway. Overall, this work highlights the power of mechanism-based computational systems biology as a discovery tool that can leverage available information to open new research areas.
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Affiliation(s)
- Michael Trogdon
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Pfizer, La Jolla, CA, 92037, USA
| | - Kodye Abbott
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Nadia Arang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kathryn Lande
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Navneet Kaur
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Melinda Tong
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Mathieu Bakhoum
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Edward C Stites
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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15
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Bakina O, Conrad T, Mitic N, Vidal RO, Obrusnik T, Sai S, Nolte C, Semtner M, Kettenmann H. In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia. PLoS One 2024; 19:e0302376. [PMID: 38990806 PMCID: PMC11239014 DOI: 10.1371/journal.pone.0302376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 07/13/2024] Open
Abstract
We applied the patch-seq technique to harvest transcripts from individual microglial cells from cortex, hippocampus and corpus callosum of acute brain slices from adult mice. After recording membrane currents with the patch-clamp technique, the cytoplasm was collected via the pipette and underwent adapted SMART-seq2 preparation with subsequent sequencing. On average, 4138 genes were detected in 113 cells from hippocampus, corpus callosum and cortex, including microglia markers such as Tmem119, P2ry12 and Siglec-H. Comparing our dataset to previously published single cell mRNA sequencing data from FACS-isolated microglia indicated that two clusters of cells were absent in our patch-seq dataset. Pathway analysis of marker genes in FACS-specific clusters revealed association with microglial activation and stress response. This indicates that under normal conditions microglia in situ lack transcripts associated with a stress-response, and that the microglia-isolation procedure by mechanical dissociation and FACS triggers the expression of genes related to activation and stress.
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Affiliation(s)
- Olga Bakina
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Humboldt Universität, Berlin, Germany
| | - Thomas Conrad
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nina Mitic
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ramon Oliveira Vidal
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Tessa Obrusnik
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Somesh Sai
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christiane Nolte
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marcus Semtner
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Helmut Kettenmann
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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16
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Huang Y, Dong D, Zhang W, Wang R, Lin YCD, Zuo H, Huang HY, Huang HD. DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning. Database (Oxford) 2024; 2024:baae051. [PMID: 38994794 PMCID: PMC11240114 DOI: 10.1093/database/baae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/25/2024] [Accepted: 06/29/2024] [Indexed: 07/13/2024]
Abstract
In recent years, drug repositioning has emerged as a promising alternative to the time-consuming, expensive and risky process of developing new drugs for diseases. However, the current database for drug repositioning faces several issues, including insufficient data volume, restricted data types, algorithm inaccuracies resulting from the neglect of multidimensional or heterogeneous data, a lack of systematic organization of literature data associated with drug repositioning, limited analytical capabilities and user-unfriendly webpage interfaces. Hence, we have established the first all-encompassing database called DrugRepoBank, consisting of two main modules: the 'Literature' module and the 'Prediction' module. The 'Literature' module serves as the largest repository of literature-supported drug repositioning data with experimental evidence, encompassing 169 repositioned drugs from 134 articles from 1 January 2000 to 1 July 2023. The 'Prediction' module employs 18 efficient algorithms, including similarity-based, artificial-intelligence-based, signature-based and network-based methods to predict repositioned drug candidates. The DrugRepoBank features an interactive and user-friendly web interface and offers comprehensive functionalities such as bioinformatics analysis of disease signatures. When users provide information about a drug, target or disease of interest, DrugRepoBank offers new indications and targets for the drug, proposes new drugs that bind to the target or suggests potential drugs for the queried disease. Additionally, it provides basic information about drugs, targets or diseases, along with supporting literature. We utilize three case studies to demonstrate the feasibility and effectiveness of predictively repositioned drugs within DrugRepoBank. The establishment of the DrugRepoBank database will significantly accelerate the pace of drug repositioning. Database URL: https://awi.cuhk.edu.cn/DrugRepoBank.
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Affiliation(s)
- Yixian Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Danhong Dong
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Wenyang Zhang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Ruiting Wang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Huali Zuo
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
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17
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Qian F, Zuo D, Xue Y, Guan W, Ullah N, Zhu J, Cai G, Zhu B, Wu X. Comprehensive genome-wide identification of Snf2 gene family and their expression profile under salt stress in six Brassica species of U's triangle model. PLANTA 2024; 260:49. [PMID: 38985323 DOI: 10.1007/s00425-024-04473-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024]
Abstract
MAIN CONCLUSION We comprehensively identified and analyzed the Snf2 gene family. Some Snf2 genes were involved in responding to salt stress based on the RNA-seq and qRT-PCR analysis. Sucrose nonfermenting 2 (Snf2) proteins are core components of chromatin remodeling complexes that not only alter DNA accessibility using the energy of ATP hydrolysis, but also play a critical regulatory role in growth, development, and stress response in eukaryotes. However, the comparative study of Snf2 gene family in the six Brassica species in U's triangle model remains unclear. Here, a total of 405 Snf2 genes were identified, comprising 53, 50, and 46 in the diploid progenitors: Brassica rapa (AA, 2n = 20), Brassica nigra (BB, 2n = 16), and Brassica oleracea (CC, 2n = 18), and 93, 91, and 72 in the allotetraploid: Brassica juncea (AABB, 2n = 36), Brassica napus (AACC, 2n = 38), and Brassica carinata (BBCC, 2n = 34), respectively. These genes were classified into six clades and further divided into 18 subfamilies based on their conserved motifs and domains. Intriguingly, these genes showed highly conserved chromosomal distributions and gene structures, indicating that few dynamic changes occurred during the polyploidization. The duplication modes of the six Brassica species were diverse, and the expansion of most Snf2 in Brassica occurred primarily through dispersed duplication (DSD) events. Additionally, the majority of Snf2 genes were under purifying selection during polyploidization, and some Snf2 genes were associated with various abiotic stresses. Both RNA-seq and qRT-PCR analysis showed that the expression of BnaSnf2 genes was significantly induced under salt stress, implying their involvement in salt tolerance response in Brassica species. The results provide a comprehensive understanding of the Snf2 genes in U's triangle model species, which will facilitate further functional analysis of the Snf2 genes in Brassica plants.
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Affiliation(s)
- Fang Qian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Dan Zuo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Yujun Xue
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Wenjie Guan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Naseeb Ullah
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Jiarong Zhu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Guangqin Cai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
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Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2664-0. [PMID: 38987431 DOI: 10.1007/s11427-024-2664-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
Winter plants rely on vernalization, a crucial process for adapting to cold conditions and ensuring successful reproduction. However, understanding the role of histone modifications in guiding the vernalization process in winter wheat remains limited. In this study, we investigated the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the field. Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS), components of the writer complex for H3K27me3 and H3K36me3, respectively, affected flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure memory in the absence of H3K36me3. During embryo development, VRN1 was silenced with the removal of active histone modifications in both winter and spring wheat, with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87, a component of H3K27me3 "writer" complex, did not influence the silence of VRN1 during embryo development, but rather attenuated the cold exposure requirement of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of flowering. This study unveils distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and resetting in winter wheat.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Deng
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxin Shi
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinchao Chen
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shujuan Xu
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, 3400, Austria
| | - Xiaomin Bie
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiansheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, 100101, China.
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19
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McQuarrie DWJ, Alizada A, Nicholson BC, Soller M. Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors. BMC Genomics 2024; 25:678. [PMID: 38977960 PMCID: PMC11229233 DOI: 10.1186/s12864-024-10584-9] [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: 04/10/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The piRNA pathway in animal gonads functions as an 'RNA-based immune system', serving to silence transposable elements and prevent inheritance of novel invaders. In Drosophila, this pathway relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine and Piwi) that associate with 23-28 nucleotide piRNAs, directing the silencing of transposon-derived transcripts. Transposons constitute a primary driver of genome evolution, yet the evolution of piRNA pathway factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact piRNA processing, exhibit regions of rapid evolution in their promoters. Consequently, the question arises whether such a mode of evolution is a general feature of transposon silencing pathways. RESULTS By employing genomic analysis of coding and promoter regions within genes that function in transposon silencing in Drosophila, we demonstrate that the promoters of germ cell-specific piRNA factors are undergoing rapid evolution. Our findings indicate that rapid promoter evolution is a common trait among piRNA factors engaged in germline silencing across insect species, potentially contributing to gene expression divergence in closely related taxa. Furthermore, we observe that the promoters of genes exclusively expressed in germ cells generally exhibit rapid evolution, with some divergence in gene expression. CONCLUSION Our results suggest that increased germline promoter evolution, in partnership with other factors, could contribute to transposon silencing and evolution of species through differential expression of genes driven by invading transposons.
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Affiliation(s)
- David W J McQuarrie
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Azad Alizada
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Benjamin Czech Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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20
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Delvenne A, Gobom J, Schindler SE, Kate MT, Reus LM, Dobricic V, Tijms BM, Benzinger TLS, Cruchaga C, Teunissen CE, Ramakers I, Martinez-Lage P, Tainta M, Vandenberghe R, Schaeverbeke J, Engelborghs S, Roeck ED, Popp J, Peyratout G, Tsolaki M, Freund-Levi Y, Lovestone S, Streffer J, Barkhof F, Bertram L, Blennow K, Zetterberg H, Visser PJ, Vos SJB. CSF proteomic profiles of neurodegeneration biomarkers in Alzheimer's disease. Alzheimers Dement 2024. [PMID: 38970402 DOI: 10.1002/alz.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 07/08/2024]
Abstract
INTRODUCTION We aimed to unravel the underlying pathophysiology of the neurodegeneration (N) markers neurogranin (Ng), neurofilament light (NfL), and hippocampal volume (HCV), in Alzheimer's disease (AD) using cerebrospinal fluid (CSF) proteomics. METHODS Individuals without dementia were classified as A+ (CSF amyloid beta [Aβ]42), T+ (CSF phosphorylated tau181), and N+ or N- based on Ng, NfL, or HCV separately. CSF proteomics were generated and compared between groups using analysis of covariance. RESULTS Only a few individuals were A+T+Ng-. A+T+Ng+ and A+T+NfL+ showed different proteomic profiles compared to A+T+Ng- and A+T+NfL-, respectively. Both Ng+ and NfL+ were associated with neuroplasticity, though in opposite directions. Compared to A+T+HCV-, A+T+HCV+ showed few proteomic changes, associated with oxidative stress. DISCUSSION Different N markers are associated with distinct neurodegenerative processes and should not be equated. N markers may differentially complement disease staging beyond amyloid and tau. Our findings suggest that Ng may not be an optimal N marker, given its low incongruency with tau pathophysiology. HIGHLIGHTS In Alzheimer's disease, neurogranin (Ng)+, neurofilament light (NfL)+, and hippocampal volume (HCV)+ showed differential protein expression in cerebrospinal fluid. Ng+ and NfL+ were associated with neuroplasticity, although in opposite directions. HCV+ showed few proteomic changes, related to oxidative stress. Neurodegeneration (N) markers may differentially refine disease staging beyond amyloid and tau. Ng might not be an optimal N marker, as it relates more closely to tau.
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Affiliation(s)
- Aurore Delvenne
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mara Ten Kate
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Tammie L S Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Inez Ramakers
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | | | - Mikel Tainta
- Fundación CITA-Alzhéimer Fundazioa, Donostia, Spain
| | - Rik Vandenberghe
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jolien Schaeverbeke
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Bru-BRAIN, Universitair Ziekenhuis Brussel and NEUR Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen De Roeck
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Julius Popp
- Old Age Psychiatry, University Hospital Lausanne, Lausanne, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatry University Hospital Zürich, Zürich, Switzerland
| | | | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Makedonia, Thessaloniki, Greece
| | - Yvonne Freund-Levi
- Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Old Age Psychiatry, Psychology & Neuroscience, King's College, London, UK
| | - Simon Lovestone
- University of Oxford, United Kingdom (currently at Johnson and Johnson Medical Ltd., Oxford, UK
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- H. Lundbeck A/S, Valby, Denmark
| | - Frederik Barkhof
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, P.R. China
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
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21
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Bomba-Warczak EK, Velez KM, Zhou LT, Guillermier C, Edassery S, Steinhauser M, Savas JN, Duncan FE. Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.18.562852. [PMID: 37905022 PMCID: PMC10614913 DOI: 10.1101/2023.10.18.562852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The mechanisms contributing to age-related deterioration of the female reproductive system are complex, but aberrant protein homeostasis is a major contributor. We elucidated the exceptionally stable proteins, structures, and macromolecules that persist in mammalian ovaries and gametes across the reproductive lifespan. Ovaries exhibit localized structural and cell-type specific enrichment of stable macromolecules in both the follicular and extrafollicular environments. Moreover, both ovaries and oocytes harbor a panel of exceptionally long-lived proteins, including cytoskeletal components, mitochondrial, and oocyte-derived proteins. The exceptional persistence of these long-lived molecules might play a critical role in both lifelong maintenance and age-dependent deterioration of reproductive tissues.
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Affiliation(s)
- Ewa K. Bomba-Warczak
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Karen M. Velez
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Luhan T Zhou
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Seby Edassery
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Matthew Steinhauser
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, MA
| | - Jeffrey N. Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Francesca E. Duncan
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
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22
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Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization Using Large Language Models. ARXIV 2024:arXiv:2305.13338v3. [PMID: 37292480 PMCID: PMC10246080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of biological function terms associated with genes or their properties, based on curated assertions from a knowledge base (KB) such as the Gene Ontology (GO). Interpreting gene lists can also be framed as a textual summarization task, enabling Large Language Models (LLMs) to use scientific texts directly and avoid reliance on a KB. TALISMAN (Terminological ArtificiaL Intelligence SuMmarization of Annotation and Narratives) uses generative AI to perform gene set function summarization as a complement to standard enrichment analysis. This method can use different sources of gene functional information: (1) structured text derived from curated ontological KB annotations, (2) ontology-free narrative gene summaries, or (3) direct retrieval from the model. We demonstrate that these methods are able to generate plausible and biologically valid summary GO term lists for an input gene set. However, LLM-based approaches are unable to deliver reliable scores or p-values and often return terms that are not statistically significant. Crucially, in our experiments these methods were rarely able to recapitulate the most precise and informative term from standard enrichment analysis. We also observe minor differences depending on prompt input information, with GO term descriptions leading to higher recall but lower precision. However, newer LLM models perform statistically significantly better than the oldest model across all performance metrics, suggesting that future models may lead to further improvements. Overall, the results are nondeterministic, with minor variations in prompt resulting in radically different term lists, true to the stochastic nature of LLMs. Our results show that at this point, LLM-based methods are unsuitable as a replacement for standard term enrichment analysis, however they may provide summarization benefits for implicit knowledge integration across extant but unstandardized knowledge, for large sets of features, and where the amount of information is difficult for humans to process.
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Affiliation(s)
- Marcin P Joachimiak
- Biosystems Data Science Department, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - J Harry Caufield
- Biosystems Data Science Department, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nomi L Harris
- Biosystems Data Science Department, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | | | - Christopher J Mungall
- Biosystems Data Science Department, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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23
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Fabregat-Cid G, Cedeno DL, De Andrés J, Harutyunyan A, Monsalve-Dolz V, Mínguez-Martí A, Escrivá-Matoses N, Asensio-Samper JM, Carnaval T, Villoria J, Rodríguez-López R, Vallejo R. Insights into the pathophysiology and response of persistent spinal pain syndrome type 2 to spinal cord stimulation: a human genome-wide association study. Reg Anesth Pain Med 2024:rapm-2024-105517. [PMID: 38960591 DOI: 10.1136/rapm-2024-105517] [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: 03/29/2024] [Accepted: 06/15/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Spinal cord stimulation (SCS) provides pain relief for some patients with persistent spinal pain syndrome type 2 (PSPS 2), but the precise mechanisms of action and prognostic factors for a favorable pain response remain obscure. This in vivo human genome-wide association study provides some pathophysiological clues. METHODS We performed a high-density oligonucleotide microarray analysis of serum obtained from both PSPS 2 cases and pain-free controls who had undergone lower back spinal surgery at the study site. Using multivariate discriminant analysis, we tried to identify different expressions between mRNA transcripts from PSPS 2 patients relative to controls, SCS responders to non-responders, or SCS responders to themselves before starting SCS. Gene ontology enrichment analysis was used to identify the biological processes that best discriminate between the groups of clinical interest. RESULTS Thirty PSPS 2 patients, of whom 23 responded to SCS, were evaluated together with 15 pain-free controls. We identified 11 significantly downregulated genes in serum of PSPS 2 patients compared with pain-free controls and two significantly downregulated genes once the SCS response became apparent. All were suggestive of enhanced inflammation, tissue repair mechanisms and proliferative responses among the former. We could not identify any gene differentiating patients who responded to SCS from those who did not respond. CONCLUSIONS This study points out various biological processes that may underlie PSPS 2 pain and SCS therapeutic effects, including the modulation of neuroimmune response, inflammation and restorative processes.
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Affiliation(s)
- Gustavo Fabregat-Cid
- Multidisciplinary Pain Management Department, General University Hospital Consortium of Valencia, Valencia, Spain
- Surgery Department, University of Valencia, Valencia, Spain
| | | | - José De Andrés
- Multidisciplinary Pain Management Department, General University Hospital Consortium of Valencia, Valencia, Spain
- Surgery Department, University of Valencia, Valencia, Spain
| | - Anushik Harutyunyan
- Multidisciplinary Pain Management Department, General University Hospital Consortium of Valencia, Valencia, Spain
| | - Vicente Monsalve-Dolz
- Multidisciplinary Pain Management Department, General University Hospital Consortium of Valencia, Valencia, Spain
| | - Ana Mínguez-Martí
- Multidisciplinary Pain Management Department, General University Hospital Consortium of Valencia, Valencia, Spain
| | | | - Juan Marcos Asensio-Samper
- Multidisciplinary Pain Management Department, General University Hospital Consortium of Valencia, Valencia, Spain
- Surgery Department, University of Valencia, Valencia, Spain
| | - Thiago Carnaval
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, Barcelona, Spain
- Design and Biometrics Department, Medicxact, Madrid, Spain
| | - Jesús Villoria
- Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, Barcelona, Spain
- Design and Biometrics Department, Medicxact, Madrid, Spain
| | - Raquel Rodríguez-López
- Genetics Laboratory; Clinical Analysis Service, General University Hospital Consortium of Valencia, Valencia, Spain
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24
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Pahari S, Vaid N, Soolanayakanahally R, Kagale S, Pasha A, Esteban E, Provart N, Stobbs JA, Vu M, Meira D, Karunakaran C, Boda P, Prasannakumar MK, Nagaraja A, Jain AK. Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:577-594. [PMID: 38576267 DOI: 10.1111/tpj.16749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK-8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high-quality, in-depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user-friendly interface, allowing interactive visualizations of tissue-specific gene expression. Using these data, we identified transcripts, the orthologs of which in Arabidopsis and rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of "hidden hunger" and to attain nutritional security, making it a valuable asset for translational research.
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Affiliation(s)
- Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Miranda Vu
- Canadian Light Source Inc, Saskatoon, Saskatchewan, Canada
| | - Debora Meira
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, United States
| | | | - Praveen Boda
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | | | - Alur Nagaraja
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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25
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Wojciechowska I, Mukherjee T, Knox-Brown P, Hu X, Khosla A, Subedi B, Ahmad B, Mathews GL, Panagakis AA, Thompson KA, Peery ST, Szlachetko J, Thalhammer A, Hincha DK, Skirycz A, Schrick K. Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism. THE NEW PHYTOLOGIST 2024. [PMID: 38952028 DOI: 10.1111/nph.19917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/06/2024] [Indexed: 07/03/2024]
Abstract
Plant homeodomain leucine zipper IV (HD-Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain. While the START domain is required for TF activity, its presumed role as a lipid sensor is not clear. Here we used tandem affinity purification from Arabidopsis cell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative member that controls epidermal differentiation, recruits lysophosphatidylcholines (LysoPCs) in a START-dependent manner. Microscale thermophoresis assays confirmed that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding. We additionally found that PDF2 acts as a transcriptional regulator of phospholipid- and phosphate (Pi) starvation-related genes and binds to a palindromic octamer with consensus to a Pi response element. Phospholipid homeostasis and elongation growth were altered in pdf2 mutants according to Pi availability. Cycloheximide chase experiments revealed a role for START in maintaining protein levels, and Pi starvation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity. We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Our data provide insights toward understanding how the lipid metabolome integrates Pi availability with gene expression.
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Affiliation(s)
| | - Thiya Mukherjee
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan, KS, 66506, USA
- Donald Danforth Plant Science Center, Olivette, MO, 63132, USA
| | | | - Xueyun Hu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Aashima Khosla
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bibek Subedi
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bilal Ahmad
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Graham L Mathews
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Kyle A Thompson
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophie T Peery
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jagoda Szlachetko
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Anja Thalhammer
- Physical Biochemistry, University of Potsdam, 14476, Potsdam, Germany
| | - Dirk K Hincha
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Kathrin Schrick
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
- Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan, KS, 66506, USA
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26
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Neupane S, Williamson DB, Roth RA, Halabi CM, Haltiwanger RS, Holdener BC. Poglut2/3 double knockout in mice results in neonatal lethality with reduced levels of fibrillin in lung tissues. J Biol Chem 2024; 300:107445. [PMID: 38844137 PMCID: PMC11261140 DOI: 10.1016/j.jbc.2024.107445] [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: 03/24/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/30/2024] Open
Abstract
Fibrillin microfibrils play a critical role in the formation of elastic fibers, tissue/organ development, and cardiopulmonary function. These microfibrils not only provide structural support and flexibility to tissues, but they also regulate growth factor signaling through a plethora of microfibril-binding proteins in the extracellular space. Mutations in fibrillins are associated with human diseases affecting cardiovascular, pulmonary, skeletal, and ocular systems. Fibrillins consist of up to 47 epidermal growth factor-like repeats, of which more than half are modified by protein O-glucosyltransferase 2 (POGLUT2) and/or POGLUT3. Loss of these modifications reduces secretion of N-terminal fibrillin constructs overexpressed in vitro. Here, we investigated the role of POGLUT2 and POGLUT3 in vivo using a Poglut2/3 double knockout (DKO) mouse model. Blocking O-glucosylation caused neonatal death with skeletal, pulmonary, and eye defects reminiscent of fibrillin/elastin mutations. Proteomic analyses of DKO dermal fibroblast medium and extracellular matrix provided evidence that fibrillins were more sensitive to loss of O-glucose compared to other POGLUT2/3 substrates. This conclusion was supported by immunofluorescent analyses of late gestation DKO lungs where FBN levels were reduced and microfibrils appeared fragmented in the pulmonary arteries and veins, bronchioles, and developing saccules. Defects in fibrillin microfibrils likely contributed to impaired elastic fiber formation and histological changes observed in DKO lung blood vessels, bronchioles, and saccules. Collectively, these results highlight the importance of POGLUT2/3-mediated O-glucosylation in vivo and open the possibility that O-glucose modifications on fibrillin influence microfibril assembly and or protein interactions in the ECM environment.
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Affiliation(s)
- Sanjiv Neupane
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Daniel B Williamson
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Robyn A Roth
- Division of Nephrology, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Carmen M Halabi
- Division of Nephrology, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Robert S Haltiwanger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
| | - Bernadette C Holdener
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA.
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27
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Fuentes RR, Nieuwenhuis R, Chouaref J, Hesselink T, van Dooijeweert W, van den Broeck HC, Schijlen E, Schouten HJ, Bai Y, Fransz P, Stam M, de Jong H, Trivino SD, de Ridder D, van Dijk ADJ, Peters SA. A catalogue of recombination coldspots in interspecific tomato hybrids. PLoS Genet 2024; 20:e1011336. [PMID: 38950081 PMCID: PMC11244794 DOI: 10.1371/journal.pgen.1011336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 07/12/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024] Open
Abstract
Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
- Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ronald Nieuwenhuis
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Jihed Chouaref
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thamara Hesselink
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem van Dooijeweert
- Centre for Genetic Resources, Wageningen University and Research, Wageningen, The Netherlands
| | - Hetty C van den Broeck
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Henk J Schouten
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
| | - Sara Diaz Trivino
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
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Kappler U, Henningham A, Nasreen M, Yamamoto A, Buultjens AH, Stinear TP, Sly P, Fantino E. Tolerance to Haemophilus influenzae infection in human epithelial cells: Insights from a primary cell-based model. PLoS Pathog 2024; 20:e1012282. [PMID: 38990812 PMCID: PMC11239077 DOI: 10.1371/journal.ppat.1012282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/22/2024] [Indexed: 07/13/2024] Open
Abstract
Haemophilus influenzae is a human respiratory pathogen and inhabits the human respiratory tract as its only niche. Despite this, the molecular mechanisms that allow H. influenzae to establish persistent infections of human epithelia are not well understood. Here, we have investigated how H. influenzae adapts to the host environment and triggers the host immune response using a human primary cell-based infection model that closely resembles human nasal epithelia (NHNE). Physiological assays combined with dualRNAseq revealed that NHNE from five healthy donors all responded to H. influenzae infection with an initial, 'unproductive' inflammatory response that included a strong hypoxia signature but did not produce pro-inflammatory cytokines. Subsequently, an apparent tolerance to large extracellular and intraepithelial burdens of H. influenzae developed, with NHNE transcriptional profiles resembling the pre-infection state. This occurred in parallel with the development of intraepithelial bacterial populations, and appears to involve interruption of NFκB signalling. This is the first time that large-scale, persistence-promoting immunomodulatory effects of H. influenzae during infection have been observed, and we were able to demonstrate that only infections with live, but not heat-killed H. influenzae led to immunomodulation and reduced expression of NFκB-controlled cytokines such as IL-1β, IL-36γ and TNFα. Interestingly, NHNE were able to re-activate pro-inflammatory responses towards the end of the 14-day infection, resulting in release of IL-8 and TNFα. In addition to providing first molecular insights into mechanisms enabling persistence of H. influenzae in the host, our data further indicate the presence of infection stage-specific gene expression modules, highlighting fundamental similarities between immune responses in NHNE and canonical immune cells, which merit further investigation.
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Affiliation(s)
- Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Anna Henningham
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Marufa Nasreen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Ayaho Yamamoto
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Andrew H. Buultjens
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Peter Sly
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Emmanuelle Fantino
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
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29
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Sanjay, Sood R, Jaiswal V, Kang SU, Park M, Lee HJ. Nobiletin regulates intracellular Ca 2+ levels via IP 3R and ameliorates neuroinflammation in Aβ42-induced astrocytes. Redox Biol 2024; 73:103197. [PMID: 38781730 PMCID: PMC11145555 DOI: 10.1016/j.redox.2024.103197] [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: 04/25/2024] [Revised: 05/12/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Astrocytes are the major glial cells in the human brain and provide crucial metabolic and trophic support to neurons. The amyloid-β peptide (Aβ) alter the morphological and functional properties of astrocytes and induce inflammation and calcium dysregulation, contributing to Alzheimer's disease (AD) pathology. Recent studies highlight the role of Toll-like receptor (TLR) 4/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling in inflammation. Reactive oxygen species (ROS) generated due to Aβ, induce apoptosis in the brain cells worsening AD progression. Astrocytic cell surface receptors, such as purinergic receptors (P2Y1 and P2Y2), metabotropic glutamate receptor (mGLUR)5, α7 nicotinic acetylcholine receptor (α7nAChR), and N-methyl-d-aspartate receptors (NMDARs), have been suggested to interact with inositol trisphosphate receptor (IP3R) on the endoplasmic reticulum (ER) to induce Ca2+ movement from ER to cytoplasm, causing Ca2+ dysregulation. We found that the citrus flavonoid nobiletin (NOB) protected primary astrocytes from Aβ42-induced cytotoxicity and inhibited TLR4/NF-κB signaling in Aβ42-induced primary rat astrocytes. NOB was found to regulate Aβ42-induced ROS levels through Keap1-Nrf2 pathway. The receptors P2Y1, P2Y2, mGLUR5, α7nAChR, and NMDARs induced intracellular Ca2+ levels by activating IP3R and NOB regulated them, thereby regulating intracellular Ca2+ levels. Molecular docking analysis revealed a possible interaction between NOB and IP3R in IP3R regulation. Furthermore, RNA sequencing revealed various NOB-mediated biological signaling pathways, such as the AD-presenilin, AD-amyloid secretase, and Wnt signaling pathway, suggesting possible neuroprotective roles of NOB. To conclude, NOB is a promising therapeutic agent for AD and works by modulating AD pathology at various levels in Aβ42-induced primary rat astrocytes.
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Affiliation(s)
- Sanjay
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
| | - Rachit Sood
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea; Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
| | - Varun Jaiswal
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea; Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Miey Park
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea; Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
| | - Hae-Jeung Lee
- Institute for Aging and Clinical Nutrition Research, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea; Department of Food and Nutrition, College of BioNano Technology, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea; Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, 21999, Republic of Korea.
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30
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms. Life Sci Alliance 2024; 7:e202302501. [PMID: 38803235 PMCID: PMC11109482 DOI: 10.26508/lsa.202302501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the developmental transcription factor CCAAT/enhancer-binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This choice between alternative start sites depends on sequence features of the CEBPA transcript, including a regulatory uORF, but the molecular basis is not fully understood. Here, we identify the factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescent reporter coupled with CRISPRi screening. Our screen uncovered a role of the ribosome rescue factor PELOTA (PELO) in promoting the expression of the longer C/EBPα isoform by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin kinase. Our work uncovers further links between ribosome recycling and translation reinitiation that regulate a key transcription factor, with implications for normal hematopoiesis and leukemogenesis.
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Affiliation(s)
- Samantha G Fernandez
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas Ferguson
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Nicholas T Ingolia
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
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31
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Takeda S, Yoza M, Ueda S, Takeuchi S, Maeno A, Sakamoto T, Kimura S. Exploring the diversity of galls on Artemisia indica induced by Rhopalomyia species through morphological and transcriptome analyses. PLANT DIRECT 2024; 8:e619. [PMID: 38962171 PMCID: PMC11219473 DOI: 10.1002/pld3.619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Plant galls generated by insects have highly organized structures, providing nutrients and shelter to the insects living within them. Most research on the physiological and molecular mechanisms of gall development has focused on single galls. To understand the diversity of gall development, we examined five galls with different morphologies generated by distinct species of Rhopalomyia (gall midge; Diptera: Cecidomyiidae) on a single host plant of Artemisia indica var. maximowiczii (Asteraceae). Vasculature developed de novo within the galls, indicating active transport of nutrients between galls and the host plant. Each gall had a different pattern of vasculature and lignification, probably due to differences in the site of gall generation and the gall midge species. Transcriptome analysis indicated that photosynthetic and cell wall-related genes were down-regulated in leaf and stem galls, respectively, compared with control leaf and stem tissues, whereas genes involved in floral organ development were up-regulated in all types of galls, indicating that transformation from source to sink organs occurs during gall development. Our results help to understand the diversity of galls on a single herbaceous host plant.
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Affiliation(s)
- Seiji Takeda
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
- Biotechnology Research Department, Kyoto Prefectural Agriculture Forestry and Fisheries Technology CenterSeikaJapan
| | - Makiko Yoza
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Sawako Ueda
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Sakura Takeuchi
- Graduate School of Life and Environmental SciencesKyoto Prefectural UniversityKyotoJapan
| | - Akiteru Maeno
- Cell Architecture LaboratoryNational Institute of GeneticsShizuokaJapan
| | | | - Seisuke Kimura
- Center for Plant SciencesKyoto Sangyo UniversityKyotoJapan
- Department of Industrial Life Sciences, Faculty of Life SciencesKyoto Sangyo UniversityKyotoJapan
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Gao X, Ma Q, Zhang X, Wang X, Wang N, Cui Y, Li S, Ma S, Wang H, Zhang K. The reference genome sequence of Artemisia argyi provides insights into secondary metabolism biosynthesis. FRONTIERS IN PLANT SCIENCE 2024; 15:1406592. [PMID: 39006964 PMCID: PMC11239399 DOI: 10.3389/fpls.2024.1406592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Artemisia argyi, a perennial herb of the genus Artemisia in the family Asteraceae, holds significant importance in Chinese traditional medicine, referred to as "Aicao". Here, we report a high-quality reference genome of Artemisia argyi L. cv. beiai, with a genome size up to 4.15 Gb and a contig N50 of 508.96 Kb, produced with third-generation Nanopore sequencing technology. We predicted 147,248 protein-coding genes, with approximately 68.86% of the assembled sequences comprising repetitive elements, primarily long terminal repeat retrotransposons(LTRs). Comparative genomics analysis shows that A. argyi has the highest number of specific gene families with 5121, and much more families with four or more members than the other 6 plant species, which is consistent with its more expanded gene families and fewer contracted gene families. Furthermore, through transcriptome sequencing of A. argyi in response to exogenous MeJA treatment, we have elucidated acquired regulatory insights into MeJA's impact on the phenylpropanoid, flavonoid, and terpenoid biosynthesis pathways of A. argyi. The whole-genome information obtained in this study serves as a valuable resource for delving deeper into the cultivation and molecular breeding of A. argyi. Moreover, it holds promise for enhancing genome assemblies across other members of the Asteraceae family. The identification of key genes establishes a solid groundwork for developing new varieties of Artemisia with elevated concentrations of active compounds.
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Affiliation(s)
- Xinqiang Gao
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Qiang Ma
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xiaomeng Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xingyun Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yupeng Cui
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Shuyan Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Shengming Ma
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Hong Wang
- Henan Artemisia Argyi Medical Research Center, Anyang, China
| | - Kunpeng Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
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Xie XZ, Zuo L, Huang W, Fan QM, Weng YY, Yao WD, Jiang JL, Jin JQ. FDX1 as a novel biomarker and treatment target for stomach adenocarcinoma. World J Gastrointest Surg 2024; 16:1803-1824. [PMID: 38983344 PMCID: PMC11230022 DOI: 10.4240/wjgs.v16.i6.1803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Stomach adenocarcinoma (STAD) is one of the main reasons for cancer-related deaths worldwide. This investigation aimed to define the connection between STAD and Cuproptosis-related genes (CRGs). Cuproptosis is a newly identified form of mitochondrial cell death triggered by copper. AIM To explore the identification of potential biomarkers for STAD disease based on cuproptosis. METHODS A predictive model using Gene Ontology (GO), Least Absolute Shrinkage and Selection Operator (LASSO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Variation Analysis (GSVA), and Gene Set Enrichment Analysis analyzed gene interconnections, focusing on 3 copper-related genes and their expression in The Cancer Genome Atlas-STAD. Networks for mRNA-miRNA and mRNA-transcription factor interactions were constructed. The prognostic significance of CRG scores was evaluated using time-receiver operating characteristic, Kaplan-Meier curves, and COX regression analysis. Validation was conducted with datasets GSE26942, GSE54129, and GSE66229. Expression of copper-related differentially expressed genes was also analyzed in various human tissues and gastric cancer subpopulations using the human protein atlas. RESULTS Three significant genes (FDX1, LIAS, MTF1) were identified and selected via LASSO analysis to predict and classify individuals with STAD into high and low CRG score subgroups. These genes were down-regulated in both risk categories. GO and KEGG analyses highlighted their involvement mainly in the electron transport chain. After validating their differential expression, FDX1 emerged as the most accurate diagnostic marker for gastric cancer. Additionally, the RCircos package localized FDX1 on chromosome 11. CONCLUSION Our study revealed that FDX1 could be a potential biomarker and treatment target for gastric malignancy, providing new ideas for further scientific research.
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Affiliation(s)
- Xian-Ze Xie
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
| | - Lei Zuo
- Anhui Province Huainan City Shou County Agricultural Machinery Affairs Management Center, Huainan 232200, Anhui Province, China
| | - Wei Huang
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
| | - Qiao-Mei Fan
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
| | - Ya-Yun Weng
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
| | - Wen-Dong Yao
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
| | - Jia-Li Jiang
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
| | - Jia-Qi Jin
- Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310018, Zhejiang Province, China
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Kerdkumthong K, Nanarong S, Roytrakul S, Pitakpornpreecha T, Tantimetta P, Runsaeng P, Obchoei S. Quantitative proteomics analysis reveals possible anticancer mechanisms of 5'-deoxy-5'-methylthioadenosine in cholangiocarcinoma cells. PLoS One 2024; 19:e0306060. [PMID: 38923999 PMCID: PMC11206958 DOI: 10.1371/journal.pone.0306060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Cholangiocarcinoma (CCA) is an aggressive cancer originating from bile duct epithelium, particularly prevalent in Asian countries with liver fluke infections. Current chemotherapy for CCA often fails due to drug resistance, necessitating novel anticancer agents. This study investigates the potential of 5'-deoxy-5'-methylthioadenosine (MTA), a naturally occurring nucleoside, against CCA. While MTA has shown promise against various cancers, its effects on CCA remain unexplored. We evaluated MTA's anticancer activity in CCA cell lines and drug-resistant sub-lines, assessing cell viability, migration, invasion, and apoptosis. The potential anticancer mechanisms of MTA were explored through proteomic analysis using LC-MS/MS and bioinformatic analysis. The results show a dose-dependent reduction in CCA cell viability, with enhanced effects on cancer cells compared to normal cells. Moreover, MTA inhibits growth, induces apoptosis, and suppresses cell migration and invasion. Additionally, MTA enhanced the anticancer effects of gemcitabine on drug-resistant CCA cells. Proteomics revealed the down-regulation of multiple proteins by MTA, affecting various molecular functions, biological processes, and cellular components. Network analysis highlighted MTA's role in inhibiting proteins related to mitochondrial function and energy derivation, crucial for cell growth and survival. Additionally, MTA suppressed proteins involved in cell morphology and cytoskeleton organization, important for cancer cell motility and metastasis. Six candidate genes, including ZNF860, KLC1, GRAMD1C, MAMSTR, TANC1, and TTC13, were selected from the top 10 most down-regulated proteins identified in the proteomics results and were subsequently verified through RT-qPCR. Further, KLC1 protein suppression by MTA treatment was confirmed through Western blotting. Additionally, based on TCGA data, KLC1 mRNA was found to be upregulated in the tissue of CCA patients compared to that of normal adjacent tissues. In summary, MTA shows promising anticancer potential against CCA by inhibiting growth, inducing apoptosis, and suppressing migration and invasion, while enhancing gemcitabine's effects. Proteomic analysis elucidates possible molecular mechanisms underlying MTA's anticancer activity, laying the groundwork for future research and development of MTA as a treatment for advanced CCA.
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Affiliation(s)
- Kankamol Kerdkumthong
- Faculty of Science, Division of Health and Applied Sciences, Biochemistry Graduate Program, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Sutthipong Nanarong
- Faculty of Science, Division of Health and Applied Sciences, Biochemistry Graduate Program, Prince of Songkla University, Hatyai, Songkhla, Thailand
- Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumtani, Thailand
| | - Thanawat Pitakpornpreecha
- Faculty of Science, Division of Health and Applied Sciences, Biochemistry Graduate Program, Prince of Songkla University, Hatyai, Songkhla, Thailand
- Faculty of Science, Center of Excellence for Biochemistry, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Phonprapavee Tantimetta
- Faculty of Science, Division of Health and Applied Sciences, Biochemistry Graduate Program, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Phanthipha Runsaeng
- Faculty of Science, Division of Health and Applied Sciences, Biochemistry Graduate Program, Prince of Songkla University, Hatyai, Songkhla, Thailand
- Faculty of Science, Center of Excellence for Biochemistry, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Sumalee Obchoei
- Faculty of Science, Division of Health and Applied Sciences, Biochemistry Graduate Program, Prince of Songkla University, Hatyai, Songkhla, Thailand
- Faculty of Science, Center of Excellence for Biochemistry, Prince of Songkla University, Hatyai, Songkhla, Thailand
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Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience 2024; 27:110083. [PMID: 38872974 PMCID: PMC11170199 DOI: 10.1016/j.isci.2024.110083] [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: 10/06/2023] [Revised: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Ochocka
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Richard Ho
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
- The Njord Centre, Department of Physics, University of Oslo, Oslo, Norway
| | - Bożena Kamińska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
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Windisch R, Soliman S, Hoffmann A, Chen-Wichmann L, Danese A, Vosberg S, Bravo J, Lutz S, Kellner C, Fischer A, Gebhard C, Redondo Monte E, Hartmann L, Schneider S, Beier F, Strobl CD, Weigert O, Peipp M, Schündeln M, Stricker SH, Rehli M, Bernhagen J, Humpe A, Klump H, Brendel C, Krause DS, Greif PA, Wichmann C. Engineering an inducible leukemia-associated fusion protein enables large-scale ex vivo production of functional human phagocytes. Proc Natl Acad Sci U S A 2024; 121:e2312499121. [PMID: 38857395 PMCID: PMC11194515 DOI: 10.1073/pnas.2312499121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/20/2024] [Indexed: 06/12/2024] Open
Abstract
Ex vivo expansion of human CD34+ hematopoietic stem and progenitor cells remains a challenge due to rapid differentiation after detachment from the bone marrow niche. In this study, we assessed the capacity of an inducible fusion protein to enable sustained ex vivo proliferation of hematopoietic precursors and their capacity to differentiate into functional phagocytes. We fused the coding sequences of an FK506-Binding Protein 12 (FKBP12)-derived destabilization domain (DD) to the myeloid/lymphoid lineage leukemia/eleven nineteen leukemia (MLL-ENL) fusion gene to generate the fusion protein DD-MLL-ENL and retrovirally expressed the protein switch in human CD34+ progenitors. Using Shield1, a chemical inhibitor of DD fusion protein degradation, we established large-scale and long-term expansion of late monocytic precursors. Upon Shield1 removal, the cells lost self-renewal capacity and spontaneously differentiated, even after 2.5 y of continuous ex vivo expansion. In the absence of Shield1, stimulation with IFN-γ, LPS, and GM-CSF triggered terminal differentiation. Gene expression analysis of the obtained phagocytes revealed marked similarity with naïve monocytes. In functional assays, the novel phagocytes migrated toward CCL2, attached to VCAM-1 under shear stress, produced reactive oxygen species, and engulfed bacterial particles, cellular particles, and apoptotic cells. Finally, we demonstrated Fcγ receptor recognition and phagocytosis of opsonized lymphoma cells in an antibody-dependent manner. Overall, we have established an engineered protein that, as a single factor, is useful for large-scale ex vivo production of human phagocytes. Such adjustable proteins have the potential to be applied as molecular tools to produce functional immune cells for experimental cell-based approaches.
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Affiliation(s)
- Roland Windisch
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Sarah Soliman
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Adrian Hoffmann
- Vascular Biology, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Linping Chen-Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Anna Danese
- Biomedical Center, Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz8010, Austria
| | - Jimena Bravo
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main60596, Germany
| | - Sebastian Lutz
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Christian Kellner
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg93053, Germany
| | - Claudia Gebhard
- Leibniz Institute for Immunotherapy, Regensburg93053, Germany
| | - Enric Redondo Monte
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Luise Hartmann
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Stephanie Schneider
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen52074, Germany
| | - Carolin Dorothea Strobl
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Medicine II, Christian Albrechts University of Kiel, Kiel24105, Germany
| | - Michael Schündeln
- Pediatric Hematology and Oncology, Department of Pediatrics III, University Hospital Essen and the University of Duisburg-Essen, Essen45147, Germany
| | - Stefan H. Stricker
- Biomedical Center, Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg93053, Germany
- Leibniz Institute for Immunotherapy, Regensburg93053, Germany
| | - Jürgen Bernhagen
- Vascular Biology, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Munich Cluster for Systems Neurology, Munich81377, Germany
| | - Andreas Humpe
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, Essen45147, Germany
- Institute for Transfusion Medicine and Cell Therapeutics, University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen52074, Germany
| | - Christian Brendel
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA02115
| | - Daniela S. Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main60596, Germany
- Institute of General Pharmacology and Toxicology, University Hospital Frankfurt, Goethe-University, Frankfurt am Main60596, Germany
| | - Philipp A. Greif
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
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Dash S, Jagadeesan R, Baptista ISC, Chauhan V, Kandavalli V, Oliveira SMD, Ribeiro AS. A library of reporters of the global regulators of gene expression in Escherichia coli. mSystems 2024; 9:e0006524. [PMID: 38687030 PMCID: PMC11237500 DOI: 10.1128/msystems.00065-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
The topology of the transcription factor network (TFN) of Escherichia coli is far from uniform, with 22 global regulator (GR) proteins controlling one-third of all genes. So far, their production rates cannot be tracked by comparable fluorescent proteins. We developed a library of fluorescent reporters for 16 GRs for this purpose. Each consists of a single-copy plasmid coding for green fluorescent protein (GFP) fused to the full-length copy of the native promoter. We tracked their activity in exponential and stationary growth, as well as under weak and strong stresses. We show that the reporters have high sensitivity and specificity to all stresses tested and detect single-cell variability in transcription rates. Given the influence of GRs on the TFN, we expect that the new library will contribute to dissecting global transcriptional stress-response programs of E. coli. Moreover, the library can be invaluable in bioindustrial applications that tune those programs to, instead of cell growth, favor productivity while reducing energy consumption.IMPORTANCECells contain thousands of genes. Many genes are involved in the control of cellular activities. Some activities require a few hundred genes to run largely synchronous transcriptional programs. To achieve this, cells have evolved global regulator (GR) proteins that can influence hundreds of genes simultaneously. We have engineered a library of Escherichia coli strains to track the levels over time of these, phenotypically critical, GRs. Each strain has a single-copy plasmid coding for a fast-maturing green fluorescent protein whose transcription is controlled by a copy of the natural GR promoter. By allowing the tracking of GR levels, with sensitivity and specificity, this library should become of wide use in scientific research on bacterial gene expression (from molecular to synthetic biology) and, later, be used in applications in therapeutics and bioindustries.
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Affiliation(s)
- Suchintak Dash
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rahul Jagadeesan
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ines S. C. Baptista
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vatsala Chauhan
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vinodh Kandavalli
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Samuel M. D. Oliveira
- Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - Andre S. Ribeiro
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Seenak P, Nernpermpisooth N, Kumphune S, Songjang W, Jiraviriyakul A, Jumroon N, Pankhong P, Roytrakul S, Thaisakun S, Phaonakrop N, Nuengchamnong N. Secretome profiling of human epithelial cells exposed to cigarette smoke extract and their effect on human lung microvascular endothelial cells. Sci Rep 2024; 14:13740. [PMID: 38877184 PMCID: PMC11178828 DOI: 10.1038/s41598-024-64717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/12/2024] [Indexed: 06/16/2024] Open
Abstract
Cigarette smoke (CS) is one of the leading causes of pulmonary diseases and can induce lung secretome alteration. CS exposure-induced damages to human pulmonary epithelial cells and microvascular endothelial cells have been extensively demonstrated; however, the effects of the secretome of lung epithelial cells exposed to CS extracts (CSE) on lung microvascular endothelial cells are not fully understood. In this study, we aimed to determine the effects of the secretome of lung epithelial cells exposed to CSE on lung microvascular endothelial cells. Human lung epithelial cells, A549, were exposed to CSE, and the secretome was collected. Human lung microvascular endothelial cells, HULEC-5a, were used to evaluate the effect of the secretome of A549 exposed to CSE. Secretome profile, endothelial cell death, inflammation, and permeability markers were determined. CSE altered the secretome expression of A549 cells, and secretome derived from CSE-exposed A549 cells caused respiratory endothelial cell death, inflammation, and moderately enhanced endothelial permeability. This study demonstrates the potential role of cellular interaction between endothelial and epithelial cells during exposure to CSE and provides novel therapeutic targets or beneficial biomarkers using secretome analysis for CSE-related respiratory diseases.
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Affiliation(s)
- Porrnthanate Seenak
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand.
- Department of Cardio-Thoracic Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand.
| | - Nitirut Nernpermpisooth
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Department of Cardio-Thoracic Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Sarawut Kumphune
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Biomedical Engineering and Innovation Research Centre, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
- Biomedical Engineering Institute, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Worawat Songjang
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Arunya Jiraviriyakul
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Noppadon Jumroon
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Panyupa Pankhong
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Sittiruk Roytrakul
- National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Siriwan Thaisakun
- National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Narumon Phaonakrop
- National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Nitra Nuengchamnong
- Science Laboratory Center, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
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Polyong CP, Roytrakul S, Sirivarasai J, Yingratanasuk T, Thetkathuek A. Novel Serum Proteomes Expressed from Benzene Exposure Among Gasoline Station Attendants. Biomark Insights 2024; 19:11772719241259604. [PMID: 38868168 PMCID: PMC11168042 DOI: 10.1177/11772719241259604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
Background Research on the proteomes impact of benzene exposure in fuel station employees remains sparse, underscoring the need for detailed health impact assessments focusing on biomarker evaluation. Objectives This investigation aimed to analyze the differences in blood parameters and serum proteomes resulting from benzene exposure between gasoline station attendants (B-GSA) and a control group. Design and methods A cross-sectional analytical study was conducted with 96 participants, comprising 54 in the B-GSA group and 42 in the control group. The methodology employed included an interview questionnaire alongside urine and blood sample collections. The urine samples were analyzed for trans,trans-muconic acid (t,t-MA) levels, while the blood samples underwent complete blood count analysis and proteome profiling. Results Post-shift analysis indicated that the B-GSA group exhibited significantly higher levels of t,t-MA and monocytes compared to the control group (P < .05). Proteome quantification identified 1448 proteins differentially expressed between the B-GSA and control groups. Among these, 20 proteins correlated with the levels of t,t-MA in urine. Notably, 4 proteins demonstrated more than a 2-fold down-regulation in the B-GSA group: HBS1-like, non-structural maintenance of chromosomes element 1 homolog, proprotein convertase subtilisin/kexin type 4, and zinc finger protein 658. The KEGG pathway analysis revealed associations with apoptosis, cancer pathways, p53 signaling, and the TNF signaling pathway. Conclusion The changes in these 4 significant proteins may elucidate the molecular mechanisms underlying benzene toxicity and suggest their potential as biomarkers for benzene poisoning in future assessments.
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Affiliation(s)
- Chan Pattama Polyong
- Occupational Health and Safety Program, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jintana Sirivarasai
- Nutrition Division, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Tanongsak Yingratanasuk
- Department of Industrial Hygiene and Safety, Faculty of Public Health, Burapha University, Chonburi, Thailand
| | - Anamai Thetkathuek
- Department of Industrial Hygiene and Safety, Faculty of Public Health, Burapha University, Chonburi, Thailand
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Anek P, Kumpangcum S, Roytrakul S, Khanongnuch C, Saenjum C, Phannachet K. Antibacterial Activities of Phenolic Compounds in Miang Extract: Growth Inhibition and Change in Protein Expression of Extensively Drug-Resistant Klebsiella pneumoniae. Antibiotics (Basel) 2024; 13:536. [PMID: 38927202 PMCID: PMC11201136 DOI: 10.3390/antibiotics13060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The rising incidence of extensively drug-resistant (XDR) Klebsiella pneumoniae, including carbapenem- and colistin-resistant strains, leads to the limitation of available effective antibiotics. Miang, known as chewing tea, is produced from Camellia sinensis var. assamica or Assam tea leaves fermentation. Previous studies revealed that the extract of Miang contains various phenolic and flavonoid compounds with numerous biological activities including antibacterial activity. However, the antibacterial activity of Miang against XDR bacteria especially colistin-resistant strains had not been investigated. In this study, the compositions of phenolic and flavonoid compounds in fresh, steamed, and fermented Assam tea leaves were examined by HPLC, and their antibacterial activities were evaluated by the determination of the MIC and MBC. Pyrogallol was detected only in the extract from Miang and showed the highest activities with an MIC of 0.25 mg/mL and an MBC of 0.25-0.5 mg/mL against methicillin-susceptible Staphylococcus aureus, methicillin-resistant S. aureus, Escherichia coli ATCC 25922, colistin-resistant E. coli, and colistin-resistant K. pneumoniae. The effects on morphology and proteomic changes in K. pneumoniae NH54 treated with Miang extract were characterized by SEM and label-free quantitative shotgun proteomics analysis. The results revealed that Miang extract caused the decrease in bacterial cell wall integrity and cell lysis. The up- and downregulated expression with approximately a 2 to >5-fold change in proteins involved in peptidoglycan synthesis and outer membrane, carbohydrate, and amino acid metabolism were identified. These findings suggested that Miang containing pyrogallol and other secondary metabolites from fermentation has potential as an alternative candidate with an antibacterial agent or natural active pharmaceutical ingredient against XDR bacteria including colistin-resistant bacteria.
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Affiliation(s)
- Pannita Anek
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.A.); (S.K.)
| | - Sutita Kumpangcum
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.A.); (S.K.)
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand;
| | - Chartchai Khanongnuch
- Research Center for Innovation in Analytical Science and Technology for Biodiversity-Based Economic and Society (I-ANALY-S-T_B.BES-CMU), Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center for Multidisciplinary Approaches to Miang, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chalermpong Saenjum
- Research Center for Innovation in Analytical Science and Technology for Biodiversity-Based Economic and Society (I-ANALY-S-T_B.BES-CMU), Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center for Multidisciplinary Approaches to Miang, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kulwadee Phannachet
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.A.); (S.K.)
- Research Center for Innovation in Analytical Science and Technology for Biodiversity-Based Economic and Society (I-ANALY-S-T_B.BES-CMU), Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center for Multidisciplinary Approaches to Miang, Chiang Mai University, Chiang Mai 50200, Thailand
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Darbellay F, Ramisch A, Lopez-Delisle L, Kosicki M, Rauseo A, Jouini Z, Visel A, Andrey G. Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development. Nat Commun 2024; 15:4820. [PMID: 38844479 PMCID: PMC11156918 DOI: 10.1038/s41467-024-49203-2] [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: 06/02/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Chondrocyte differentiation controls skeleton development and stature. Here we provide a comprehensive map of chondrocyte-specific enhancers and show that they provide a mechanistic framework through which non-coding genetic variants can influence skeletal development and human stature. Working with fetal chondrocytes isolated from mice bearing a Col2a1 fluorescent regulatory sensor, we identify 780 genes and 2'704 putative enhancers specifically active in chondrocytes using a combination of RNA-seq, ATAC-seq and H3K27ac ChIP-seq. Most of these enhancers (74%) show pan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. Notably, genetic variations overlapping these enhancers better explain height differences than those overlapping non-chondrogenic enhancers. Finally, targeted deletions of identified enhancers at the Fgfr3, Col2a1, Hhip and, Nkx3-2 loci confirm their role in regulating cognate genes. This enhancer map provides a framework for understanding how genes and non-coding variations influence bone development and diseases.
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Affiliation(s)
- Fabrice Darbellay
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
| | - Anna Ramisch
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
| | - Antonella Rauseo
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
| | - Zahra Jouini
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Guillaume Andrey
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211, Geneva, Switzerland.
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Abela L, Gianfrancesco L, Tagliatti E, Rossignoli G, Barwick K, Zourray C, Reid KM, Budinger D, Ng J, Counsell J, Simpson A, Pearson TS, Edvardson S, Elpeleg O, Brodsky FM, Lignani G, Barral S, Kurian MA. Neurodevelopmental and synaptic defects in DNAJC6 parkinsonism, amenable to gene therapy. Brain 2024; 147:2023-2037. [PMID: 38242634 PMCID: PMC11146427 DOI: 10.1093/brain/awae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/10/2023] [Accepted: 12/16/2023] [Indexed: 01/21/2024] Open
Abstract
DNAJC6 encodes auxilin, a co-chaperone protein involved in clathrin-mediated endocytosis (CME) at the presynaptic terminal. Biallelic mutations in DNAJC6 cause a complex, early-onset neurodegenerative disorder characterized by rapidly progressive parkinsonism-dystonia in childhood. The disease is commonly associated with additional neurodevelopmental, neurological and neuropsychiatric features. Currently, there are no disease-modifying treatments for this condition, resulting in significant morbidity and risk of premature mortality. To investigate the underlying disease mechanisms in childhood-onset DNAJC6 parkinsonism, we generated induced pluripotent stem cells (iPSC) from three patients harbouring pathogenic loss-of-function DNAJC6 mutations and subsequently developed a midbrain dopaminergic neuronal model of disease. When compared to age-matched and CRISPR-corrected isogenic controls, the neuronal cell model revealed disease-specific auxilin deficiency as well as disturbance of synaptic vesicle recycling and homeostasis. We also observed neurodevelopmental dysregulation affecting ventral midbrain patterning and neuronal maturation. To explore the feasibility of a viral vector-mediated gene therapy approach, iPSC-derived neuronal cultures were treated with lentiviral DNAJC6 gene transfer, which restored auxilin expression and rescued CME. Our patient-derived neuronal model provides deeper insights into the molecular mechanisms of auxilin deficiency as well as a robust platform for the development of targeted precision therapy approaches.
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Affiliation(s)
- Lucia Abela
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Lorita Gianfrancesco
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Erica Tagliatti
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Laboratory of Pharmacology and Brain Pathology, Humanitas Clinical and Research Center, 20089 Milano, Italy
| | - Giada Rossignoli
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Katy Barwick
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Clara Zourray
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Kimberley M Reid
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Dimitri Budinger
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Joanne Ng
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Genetic Therapy Accelerator Centre, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - John Counsell
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Arlo Simpson
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Toni S Pearson
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032-3784, USA
- Department of Pediatrics, Nationwide Children’s Hospital, Ohio State University, Columbus, OH 43210, USA
- Department of Neurology, Nationwide Children’s Hospital, Ohio State University, Columbus, OH 43210, USA
| | - Simon Edvardson
- Department of Genetics, Hadassah, Hebrew University Medical Center, 9574869 Jerusalem, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, 9574869 Jerusalem, Israel
| | - Frances M Brodsky
- Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Gabriele Lignani
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Serena Barral
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Department of Neurology, Great Ormond Street Hospital, London, WC1N 3JH, UK
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Duan M, Plemel RL, Takenaka T, Lin A, Delgado BM, Nattermann U, Nickerson DP, Mima J, Miller EA, Merz AJ. SNARE chaperone Sly1 directly mediates close-range vesicle tethering. J Cell Biol 2024; 223:e202001032. [PMID: 38478018 PMCID: PMC10943277 DOI: 10.1083/jcb.202001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
The essential Golgi protein Sly1 is a member of the Sec1/mammalian Unc-18 (SM) family of SNARE chaperones. Sly1 was originally identified through remarkable gain-of-function alleles that bypass requirements for diverse vesicle tethering factors. Employing genetic analyses and chemically defined reconstitutions of ER-Golgi fusion, we discovered that a loop conserved among Sly1 family members is not only autoinhibitory but also acts as a positive effector. An amphipathic lipid packing sensor (ALPS)-like helix within the loop directly binds high-curvature membranes. Membrane binding is required for relief of Sly1 autoinhibition and also allows Sly1 to directly tether incoming vesicles to the Qa-SNARE on the target organelle. The SLY1-20 mutation bypasses requirements for diverse tethering factors but loses this ability if the tethering activity is impaired. We propose that long-range tethers, including Golgins and multisubunit tethering complexes, hand off vesicles to Sly1, which then tethers at close range to initiate trans-SNARE complex assembly and fusion in the early secretory pathway.
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Affiliation(s)
- Mengtong Duan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachael L. Plemel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Ariel Lin
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biology, California State University, San Bernardino, CA, USA
| | | | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Biophysics, Structure, and Design Graduate Program, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Joji Mima
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Alexey J. Merz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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Pitchika GK, Naik BK, Ramana GVV, Nirupama R, Ranjani TS, Venkaiah K, Reddy MH, Sainath SB, Pradeepkiran JA. Transcriptomic profile in carbendazim-induced developmental defects in zebrafish (Danio rerio) embryos/larvae. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109907. [PMID: 38522711 DOI: 10.1016/j.cbpc.2024.109907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/26/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Carbendazim is a widely used fungicide to protect agricultural and horticultural crops against a wide array of fungal species. Published reports have shown that the wide usage of carbendazim resulted in reprotoxicity, carcinogenicity, immunotoxicity, and developmental toxicity in mammalian models. However, studies related to the developmental toxicity of carbendazim in aquatic organisms are not clear. To address this gap, an attempt was made by exposing zebrafish embryos to carbendazim (800 μg/L) and assessing the phenotypic and transcriptomic profile at different developmental stages [24 hour post fertilization (hpf), 48 hpf, 72 hpf and 96 hpf). At 48 hpf, phenotypic abnormalities such as delay in hatching rate, deformed spinal axial curvature, and pericardial edema were observed in zebrafish larvae over its respective controls. At 72 hpf, exposure of zebrafish embryos exposed to carbendazim resulted in scoliosis; however, unexposed larvae did not exhibit signs of scoliosis. Interestingly, the transcriptomic analysis revealed a total of 1253 DEGs were observed at selected time points, while unique genes at 24 hpf, 48 hpf, 72 hpf and 96 hpf was found to be 76.54 %, 61.14 %, 92.98 %, and 68.28 %, respectively. Functional profiling of downregulated genes revealed altered transcriptomic markers associated with phototransduction (24 hpf and 72 hpf), immune system (48 hpf), and SNARE interactions in the vesicular pathway (96 hpf). Whereas functional profiling of upregulated genes revealed altered transcriptomic markers associated with riboflavin metabolism (24 hpf), basal transcription factors (48 hpf), insulin signaling pathway (72 hpf), and primary bile acid biosynthesis (96 hpf). Taken together, carbendazim-induced developmental toxicity could be ascribed to pleiotropic responses at the molecular level, which in turn might reflect phenotypic abnormalities.
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Affiliation(s)
- Gopi Krishna Pitchika
- Department of Zoology, Vikrama Simhapuri University College, Kavali 524201, A.P., India.
| | - B Krishna Naik
- Department of Zoology, Vikrama Simhapuri University College, Kavali 524201, A.P., India
| | - G V V Ramana
- Department of Zoology, Vikrama Simhapuri University College, Kavali 524201, A.P., India
| | - R Nirupama
- Department of Zoology, Vikrama Simhapuri University College, Kavali 524201, A.P., India
| | - T Sri Ranjani
- Department of Zoology, D.K. Govt. College for Women (A), Dargamitta, Nellore 524003, A.P., India
| | - K Venkaiah
- Department of Biotechnology, Vikrama Simhapuri University, Nellore 524324, A.P., India
| | - M Hanuma Reddy
- Department of Marine Biology, Vikrama Simhapuri University, Nellore 524324, A.P., India
| | - S B Sainath
- Department of Biotechnology, Vikrama Simhapuri University, Nellore 524324, A.P., India.
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Liu Z, Bai T, Liu B, Yu L. MulStack: An ensemble learning prediction model of multilabel mRNA subcellular localization. Comput Biol Med 2024; 175:108289. [PMID: 38688123 DOI: 10.1016/j.compbiomed.2024.108289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 05/02/2024]
Abstract
Subcellular localization of mRNA is related to protein synthesis, cell polarity, cell movement and other biological regulation mechanisms. The distribution of mRNAs in subcellulars is similar to that of proteins, and most mRNAs are distributed in multiple subcellulars. Recently, some computational methods have been designed to predict the subcellular localization of mRNA. However, these methods only employed a sin-gle level of mRNA features and did not employ the position encoding of nucleotides in mRNA. In this paper, an ensemble learning prediction model is proposed, named MulStack, which is based on random forest and deep learning for multilabel mRNA subcellular localization. The proposed method employs two levels of mRNA features, including sequence-level and residue-level features, and position encoding is employed for the first time in the field of subcellular localization of mRNA. Random forest is employed to learn mRNA sequence-level feature, deep learning is employed to learn mRNA sequence-level feature and mRNA residue-level combined with position encoding. And the outputs of random forest and deep learning model will be weighted sum as the prediction probability. Compared with existing methods, the results show that MulStack is the best in the localization of the nucleus, cytosol and exosome. In addition, position weight matrices (PWMs) are extracted by convolutional neural networks (CNNs) that can be matched with known RNA binding protein motifs. Gene ontology (GO) enrichment analysis shows biological processes, molecular functions and cellular components of mRNA genes. The prediction web server of MulStack is freely accessible at http://bliulab.net/MulStack.
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Affiliation(s)
- Ziqi Liu
- School of Computer Science and Technology, Xidian University, Xian, 710075, China.
| | - Tao Bai
- School of Mathematics & Computer Science, Yan'an University, Shaanxi, 716000, China; School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xian, 710075, China.
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Sales Conniff A, Tur J, Kohena K, Zhang M, Gibbons J, Heller LC. DNA Electrotransfer Regulates Molecular Functions in Skeletal Muscle. Bioelectricity 2024; 6:80-90. [PMID: 39119567 PMCID: PMC11304878 DOI: 10.1089/bioe.2022.0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Background Tissues, such as skeletal muscle, have been targeted for the delivery of plasmid DNA (pDNA) encoding vaccines and therapeutics. The application of electric pulses (electroporation or electrotransfer) increases cell membrane permeability to enhance plasmid delivery and expression. However, the molecular effects of DNA electrotransfer on the muscle tissue are poorly characterized. Materials and Methods Four hours after intramuscular plasmid electrotransfer, we evaluated gene expression changes by RNA sequencing. Differentially expressed genes were analyzed by gene ontology (GO) pathway enrichment analysis. Results GO analysis highlighted many enriched molecular functions. The terms regulated by pulse application were related to muscle stress, the cytoskeleton and inflammation. The terms regulated by pDNA injection were related to a DNA-directed response and its control. Several terms regulated by pDNA electrotransfer were similar to those regulated by pulse application. However, the terms related to pDNA injection differed, focusing on entry of the plasmid into the cells and intracellular trafficking. Conclusion Each muscle stimulus resulted in specific regulated molecular functions. Identifying the unique intrinsic molecular changes driven by intramuscular DNA electrotransfer will aid in the design of preventative and therapeutic gene therapies.
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Affiliation(s)
- Amanda Sales Conniff
- Department of Medical Engineering, University of South Florida, Tampa, Florida, USA
| | - Jared Tur
- Department of Medical Engineering, University of South Florida, Tampa, Florida, USA
| | - Kristopher Kohena
- Department of Medical Engineering, University of South Florida, Tampa, Florida, USA
| | - Min Zhang
- USF Genomics Core, University of South Florida, Tampa, Florida, USA
| | - Justin Gibbons
- USF Omics Hub, University of South Florida, Tampa, Florida, USA
| | - Loree C. Heller
- Department of Medical Engineering, University of South Florida, Tampa, Florida, USA
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Soussi G, Girdziusaite A, Jhanwar S, Palacio V, Notaro M, Sheth R, Zeller R, Zuniga A. TBX3 is essential for establishment of the posterior boundary of anterior genes and upregulation of posterior genes together with HAND2 during the onset of limb bud development. Development 2024; 151:dev202722. [PMID: 38828908 PMCID: PMC11190573 DOI: 10.1242/dev.202722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/26/2024] [Indexed: 06/05/2024]
Abstract
During limb bud formation, axis polarities are established as evidenced by the spatially restricted expression of key regulator genes. In particular, the mutually antagonistic interaction between the GLI3 repressor and HAND2 results in distinct and non-overlapping anterior-distal Gli3 and posterior Hand2 expression domains. This is a hallmark of the establishment of antero-posterior limb axis polarity, together with spatially restricted expression of homeodomain and other transcriptional regulators. Here, we show that TBX3 is required for establishment of the posterior expression boundary of anterior genes in mouse limb buds. ChIP-seq and differential gene expression analysis of wild-type and mutant limb buds identifies TBX3-specific and shared TBX3-HAND2 target genes. High sensitivity fluorescent whole-mount in situ hybridisation shows that the posterior expression boundaries of anterior genes are positioned by TBX3-mediated repression, which excludes anterior genes such as Gli3, Alx4, Hand1 and Irx3/5 from the posterior limb bud mesenchyme. This exclusion delineates the posterior mesenchymal territory competent to establish the Shh-expressing limb bud organiser. In turn, HAND2 is required for Shh activation and cooperates with TBX3 to upregulate shared posterior identity target genes in early limb buds.
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Affiliation(s)
- Geoffrey Soussi
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Ausra Girdziusaite
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Shalu Jhanwar
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Victorio Palacio
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | | | - Rushikesh Sheth
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
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Huang X, Chen M, Xiao Y, Zhu F, Chen L, Tian X, Hong L. The influence of biological sex in human skeletal muscle transcriptome during ageing. Biogerontology 2024; 25:461-478. [PMID: 37792135 DOI: 10.1007/s10522-023-10070-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/16/2023] [Indexed: 10/05/2023]
Abstract
Sex is a crucial biological variable, and influence of biological sex on the change of gene expression in ageing skeletal muscle has not yet been fully revealed. In this study, the mRNA expression profiles were obtained from the Gene Expression Omnibus database. Key genes were identified by differential expression analysis and weighted gene co-expression network analysis. The gene set enrichment analysis software and Molecular Signatures Database were used for functional and enrichment analysis. A protein-protein interaction network was constructed using STRING and visualized in Cytoscape. The results were compared between female and male subgroups. Differentially expressed genes and enriched pathways in different sex subgroups shared only limited similarities. The pathways enriched in the female subgroup were more similar to the pathways enriched in the older groups without taking sex difference into consideration. The pathways enriched in the female subgroup were more similar to the pathways enriched in the older groups without taking sex difference into consideration. The muscle myosin filament pathways were downregulated in the both aged female and male samples whereas transforming growth factor beta pathway and extracellular matrix-related pathways were upregulated. With muscle ageing, the metabolism-related pathways, protein synthesis and degradation pathways, results of predicted immune cell infiltration, and gene cluster associated with slow-type myofibers drastically different between the female and male subgroups. This finding may indicate that changes in muscle type with ageing may differ between the sexes in vastus lateralis muscle.
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Affiliation(s)
- Xiaoyu Huang
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mao Chen
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ya Xiao
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fangyi Zhu
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Liying Chen
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaoyu Tian
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Hong
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China.
- Pelvic Floor Research Centre of Hubei Province, Renmin Hospital of Wuhan University, Wuhan, China.
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49
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Getzke F, Wang L, Chesneau G, Böhringer N, Mesny F, Denissen N, Wesseler H, Adisa PT, Marner M, Schulze-Lefert P, Schäberle TF, Hacquard S. Physiochemical interaction between osmotic stress and a bacterial exometabolite promotes plant disease. Nat Commun 2024; 15:4438. [PMID: 38806462 PMCID: PMC11133316 DOI: 10.1038/s41467-024-48517-5] [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: 09/08/2023] [Accepted: 05/01/2024] [Indexed: 05/30/2024] Open
Abstract
Various microbes isolated from healthy plants are detrimental under laboratory conditions, indicating the existence of molecular mechanisms preventing disease in nature. Here, we demonstrated that application of sodium chloride (NaCl) in natural and gnotobiotic soil systems is sufficient to induce plant disease caused by an otherwise non-pathogenic root-derived Pseudomonas brassicacearum isolate (R401). Disease caused by combinatorial treatment of NaCl and R401 triggered extensive, root-specific transcriptional reprogramming that did not involve down-regulation of host innate immune genes, nor dampening of ROS-mediated immunity. Instead, we identified and structurally characterized the R401 lipopeptide brassicapeptin A as necessary and sufficient to promote disease on salt-treated plants. Brassicapeptin A production is salt-inducible, promotes root colonization and transitions R401 from being beneficial to being detrimental on salt-treated plants by disturbing host ion homeostasis, thereby bolstering susceptibility to osmolytes. We conclude that the interaction between a global change stressor and a single exometabolite from a member of the root microbiome promotes plant disease in complex soil systems.
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Affiliation(s)
- Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Lei Wang
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Guillaume Chesneau
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany
| | - Fantin Mesny
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institute for Plant Sciences, University of Cologne, 50674, Cologne, Germany
| | - Nienke Denissen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Hidde Wesseler
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Priscilla Tijesuni Adisa
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany.
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany.
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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Rajacharya GH, Sharma A, Yazdani SS. Proteomics and metabolic burden analysis to understand the impact of recombinant protein production in E. coli. Sci Rep 2024; 14:12271. [PMID: 38806637 PMCID: PMC11133349 DOI: 10.1038/s41598-024-63148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
The impact of recombinant protein production (RPP) on host cells and the metabolic burden associated with it undermine the efficiency of the production system. This study utilized proteomics to investigate the dynamics of parent and recombinant cells induced at different time points for RPP. The results revealed significant changes in both transcriptional and translational machinery that may have impacted the metabolic burden, growth rate of the culture and the RPP. The timing of protein synthesis induction also played a critical role in the fate of the recombinant protein within the host cell, affecting protein and product yield. The study identified significant differences in the expression of proteins involved in fatty acid and lipid biosynthesis pathways between two E. coli host strains (M15 and DH5⍺), with the E. coli M15 strain demonstrating superior expression characteristics for the recombinant protein. Overall, these findings contribute to the knowledge base for rational strain engineering for optimized recombinant protein production.
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Affiliation(s)
- Girish H Rajacharya
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Interdisciplinary Research (SIRe), Indian Institute of Technology, New Delhi, India
| | - Ashima Sharma
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Life Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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